From dfc2976df4cc73e4dcc904b307b56c60eb4690a2 Mon Sep 17 00:00:00 2001 From: walaj Date: Tue, 22 Jan 2019 23:18:40 -0500 Subject: [PATCH 1/6] fixes for issue #47 --- SeqLib | 2 +- src/svaba/AlignedContig.cpp | 100 ++++++++++++++++---------------- src/svaba/AlignedContig.h | 2 +- src/svaba/AlignmentFragment.cpp | 67 +++++++++++---------- src/svaba/AlignmentFragment.h | 2 +- src/svaba/BreakPoint.cpp | 44 +++++++++++--- src/svaba/BreakPoint.h | 12 ++-- src/svaba/DiscordantCluster.cpp | 3 +- 8 files changed, 134 insertions(+), 98 deletions(-) diff --git a/SeqLib b/SeqLib index 770cd10..af5dbb1 160000 --- a/SeqLib +++ b/SeqLib @@ -1 +1 @@ -Subproject commit 770cd10c308430e1719d54ebedcfe708db560bec +Subproject commit af5dbb16e71879d1e306c092b0794b6732f45696 diff --git a/src/svaba/AlignedContig.cpp b/src/svaba/AlignedContig.cpp index d651a33..523387b 100644 --- a/src/svaba/AlignedContig.cpp +++ b/src/svaba/AlignedContig.cpp @@ -160,67 +160,69 @@ void AlignedContig::blacklist(SeqLib::GRC &grv) { m_global_bp.splitCoverage(m_bamreads); } + +std::string AlignedContig::print(const SeqLib::BamHeader& h) const { - std::ostream& operator<<(std::ostream& out, const AlignedContig &ac) { - - // print the global breakpoint - if (!ac.m_global_bp.isEmpty()) - out << "Global BP: " << ac.m_global_bp << - " ins_aginst_contig " << ac.insertion_against_contig_read_count << - " del_against_contig " << ac.deletion_against_contig_read_count << " " << - ac.getContigName() << std::endl; - - // print the global breakpoint for secondaries - if (ac.m_global_bp_secondaries.size()) - out << "SECONDARY Global BP: " << ac.m_global_bp << - " ins_aginst_contig " << ac.insertion_against_contig_read_count << - " del_against_contig " << ac.deletion_against_contig_read_count << " " << - ac.getContigName() << std::endl; - - // print the multi-map breakpoints - for (auto& i : ac.m_local_breaks) - if (!i.isEmpty()) - out << "Multi-map BP: " << i << " -- " << ac.getContigName() << std::endl; - // print the multi-map breakpoints for secondary - for (auto& i : ac.m_local_breaks_secondaries) - if (!i.isEmpty()) - out << "SECONDARY Multi-map BP: " << i << " -- " << ac.getContigName() << std::endl; - - // print the indel breakpoints - for (auto& i : ac.m_frag_v) + std::stringstream out; + + // print the global breakpoint + if (!m_global_bp.isEmpty()) + out << "Global BP: " << m_global_bp.print(h) << + " ins_aginst_contig " << insertion_against_contig_read_count << + " del_against_contig " << deletion_against_contig_read_count << " " << + getContigName() << std::endl; + + // print the global breakpoint for secondaries + if (m_global_bp_secondaries.size()) + out << "SECONDARY Global BP: " << m_global_bp.print(h) << + " ins_aginst_contig " << insertion_against_contig_read_count << + " del_against_contig " << deletion_against_contig_read_count << " " << + getContigName() << std::endl; + + // print the multi-map breakpoints + for (auto& i : m_local_breaks) + if (!i.isEmpty()) + out << "Multi-map BP: " << i.print(h) << " -- " << getContigName() << std::endl; + // print the multi-map breakpoints for secondary + for (auto& i : m_local_breaks_secondaries) + if (!i.isEmpty()) + out << "SECONDARY Multi-map BP: " << i.print(h) << " -- " << getContigName() << std::endl; + + // print the indel breakpoints + for (auto& i : m_frag_v) for (auto& j : i.getIndelBreaks()) if (!j.isEmpty()) - out << "Indel: " << j << " -- " << ac.getContigName() << " ins_a_contig " << ac.insertion_against_contig_read_count << - " del_a_contig " << ac.deletion_against_contig_read_count << std::endl; + out << "Indel: " << j.print(h) << " -- " << getContigName() << " ins_a_contig " << insertion_against_contig_read_count << + " del_a_contig " << deletion_against_contig_read_count << std::endl; // print the AlignmentFragments alignments - for (auto& i : ac.m_frag_v) - out << i << " Disc: " << ac.printDiscordantClusters() << " -- " << ac.getContigName() << std::endl; + for (auto& i : m_frag_v) + out << i.print() << " Disc: " << printDiscordantClusters() << " -- " << getContigName() << std::endl; bool draw_divider = true; - for (auto& i : ac.m_frag_v) { + for (auto& i : m_frag_v) { for (auto& j : i.secondaries) { if (draw_divider) { - out << std::string(ac.m_seq.length(), 'S') << std::endl; + out << std::string(m_seq.length(), 'S') << std::endl; draw_divider = false; } - out << j << " Disc: " << ac.printDiscordantClusters() << " -- " << ac.getContigName() << std::endl; + out << j.print() << " Disc: " << printDiscordantClusters() << " -- " << getContigName() << std::endl; } } - + // print the break locations for indel deletions - for (auto& i : ac.m_frag_v) { + for (auto& i : m_frag_v) { for (auto& j : i.getIndelBreaks()) { if (j.num_align == 1 && j.insertion == "") // deletion //std::cerr << j.b1.cpos << " " << j.b2.cpos << " name " << ac.getContigName() << " ins " << j.insertion << std::endl; - out << std::string(j.b1.cpos, ' ') << "|" << std::string(j.b2.cpos-j.b1.cpos-1, ' ') << '|' << " " << ac.getContigName() << std::endl; + out << std::string(j.b1.cpos, ' ') << "|" << std::string(j.b2.cpos-j.b1.cpos-1, ' ') << '|' << " " << getContigName() << std::endl; } } - out << ac.getSequence() << " " << ac.getContigName() << std::endl; + out << getSequence() << " " << getContigName() << std::endl; PlottedReadVector plot_vec; // print out the individual reads - for (auto& i : ac.m_bamreads) { + for (auto& i : m_bamreads) { //std::string seq = i.QualitySequence(); std::string seq = i.Seq(); @@ -243,7 +245,7 @@ void AlignedContig::blacklist(SeqLib::GRC &grv) { assert(cnvec.size() == posvec.size()); size_t kk = 0; for (; kk < cnvec.size(); kk++) - if (cnvec[kk] == ac.getContigName()) { + if (cnvec[kk] == getContigName()) { pos = posvec[kk]; aln = alnvec[kk]; rc = rcvec[kk]; @@ -257,7 +259,7 @@ void AlignedContig::blacklist(SeqLib::GRC &grv) { */ // get the read to contig alignment information - r2c this_r2c = i.GetR2C(ac.getContigName()); + r2c this_r2c = i.GetR2C(getContigName()); int pos = this_r2c.start_on_contig; int aln = this_r2c.start_on_read; @@ -290,19 +292,19 @@ void AlignedContig::blacklist(SeqLib::GRC &grv) { seq.length() << " start " << aln << " length " << (seq.length() - aln) << std::endl; } - if ( (pos + seq.length() ) > ac.getSequence().length()) + if ( (pos + seq.length() ) > getSequence().length()) try { - seq = seq.substr(0, ac.getSequence().length() - pos); + seq = seq.substr(0, getSequence().length() - pos); } catch (...) { std::cerr << "AlignedContig::operator<< (2) error: substring out of bounds. seqlen " << - seq.length() << " start " << 0 << " pos " << pos << " ac.getSequence().length() " << - ac.getSequence().length() << std::endl; + seq.length() << " start " << 0 << " pos " << pos << " getSequence().length() " << + getSequence().length() << std::endl; } //assert(kk != cnvec.size()); // assure that we found something pos = abs(pos); - int padlen = ac.getSequence().size() - pos - seq.size() + 5; + int padlen = getSequence().size() - pos - seq.size() + 5; padlen = std::max(5, padlen); std::stringstream rstream; @@ -328,7 +330,7 @@ void AlignedContig::blacklist(SeqLib::GRC &grv) { } if (!found) { // didn't fit anywhere, so make a new line PlottedReadLine prl; - prl.contig_len = ac.getSequence().length(); + prl.contig_len = getSequence().length(); prl.addRead(&i); line_vec.push_back(prl); } @@ -336,9 +338,9 @@ void AlignedContig::blacklist(SeqLib::GRC &grv) { // plot the lines. Add contig identifier to each for (auto& i : line_vec) - out << i << " " << ac.getContigName() << std::endl; + out << i << " " << getContigName() << std::endl; - return out; + return out.str(); } void AlignedContig::setMultiMapBreakPairs() { diff --git a/src/svaba/AlignedContig.h b/src/svaba/AlignedContig.h index 0447035..ecb9cf9 100644 --- a/src/svaba/AlignedContig.h +++ b/src/svaba/AlignedContig.h @@ -72,7 +72,7 @@ class AlignedContig { std::string getSequence() const; //! print this contig - friend std::ostream& operator<<(std::ostream &out, const AlignedContig &ac); + std::string print(const SeqLib::BamHeader& h) const; // Return if this contig contains a potential variant (indel or multi-map) bool hasVariant() const; diff --git a/src/svaba/AlignmentFragment.cpp b/src/svaba/AlignmentFragment.cpp index 3606039..83290ea 100644 --- a/src/svaba/AlignmentFragment.cpp +++ b/src/svaba/AlignmentFragment.cpp @@ -77,14 +77,16 @@ AlignmentFragment::AlignmentFragment(const SeqLib::BamRecord &talign, bool flip) gbreak2 = m_align.PositionEnd(); } + // shouldn't hit either of the next two conditions if (break1 >= MAX_CONTIG_SIZE || break2 >= MAX_CONTIG_SIZE || break1 < 0 || break2 < 0) - std::cerr << " break1 " << break1 << " break2 " << break2 << " " << (*this) << std::endl; + std::cerr << " break1 " << break1 << " break2 " << break2 << " " << this->print() << std::endl; assert(break1 < MAX_CONTIG_SIZE); assert(break2 < MAX_CONTIG_SIZE); if (break1 < 0 || break2 < 0) { - std::cout << (*this) << std::endl; + std::cerr << "Negative breakpoint detected. Error?" << this->print() << std::endl; } + assert(break1 >= 0); assert(break2 >= 0); @@ -104,35 +106,36 @@ void AlignmentFragment::SetIndels(const AlignedContig * c) { } } - std::ostream& operator<<(std::ostream &out, const AlignmentFragment &c) { - - // sets the direction to print - char jsign = '>'; - if (c.m_align.ReverseFlag()) - jsign = '<'; - - // print the cigar value per base - for (auto& j : /*c.m_align.GetCigar()*/ c.m_cigar) { //c.align.CigarData) { // print releative to forward strand - if (j.Type() == 'M') - out << std::string(j.Length(), jsign); - else if (j.Type() == 'I') - out << std::string(j.Length(), 'I'); - else if (j.Type() == 'S' || j.Type() == 'H') - out << std::string(j.Length(), '.'); - } - - // print contig and genome breaks - out << "\tC[" << c.break1 << "," << c.break2 << "] G[" << c.gbreak1 << "," << c.gbreak2 << "]"; - - // add local info - std::string chr_name; - c.m_align.GetZTag("MC", chr_name); - if (!chr_name.length()) - chr_name = std::to_string(c.m_align.ChrID()+1); - out << "\tLocal: " << c.local << "\tAligned to: " << chr_name << ":" << c.m_align.Position() << "(" << (c.m_align.ReverseFlag() ? "-" : "+") << ") CIG: " << c.m_align.CigarString() << " MAPQ: " << c.m_align.MapQuality() << " SUBN " << c.sub_n; +std::string AlignmentFragment::print() const { - return out; + std::stringstream out; + // sets the direction to print + char jsign = '>'; + if (m_align.ReverseFlag()) + jsign = '<'; + + // print the cigar value per base + for (auto& j : /*m_align.GetCigar()*/ m_cigar) { //align.CigarData) { // print releative to forward strand + if (j.Type() == 'M') + out << std::string(j.Length(), jsign); + else if (j.Type() == 'I') + out << std::string(j.Length(), 'I'); + else if (j.Type() == 'S' || j.Type() == 'H') + out << std::string(j.Length(), '.'); } + + // print contig and genome breaks + out << "\tC[" << break1 << "," << break2 << "] G[" << gbreak1 << "," << gbreak2 << "]"; + + // add local info + std::string chr_name; + m_align.GetZTag("MC", chr_name); + if (!chr_name.length()) + chr_name = std::to_string(m_align.ChrID()+1); + out << "\tLocal: " << local << "\tAligned to: " << chr_name << ":" << m_align.Position() << "(" << (m_align.ReverseFlag() ? "-" : "+") << ") CIG: " << m_align.CigarString() << " MAPQ: " << m_align.MapQuality() << " SUBN " << sub_n; + + return out.str(); +} void AlignmentFragment::indelCigarMatches(const std::unordered_map& cmap) { @@ -162,7 +165,7 @@ void AlignmentFragment::indelCigarMatches(const std::unordered_mapprint() << std::endl; return false; } @@ -186,8 +189,8 @@ void AlignmentFragment::indelCigarMatches(const std::unordered_map= MIN_INDEL_MATCH_BRACKET); - bool post_match = (m_cigar[loc].Type() == 'M' && m_cigar[loc].Length() >= MIN_INDEL_MATCH_BRACKET); + bool prev_match = (m_cigar[loc-2].Type() == 'M'/* && m_cigar[loc-2].Length() >= MIN_INDEL_MATCH_BRACKET*/); + bool post_match = (m_cigar[loc].Type() == 'M'/* && m_cigar[loc].Length() >= MIN_INDEL_MATCH_BRACKET*/); if (loc > idx && prev_match && post_match) { // require 15M+ folowoing I/D idx = loc; break; diff --git a/src/svaba/AlignmentFragment.h b/src/svaba/AlignmentFragment.h index 4418bd4..115f9da 100644 --- a/src/svaba/AlignmentFragment.h +++ b/src/svaba/AlignmentFragment.h @@ -37,7 +37,7 @@ class AlignedContig; void indelCigarMatches(const std::unordered_map& cmap); // print the AlignmentFragment - friend std::ostream& operator<<(std::ostream &out, const AlignmentFragment& c); + std::string print() const; BreakEnd makeBreakEnd(bool left); diff --git a/src/svaba/BreakPoint.cpp b/src/svaba/BreakPoint.cpp index 05f1dce..cbd078b 100644 --- a/src/svaba/BreakPoint.cpp +++ b/src/svaba/BreakPoint.cpp @@ -533,17 +533,41 @@ BreakPoint::BreakPoint(const std::string &line, const SeqLib::BamHeader& h) { } */ -std::ostream& operator<<(std::ostream& out, const BreakPoint& b) { + + + +std::string BreakPoint::print(const SeqLib::BamHeader& h) const { + + std::stringstream out; + if (isindel) { + out << ">" << (insertion.size() ? "INS: " : "DEL: ") << getSpan() << " " << + b1.gr.ToString(h) << " " << cname << " " << evidence; + for (auto& i : allele) + out << " " << i.first << ":" << i.second.split; + } else { + out << ": " << b1.gr.PointString(h) << " to " << b2.gr.PointString(h) << " SPAN " << getSpan() << " " << cname + << " " << evidence; + for (auto& i : allele) + out << " " << i.first << ":" << i.second.split; + } - if (b.isindel) { - out << ">" << (b.insertion.size() ? "INS: " : "DEL: ") << b.getSpan() << " " << b.b1.gr << " " << b.cname << " " << b.evidence; - //<< " T/N split: " << b.t.split << "/" << b.n.split << " T/N cigar: " + return out.str(); + +} + + +/*std::ostream& operator<<(std::ostream& out, const BreakPoint& b) { + + if (b.isindel) { + out << ">" << (b.insertion.size() ? "INS: " : "DEL: ") << b.getSpan() << " " << + b.b1.gr << " " << b.cname << " " << b.evidence; + //<< " T/N split: " << b.t.split << "/" << b.n.split << " T/N cigar: " // << b.t.cigar << "/" << b.n.cigar << " T/N Cov " << b.t.cov << "/" << b.n.cov << " DBSNP: " << rs_t; for (auto& i : b.allele) out << " " << i.first << ":" << i.second.split; } else { out << ": " << b.b1.gr.PointString() << " to " << b.b2.gr.PointString() << " SPAN " << b.getSpan() << " " << b.cname << " " << b.evidence; - //<< " T/N split: " << b.t.split << "/" << b.n.split << " T/N disc: " + //<< " T/N split: " << b.t.split << "/" << b.n.split << " T/N disc: " // << b.dc.tcount << "/" << b.dc.ncount << " " << b.evidence; for (auto& i : b.allele) out << " " << i.first << ":" << i.second.split; @@ -551,7 +575,7 @@ std::ostream& operator<<(std::ostream& out, const BreakPoint& b) { return out; - } + }*/ void BreakPoint::checkBlacklist(GRC &grv) { if (grv.CountOverlaps(b1.gr) || grv.CountOverlaps(b2.gr)) @@ -1430,10 +1454,14 @@ ReducedBreakPoint::ReducedBreakPoint(const std::string &line, const SeqLib::BamH } - std::ostream& operator<<(std::ostream& out, const BreakEnd& b) { +std::string BreakEnd::print(const SeqLib::BamHeader& h) const { + return gr.ToString(h) + " - " + id + " mapq " + std::to_string(mapq) + " subn " + std::to_string(sub_n); +} + +/* std::ostream& operator<<(std::ostream& out, const BreakEnd& b) { out << b.gr << " - " << b.id << " mapq " << b.mapq << " subn " << b.sub_n << std::endl; return out; - } + }*/ std::ostream& operator<<(std::ostream& out, const SampleInfo& a) { out << " split: " << a.split << " cigar " << a.cigar << " alt " << a.alt << " cov " << a.cov << " disc " << a.disc; diff --git a/src/svaba/BreakPoint.h b/src/svaba/BreakPoint.h index a995273..295ed62 100644 --- a/src/svaba/BreakPoint.h +++ b/src/svaba/BreakPoint.h @@ -41,6 +41,8 @@ struct ReducedBreakEnd { void checkLocal(const SeqLib::GenomicRegion& window); + std::string print(const SeqLib::BamHeader& h) const; + std::string hash(int offset = 0) const; std::string id; @@ -61,7 +63,7 @@ struct ReducedBreakEnd { double as_frac= 0; bool local; - friend std::ostream& operator<<(std::ostream& out, const BreakEnd& b); + // friend std::ostream& operator<<(std::ostream& out, const BreakEnd& b); }; struct ReducedDiscordantCluster { @@ -101,6 +103,9 @@ struct ReducedBreakEnd { // define how to sort these bool operator<(const ReducedBreakPoint& bp) const; + // print it with the correct chromsome string + std::string print(const BreakPoint& b, const SeqLib::BamHeader& h) const; + ReducedBreakPoint() {} ~ReducedBreakPoint() { smart_check_free(ref); @@ -273,8 +278,7 @@ struct ReducedBreakEnd { * it lands on a repeat */ void repeatFilter(); - //int checkPon(const PONFilter * p); - + std::string print(const SeqLib::BamHeader& h) const; void __combine_with_discordant_cluster(DiscordantClusterMap& dmap); @@ -384,7 +388,7 @@ struct ReducedBreakEnd { return false; } - friend std::ostream& operator<<(std::ostream& out, const BreakPoint& bp); + // friend std::ostream& operator<<(std::ostream& out, const BreakPoint& bp); void score_dscrd(int min_dscrd_size); void score_assembly_only(); diff --git a/src/svaba/DiscordantCluster.cpp b/src/svaba/DiscordantCluster.cpp index 0a8fb3f..e27a1b1 100644 --- a/src/svaba/DiscordantCluster.cpp +++ b/src/svaba/DiscordantCluster.cpp @@ -62,11 +62,10 @@ using namespace SeqLib; // accept as discordant if not FR, has large enough isize, is inter-chromosomal, // and has both mates mapping. Also dont cluster on weird chr if ( ( r.PairOrientation() != FRORIENTATION || r.FullInsertSize() >= cutoff || r.Interchromosomal()) && - r.PairMappedFlag() && r.ChrID() < 24 && r.MateChrID() < 24 && + r.PairMappedFlag() /* && r.ChrID() < 24 && r.MateChrID() < 24 */ && r.NumMatchBases() > r.NumHardClip()) // has to have mostly not-hardclip bav_dd.push_back(r); } - if (!bav_dd.size()) return DiscordantClusterMap(); From 40ff15da9f9cc5de16ea31a69a7e618c08c19945 Mon Sep 17 00:00:00 2001 From: walaj Date: Tue, 22 Jan 2019 23:26:46 -0500 Subject: [PATCH 2/6] compile fix --- src/svaba/run_svaba.cpp | 14 +++++++------- src/svaba/svabaBamWalker.cpp | 2 +- src/svaba/vcf.cpp | 18 +++++++++--------- 3 files changed, 17 insertions(+), 17 deletions(-) diff --git a/src/svaba/run_svaba.cpp b/src/svaba/run_svaba.cpp index b8e751e..d72bb1b 100644 --- a/src/svaba/run_svaba.cpp +++ b/src/svaba/run_svaba.cpp @@ -842,7 +842,7 @@ void parseRunOptions(int argc, char** argv) { bool runWorkItem(const SeqLib::GenomicRegion& region, svabaThreadUnit& wu, long unsigned int thread_id) { - WRITELOG("Running region " + region.ToString() + " on thread " + std::to_string(thread_id), opt::verbose > 1, true); + WRITELOG("Running region " + region.ToString(bwa_header) + " on thread " + std::to_string(thread_id), opt::verbose > 1, true); for (auto& w : wu.walkers) set_walker_params(w.second); @@ -969,15 +969,15 @@ bool runWorkItem(const SeqLib::GenomicRegion& region, svabaThreadUnit& wu, long // check that we don't have too many reads if (bav_this.size() > (size_t)(region.Width() * 20) && region.Width() > 20000) { std::stringstream ssss; - WRITELOG("TOO MANY READS IN REGION " + SeqLib::AddCommas(bav_this.size()) + "\t" + region.ToString(), opt::verbose, false); + WRITELOG("TOO MANY READS IN REGION " + SeqLib::AddCommas(bav_this.size()) + "\t" + region.ToString(bwa_header), opt::verbose, false); goto afterassembly; } // print message about assemblies if (bav_this.size() > 1) { - WRITELOG("Doing assemblies on " + region.ToString(), opt::verbose > 1, false); + WRITELOG("Doing assemblies on " + region.ToString(bwa_header), opt::verbose > 1, false); } else if (bav_this.size() < 3) { - WRITELOG("Skipping assembly (<= 2 reads) on " + region.ToString(), opt::verbose > 1, false); + WRITELOG("Skipping assembly (<= 2 reads) on " + region.ToString(bwa_header), opt::verbose > 1, false); goto afterassembly; } @@ -1457,7 +1457,7 @@ CountPair run_mate_collection_loop(const SeqLib::GenomicRegion& region, WalkerMa // print out to log for (auto& i : somatic_mate_regions) - WRITELOG("...mate region " + i.ToString() + " case read count that triggered lookup: " + + WRITELOG("...mate region " + i.ToString(bwa_header) + " case read count that triggered lookup: " + std::to_string(i.count) + " on mate-lookup round " + std::to_string(jjj+1), opt::verbose > 1, true); // collect the reads for this round @@ -1563,7 +1563,7 @@ void run_assembly(const SeqLib::GenomicRegion& region, svabaReadVector& bav_this try { lregion = refg->QueryRegion(bwa_header.IDtoName(region.chr), region.pos1, region.pos2); } catch (...) { - WRITELOG(" Caught exception for lregion with reg " + region.ToString(), true, true); + WRITELOG(" Caught exception for lregion with reg " + region.ToString(bwa_header), true, true); lregion = ""; } } @@ -1820,7 +1820,7 @@ void WriteFilesOut(svabaThreadUnit& wu) { // print the alignment plots for (const auto& i : wu.m_alc) if (i.hasVariant()) - all_align << i << std::endl; + all_align << i.print(bwa_header) << std::endl; // send the microbe to file for (const auto& b : wu.m_vir_contigs) diff --git a/src/svaba/svabaBamWalker.cpp b/src/svaba/svabaBamWalker.cpp index 4fd38cd..9d56cd8 100644 --- a/src/svaba/svabaBamWalker.cpp +++ b/src/svaba/svabaBamWalker.cpp @@ -130,7 +130,7 @@ SeqLib::GRC svabaBamWalker::readBam(std::ofstream * log) { std::stringstream ss; ss << "\tstopping read lookup at " << r.Brief() << " in window " - << (m_region.size() ? m_region[tb->m_region_idx].ToString() : " whole BAM") + << (m_region.size() ? m_region[tb->m_region_idx].ToString(tb->GetHeader()) : " whole BAM") << " with " << SeqLib::AddCommas(this_reads.size()) << " weird reads. Limit: " << SeqLib::AddCommas(m_limit) << std::endl; if (log) diff --git a/src/svaba/vcf.cpp b/src/svaba/vcf.cpp index 8f4689b..adef177 100644 --- a/src/svaba/vcf.cpp +++ b/src/svaba/vcf.cpp @@ -34,7 +34,7 @@ void __write_to_zip_vcf(const VCFEntry& v, BGZF * f) { } // forward declare -void tabixVcf(const std::string &fn); +//void tabixVcf(const std::string &fn); // comparator for info fields // lhs < rhs @@ -567,9 +567,9 @@ void VCFFile::writeIndels(string basename, bool zip, bool onefile) const { if (zip) { // tabix it - tabixVcf(gname); - if (!onefile) - tabixVcf(sname); + //tabixVcf(gname); + //if (!onefile) + // tabixVcf(sname); } } @@ -666,16 +666,16 @@ void VCFFile::writeSVs(std::string basename, bool zip, bool onefile) const { // tabix it if (zip) { - if (!onefile) - tabixVcf(sname); - tabixVcf(gname); + //if (!onefile) + //tabixVcf(sname); + //tabixVcf(gname); } } // tabix the vcf -void tabixVcf(const std::string &fn) { +/*void tabixVcf(const std::string &fn) { // tabix it tbx_conf_t conf = tbx_conf_gff; @@ -684,7 +684,7 @@ void tabixVcf(const std::string &fn) { if ( tbx_index_build(fn.c_str(), 0, &conf) ) cerr << "tbx_index_build failed: " << fn << endl; -} + }*/ VCFEntryPair::VCFEntryPair(std::shared_ptr& b) { From deb83df7f2a9ec3ec134c0ff3e15a206388d3df9 Mon Sep 17 00:00:00 2001 From: walaj Date: Fri, 1 Mar 2019 10:32:41 -0500 Subject: [PATCH 3/6] added reference genome checking. Fixed discordant printing --- src/svaba/AlignedContig.cpp | 8 ++--- src/svaba/AlignedContig.h | 2 +- src/svaba/BreakPoint.cpp | 10 +++--- src/svaba/BreakPoint.h | 2 +- src/svaba/DiscordantCluster.cpp | 35 +++++++++---------- src/svaba/DiscordantCluster.h | 9 +++-- src/svaba/run_svaba.cpp | 62 ++++++++++++++++++++++++++++----- src/svaba/svaba.cpp | 6 ++-- 8 files changed, 90 insertions(+), 44 deletions(-) diff --git a/src/svaba/AlignedContig.cpp b/src/svaba/AlignedContig.cpp index 523387b..e889e46 100644 --- a/src/svaba/AlignedContig.cpp +++ b/src/svaba/AlignedContig.cpp @@ -197,7 +197,7 @@ std::string AlignedContig::print(const SeqLib::BamHeader& h) const { // print the AlignmentFragments alignments for (auto& i : m_frag_v) - out << i.print() << " Disc: " << printDiscordantClusters() << " -- " << getContigName() << std::endl; + out << i.print() << " Disc: " << printDiscordantClusters(h) << " -- " << getContigName() << std::endl; bool draw_divider = true; for (auto& i : m_frag_v) { for (auto& j : i.secondaries) { @@ -205,7 +205,7 @@ std::string AlignedContig::print(const SeqLib::BamHeader& h) const { out << std::string(m_seq.length(), 'S') << std::endl; draw_divider = false; } - out << j.print() << " Disc: " << printDiscordantClusters() << " -- " << getContigName() << std::endl; + out << j.print() << " Disc: " << printDiscordantClusters(h) << " -- " << getContigName() << std::endl; } } @@ -460,14 +460,14 @@ std::string AlignedContig::print(const SeqLib::BamHeader& h) const { } - std::string AlignedContig::printDiscordantClusters() const { +std::string AlignedContig::printDiscordantClusters(const SeqLib::BamHeader& h) const { std::stringstream out; if (m_dc.size() == 0) return "none"; for (std::vector::const_iterator it = m_dc.begin(); it != m_dc.end(); it++) - out << *it << " "; + out << it->print(h) << " "; return out.str(); } diff --git a/src/svaba/AlignedContig.h b/src/svaba/AlignedContig.h index ecb9cf9..fbb28e3 100644 --- a/src/svaba/AlignedContig.h +++ b/src/svaba/AlignedContig.h @@ -42,7 +42,7 @@ class AlignedContig { // Loop through the vector of DiscordantCluster objects // associated with this contig and print - std::string printDiscordantClusters() const; + std::string printDiscordantClusters(const SeqLib::BamHeader& h) const; // return the name of the contig std::string getContigName() const; diff --git a/src/svaba/BreakPoint.cpp b/src/svaba/BreakPoint.cpp index cbd078b..5fbcc25 100644 --- a/src/svaba/BreakPoint.cpp +++ b/src/svaba/BreakPoint.cpp @@ -108,9 +108,9 @@ using namespace SeqLib; } - // make a breakpoint from a discordant cluster +// make a breakpoint from a discordant cluster BreakPoint::BreakPoint(DiscordantCluster& tdc, const BWAWrapper * bwa, DiscordantClusterMap& dmap, - const GenomicRegion& region) { + const GenomicRegion& region, const SeqLib::BamHeader& h) { num_align = 0; dc = tdc; @@ -123,7 +123,7 @@ BreakPoint::BreakPoint(DiscordantCluster& tdc, const BWAWrapper * bwa, Discordan chr_name1 = bwa->ChrIDToName(dc.m_reg1.chr); //bwa->ChrIDToName(tdc.reads.begin()->second.ChrID()); chr_name2 = bwa->ChrIDToName(dc.m_reg2.chr); //bwa->ChrIDToName(tdc.reads.begin()->second.ChrID()); } catch (...) { - std::cerr << "Warning: Found mismatch between reference genome and BAM genome for discordant cluster " << dc << std::endl; + std::cerr << "Warning: Found mismatch between reference genome and BAM genome for discordant cluster " << dc.print(h) << std::endl; chr_name1 = "Unknown"; chr_name2 = "Unknown"; } @@ -162,8 +162,8 @@ BreakPoint::BreakPoint(DiscordantCluster& tdc, const BWAWrapper * bwa, Discordan //i.second.alt = i.second.disc; } - // give a unique id - cname = dc.toRegionString() + "__" + std::to_string(region.chr+1) + "_" + std::to_string(region.pos1) + + // give a unique id (OK to give an empty header here, since used internally) + cname = dc.toRegionString(h) + "__" + std::to_string(region.chr+1) + "_" + std::to_string(region.pos1) + "_" + std::to_string(region.pos2) + "D"; // check if another cluster overlaps, but different strands diff --git a/src/svaba/BreakPoint.h b/src/svaba/BreakPoint.h index 295ed62..cda578f 100644 --- a/src/svaba/BreakPoint.h +++ b/src/svaba/BreakPoint.h @@ -262,7 +262,7 @@ struct ReducedBreakEnd { /** Construct a breakpoint from a cluster of discordant reads */ BreakPoint(DiscordantCluster& tdc, const SeqLib::BWAWrapper * bwa, DiscordantClusterMap& dmap, - const SeqLib::GenomicRegion& region); + const SeqLib::GenomicRegion& region, const SeqLib::BamHeader& h); BreakPoint() {} diff --git a/src/svaba/DiscordantCluster.cpp b/src/svaba/DiscordantCluster.cpp index e27a1b1..c7d188c 100644 --- a/src/svaba/DiscordantCluster.cpp +++ b/src/svaba/DiscordantCluster.cpp @@ -403,25 +403,25 @@ using namespace SeqLib; return mean; } - std::string DiscordantCluster::toRegionString() const +std::string DiscordantCluster::toRegionString(const SeqLib::BamHeader& h) const { int pos1 = (m_reg1.strand == '+') ? m_reg1.pos2 : m_reg1.pos1; int pos2 = (m_reg2.strand == '+') ? m_reg2.pos2 : m_reg2.pos1; std::stringstream ss; - ss << (m_reg1.chr+1) << ":" << pos1 << "(" << m_reg1.strand << ")" << "-" << - (m_reg2.chr+1) << ":" << pos2 << "(" << m_reg2.strand << ")"; + ss << h.IDtoName(m_reg1.chr) << ":" << pos1 << "(" << m_reg1.strand << ")" << "-" << + h.IDtoName(m_reg2.chr) << ":" << pos2 << "(" << m_reg2.strand << ")"; return ss.str(); } - // define how to print this to stdout - std::ostream& operator<<(std::ostream& out, const DiscordantCluster& dc) - { - out << dc.toRegionString() << " Tcount: " << dc.tcount << - " Ncount: " << dc.ncount << " Mean MAPQ: " - << dc.mapq1 << " Mean Mate MAPQ: " << dc.mapq2 << " Valid: " << (dc.valid() ? "TRUE" : "FALSE"); - return out; +// define how to print this +std::string DiscordantCluster::print(const SeqLib::BamHeader& h) const { + std::stringstream ss; + ss << toRegionString(h) << " Tcount: " << tcount << + " Ncount: " << ncount << " Mean MAPQ: " + << mapq1 << " Mean Mate MAPQ: " << mapq2 << " Valid: " << (valid() ? "TRUE" : "FALSE"); + return ss.str(); } bool DiscordantCluster::valid() const { @@ -444,15 +444,13 @@ using namespace SeqLib; // define how to print to file - std::string DiscordantCluster::toFileString(bool with_read_names /* false */) const - { + std::string DiscordantCluster::toFileString(const SeqLib::BamHeader& h, bool with_read_names) const { std::string sep = "\t"; // add the reads names (currently off) std::string reads_string; - if (with_read_names) - { + if (with_read_names) { std::unordered_set qnset; for (auto& i : reads) @@ -463,8 +461,7 @@ using namespace SeqLib; qnset.insert(i.second.Qname()); reads_string += tmp + ","; } - for (auto& i : mates) - { + for (auto& i : mates) { if (qnset.count(i.second.Qname())) continue; std::string tmp = i.second.SR(); @@ -483,11 +480,11 @@ using namespace SeqLib; int pos2 = m_reg2.strand == '+' ? m_reg2.pos2 : m_reg2.pos1; std::stringstream out; - out << m_reg1.chr+1 << sep << pos1 << sep << m_reg1.strand << sep - << m_reg2.chr+1 << sep << pos2 << sep << m_reg2.strand << sep + out << h.IDtoName(m_reg1.chr) << sep << pos1 << sep << m_reg1.strand << sep + << h.IDtoName(m_reg2.chr) << sep << pos2 << sep << m_reg2.strand << sep << tcount << sep << ncount << sep << tcount_hq << sep << ncount_hq << sep << mapq1 << sep - << mapq2 << sep << (m_contig.length() ? m_contig : "x") << sep << toRegionString() + << mapq2 << sep << (m_contig.length() ? m_contig : "x") << sep << toRegionString(h) << sep << (reads_string.length() ? reads_string : "x"); return (out.str()); diff --git a/src/svaba/DiscordantCluster.h b/src/svaba/DiscordantCluster.h index 88a88aa..d8ab7ce 100644 --- a/src/svaba/DiscordantCluster.h +++ b/src/svaba/DiscordantCluster.h @@ -48,16 +48,19 @@ typedef std::vector svabaReadClusterVector; void addMateReads(const svabaReadVector& bav); /** Return the discordant cluster as a string with just coordinates */ - std::string toRegionString() const; + std::string toRegionString(const SeqLib::BamHeader& h) const; /** Return the ID associated with this cluster */ std::string ID() const { return m_id; } /** Print this with region string and read counts and mapq */ - friend std::ostream& operator<<(std::ostream& out, const DiscordantCluster& dc); + //friend std::ostream& operator<<(std::ostream& out, const DiscordantCluster& dc); + + /** Print this with region string and read counts and mapq */ + std::string print(const SeqLib::BamHeader& h) const; /** Return as a string for writing to a file */ - std::string toFileString(bool with_read_names = false) const; + std::string toFileString(const SeqLib::BamHeader& h, bool with_read_names) const; /** Sort by coordinate */ bool operator < (const DiscordantCluster& b) const; diff --git a/src/svaba/run_svaba.cpp b/src/svaba/run_svaba.cpp index d72bb1b..a56d3ce 100644 --- a/src/svaba/run_svaba.cpp +++ b/src/svaba/run_svaba.cpp @@ -154,6 +154,10 @@ namespace opt { static double lod_somatic_db = 10; // same, but at DBSNP (want higher bc we have prior that its germline) static double scale_error = 1; // how much to emphasize erorrs. 1 is standard. 0 is assume no errors + // input options + static bool override_reference_check = false; // allow the user, with caution, to use two different reference genomes + // (one for BAM alignment, one as ref for svaba) + } enum { @@ -182,7 +186,8 @@ enum { OPT_CLIP3, OPT_GERMLINE, OPT_SCALE_ERRORS, - OPT_NO_UNFILTERED + OPT_NO_UNFILTERED, + OPT_OVERRIDE_REFERENCE_CHECK }; static const char* shortopts = "hzIAt:n:p:v:r:G:e:k:c:a:m:B:D:Y:S:L:s:V:R:K:E:C:x:M:"; @@ -239,6 +244,7 @@ static const struct option longopts[] = { { "max-reads", required_argument, NULL, 'x' }, { "max-reads-mate-region", required_argument, NULL, 'M' }, { "num-assembly-rounds", required_argument, NULL, OPT_NUM_ASSEMBLY_ROUNDS }, + { "override-reference-check",no_argument, NULL, OPT_OVERRIDE_REFERENCE_CHECK}, { NULL, 0, NULL, 0 } }; @@ -275,6 +281,7 @@ static const char *RUN_USAGE_MESSAGE = " --num-assembly-rounds Run assembler multiple times. > 1 will bootstrap the assembly. [2]\n" " --num-to-sample When learning about inputs, number of reads to sample. [2,000,000]\n" " --hp Highly parallel. Don't write output until completely done. More memory, but avoids all thread-locks.\n" +" --override-reference-check With much caution, allows user to run svaba with different reference genomes for BAMs and -G\n" " Output options\n" " -z, --g-zip Gzip and tabix the output VCF files. [off]\n" " -A, --all-contigs Output all contigs that were assembled, regardless of mapping or length. [off]\n" @@ -333,8 +340,8 @@ void runsvaba(int argc, char** argv) { std::cerr << "-----------------------------------------------------------" << std::endl << - "--- Running svaba SV and indel detection on " << SeqLib::AddCommas(opt::numThreads) << - " threads --" <<(opt::numThreads >= 10 ? "" : "-") << std::endl << + "--- Running svaba SV and indel detection on " << SeqLib::AddCommas(opt::numThreads) << + " threads ---" <<(opt::numThreads >= 10 ? "" : "-") << std::endl << "--- (inspect *.log for real-time progress updates) ---" << std::endl << "-----------------------------------------------------------" << std::endl; @@ -407,7 +414,7 @@ void runsvaba(int argc, char** argv) { std::cerr << "ERROR: empty header in main bam file" << std::endl; exit(EXIT_FAILURE); } - + // open some writer bams if (opt::write_extracted_reads) // open the extracted reads writer svabaUtils::__openWriterBam(b_header, opt::analysis_id + ".extracted.reads.bam", er_writer); @@ -531,13 +538,51 @@ void runsvaba(int argc, char** argv) { std::cerr << "ERROR: Unable to open index file: " << opt::refgenome << std::endl; exit(EXIT_FAILURE); } + + // check that the two headers are equivalant + if (opt::override_reference_check) { + WRITELOG("!!! Will NOT perform check of reference compatability with BAM.\n!!! Only if *sure* that reference and BAM have same chr in same order.", true, true); + } else { + bool trigger_explain = false; + if (b_header.NumSequences() != bwa_header.NumSequences()) { + trigger_explain = true; + std::stringstream ss; + ss << "!!!!!!!!!!! WARNING !!!!!!!!!!!" << std::endl + << "!!!!!! Number of sequences in BAM header mismatches reference" << std::endl + << "!!!!!! BAM: " << b_header.NumSequences() << " -- Ref: " << bwa_header.NumSequences(); + WRITELOG(ss.str(), true, true); + } + + // check that the two headers are equivalant + for (int i = 0; i < std::min(b_header.NumSequences(), bwa_header.NumSequences()); ++i) { + if (b_header.IDtoName(i) != bwa_header.IDtoName(i)) { + trigger_explain = true; + std::stringstream ss; + ss << "!!!!!! BAM sequence id " << i << ": \"" << b_header.IDtoName(i) << "\"" + << " -- Ref sequence id " << i << ": \"" << bwa_header.IDtoName(i) << "\""; + WRITELOG(ss.str(), true, true); + } + } + if (trigger_explain) { + std::stringstream ss; + ss << "!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!" << std::endl + << "!!! SvABA is being run with different reference genome than the reads were mapped to." << std::endl + << "!!! This can cause a massive failure in variant detection!" << std::endl + << "!!! If you are *sure* that the two references are functionally equivalent (e.g. chr1 vs 1)" << std::endl + << "!!! and that the order of the chromosomes is equivalent between the two," << std::endl + << "!!! you can override this error with option \"--override-reference-check\"" << std::endl + << "!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!"; + WRITELOG(ss.str(), true, true); + exit(EXIT_FAILURE); + } + } if (num_jobs) { WRITELOG("...running on " + SeqLib::AddCommas(num_jobs) + " chunks", opt::verbose, true); } else { WRITELOG("Chunk was <= 0: READING IN WHOLE GENOME AT ONCE", opt::verbose, true); } - + // loop through and construct the readgroup rules std::stringstream ss_rules; std::unordered_set rg_seen; @@ -748,6 +793,7 @@ void parseRunOptions(int argc, char** argv) { case 'z': opt::zip = true; break; case 'h': help = true; break; case OPT_GAP_OPEN : arg >> opt::bwa::gap_open_penalty; break; + case OPT_OVERRIDE_REFERENCE_CHECK : opt::override_reference_check = true; break; case 'x' : arg >> opt::max_reads_per_assembly; break; case 'M' : arg >> opt::mate_region_lookup_limit; break; case 'A' : opt::all_contigs = true; break; @@ -948,7 +994,7 @@ bool runWorkItem(const SeqLib::GenomicRegion& region, svabaThreadUnit& wu, long // print out results if (opt::verbose > 3) for (auto& i : dmap) - WRITELOG(i.first + " " + i.second.toFileString(false), true, false); + WRITELOG(i.first + " " + i.second.toFileString(b_header, false), true, false); afterdiscclustering: @@ -1059,7 +1105,7 @@ bool runWorkItem(const SeqLib::GenomicRegion& region, svabaThreadUnit& wu, long // DiscordantCluster not associated with assembly BP and has 2+ read support if (!i.second.hasAssociatedAssemblyContig() && (i.second.tcount + i.second.ncount) >= MIN_DSCRD_READS_DSCRD_ONLY && i.second.valid() && !below_size) { - BreakPoint tmpbp(i.second, main_bwa, dmap, region); + BreakPoint tmpbp(i.second, main_bwa, dmap, region, b_header); bp_glob.push_back(tmpbp); } } @@ -1829,7 +1875,7 @@ void WriteFilesOut(svabaThreadUnit& wu) { // send the discordant to file for (auto& i : wu.m_disc) if (i.second.valid()) //std::max(i.second.mapq1, i.second.mapq2) >= 5) - os_discordant << i.second.toFileString(opt::read_tracking) << std::endl; + os_discordant << i.second.toFileString(b_header, opt::read_tracking) << std::endl; // write ALL contigs if (opt::verbose > 2) diff --git a/src/svaba/svaba.cpp b/src/svaba/svaba.cpp index 39204ca..bb7b1a9 100644 --- a/src/svaba/svaba.cpp +++ b/src/svaba/svaba.cpp @@ -16,11 +16,11 @@ static const char *SVABA_USAGE_MESSAGE = "------------------------------------------------------------\n" -"--- SvABA (sah-bah) - SV and indel detection by assembly ---\n" +"-------- SvABA - SV and indel detection by assembly --------\n" "------------------------------------------------------------\n" "Program: SvABA \n" -"FH Version: 134 \n" -"Contact: Jeremiah Wala [ jwala@broadinstitute.org ]\n" +"Version: 1.0.1 \n" +"Contact: Jeremiah Wala [ jeremiah.wala@gmail.org ]\n" "Usage: svaba [options]\n\n" "Commands:\n" " run Run SvABA SV and Indel detection on BAM(s)\n" From 5674c8c144473a299496d495e42f282134d50701 Mon Sep 17 00:00:00 2001 From: Jeremiah Wala Date: Fri, 1 Mar 2019 11:16:00 -0500 Subject: [PATCH 4/6] updated compilation --- Makefile.in | 23 ++-- autogen.sh | 2 +- configure | 193 ++++++++++++++++---------------- configure.ac | 2 +- src/SGA/Algorithm/Makefile.in | 72 +++++++----- src/SGA/Bigraph/Makefile.in | 67 +++++++---- src/SGA/SGA/Makefile.in | 52 +++++---- src/SGA/SQG/Makefile.in | 57 ++++++---- src/SGA/StringGraph/Makefile.in | 83 +++++++++----- src/SGA/SuffixTools/Makefile.in | 142 ++++++++++++++++------- src/SGA/Util/Makefile.in | 152 ++++++++++++++++++------- src/svaba/Makefile.in | 134 ++++++++++++++++------ 12 files changed, 640 insertions(+), 339 deletions(-) diff --git a/Makefile.in b/Makefile.in index 7868aef..052768e 100644 --- a/Makefile.in +++ b/Makefile.in @@ -1,7 +1,7 @@ -# Makefile.in generated by automake 1.15 from Makefile.am. +# Makefile.in generated by automake 1.16.1 from Makefile.am. # @configure_input@ -# Copyright (C) 1994-2014 Free Software Foundation, Inc. +# Copyright (C) 1994-2018 Free Software Foundation, Inc. # This Makefile.in is free software; the Free Software Foundation # gives unlimited permission to copy and/or distribute it, @@ -132,7 +132,7 @@ am__recursive_targets = \ $(RECURSIVE_CLEAN_TARGETS) \ $(am__extra_recursive_targets) AM_RECURSIVE_TARGETS = $(am__recursive_targets:-recursive=) TAGS CTAGS \ - cscope distdir dist dist-all distcheck + cscope distdir distdir-am dist dist-all distcheck am__tagged_files = $(HEADERS) $(SOURCES) $(TAGS_FILES) \ $(LISP)config.h.in # Read a list of newline-separated strings from the standard input, @@ -320,8 +320,8 @@ Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status echo ' $(SHELL) ./config.status'; \ $(SHELL) ./config.status;; \ *) \ - echo ' cd $(top_builddir) && $(SHELL) ./config.status $@ $(am__depfiles_maybe)'; \ - cd $(top_builddir) && $(SHELL) ./config.status $@ $(am__depfiles_maybe);; \ + echo ' cd $(top_builddir) && $(SHELL) ./config.status $@ $(am__maybe_remake_depfiles)'; \ + cd $(top_builddir) && $(SHELL) ./config.status $@ $(am__maybe_remake_depfiles);; \ esac; $(top_builddir)/config.status: $(top_srcdir)/configure $(CONFIG_STATUS_DEPENDENCIES) @@ -454,7 +454,10 @@ distclean-tags: -rm -f TAGS ID GTAGS GRTAGS GSYMS GPATH tags -rm -f cscope.out cscope.in.out cscope.po.out cscope.files -distdir: $(DISTFILES) +distdir: $(BUILT_SOURCES) + $(MAKE) $(AM_MAKEFLAGS) distdir-am + +distdir-am: $(DISTFILES) $(am__remove_distdir) test -d "$(distdir)" || mkdir "$(distdir)" @srcdirstrip=`echo "$(srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \ @@ -519,7 +522,7 @@ distdir: $(DISTFILES) ! -type d ! -perm -444 -exec $(install_sh) -c -m a+r {} {} \; \ || chmod -R a+r "$(distdir)" dist-gzip: distdir - tardir=$(distdir) && $(am__tar) | GZIP=$(GZIP_ENV) gzip -c >$(distdir).tar.gz + tardir=$(distdir) && $(am__tar) | eval GZIP= gzip $(GZIP_ENV) -c >$(distdir).tar.gz $(am__post_remove_distdir) dist-bzip2: distdir @@ -545,7 +548,7 @@ dist-shar: distdir @echo WARNING: "Support for shar distribution archives is" \ "deprecated." >&2 @echo WARNING: "It will be removed altogether in Automake 2.0" >&2 - shar $(distdir) | GZIP=$(GZIP_ENV) gzip -c >$(distdir).shar.gz + shar $(distdir) | eval GZIP= gzip $(GZIP_ENV) -c >$(distdir).shar.gz $(am__post_remove_distdir) dist-zip: distdir @@ -563,7 +566,7 @@ dist dist-all: distcheck: dist case '$(DIST_ARCHIVES)' in \ *.tar.gz*) \ - GZIP=$(GZIP_ENV) gzip -dc $(distdir).tar.gz | $(am__untar) ;;\ + eval GZIP= gzip $(GZIP_ENV) -dc $(distdir).tar.gz | $(am__untar) ;;\ *.tar.bz2*) \ bzip2 -dc $(distdir).tar.bz2 | $(am__untar) ;;\ *.tar.lz*) \ @@ -573,7 +576,7 @@ distcheck: dist *.tar.Z*) \ uncompress -c $(distdir).tar.Z | $(am__untar) ;;\ *.shar.gz*) \ - GZIP=$(GZIP_ENV) gzip -dc $(distdir).shar.gz | unshar ;;\ + eval GZIP= gzip $(GZIP_ENV) -dc $(distdir).shar.gz | unshar ;;\ *.zip*) \ unzip $(distdir).zip ;;\ esac diff --git a/autogen.sh b/autogen.sh index 11a278c..27f7750 100755 --- a/autogen.sh +++ b/autogen.sh @@ -4,4 +4,4 @@ set -ex aclocal autoconf autoheader -automake -a +automake --add-missing --copy diff --git a/configure b/configure index e13b3a8..81e9889 100755 --- a/configure +++ b/configure @@ -644,7 +644,6 @@ am__nodep AMDEPBACKSLASH AMDEP_FALSE AMDEP_TRUE -am__quote am__include DEPDIR OBJEXT @@ -721,7 +720,8 @@ PACKAGE_VERSION PACKAGE_TARNAME PACKAGE_NAME PATH_SEPARATOR -SHELL' +SHELL +am__quote' ac_subst_files='' ac_user_opts=' enable_option_checking @@ -2134,7 +2134,7 @@ ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $ ac_compiler_gnu=$ac_cv_c_compiler_gnu -am__api_version='1.15' +am__api_version='1.16' ac_aux_dir= for ac_dir in "$srcdir" "$srcdir/.." "$srcdir/../.."; do @@ -2679,8 +2679,8 @@ MAKEINFO=${MAKEINFO-"${am_missing_run}makeinfo"} # For better backward compatibility. To be removed once Automake 1.9.x # dies out for good. For more background, see: -# -# +# +# mkdir_p='$(MKDIR_P)' # We need awk for the "check" target (and possibly the TAP driver). The @@ -2731,7 +2731,7 @@ END Aborting the configuration process, to ensure you take notice of the issue. You can download and install GNU coreutils to get an 'rm' implementation -that behaves properly: . +that behaves properly: . If you want to complete the configuration process using your problematic 'rm' anyway, export the environment variable ACCEPT_INFERIOR_RM_PROGRAM @@ -3281,45 +3281,45 @@ DEPDIR="${am__leading_dot}deps" ac_config_commands="$ac_config_commands depfiles" - -am_make=${MAKE-make} -cat > confinc << 'END' +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether ${MAKE-make} supports the include directive" >&5 +$as_echo_n "checking whether ${MAKE-make} supports the include directive... " >&6; } +cat > confinc.mk << 'END' am__doit: - @echo this is the am__doit target + @echo this is the am__doit target >confinc.out .PHONY: am__doit END -# If we don't find an include directive, just comment out the code. -{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for style of include used by $am_make" >&5 -$as_echo_n "checking for style of include used by $am_make... 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Let's play safe and only enable the eval # if we detect the quoting. - case $CONFIG_FILES in - *\'*) eval set x "$CONFIG_FILES" ;; - *) set x $CONFIG_FILES ;; - esac + # TODO: see whether this extra hack can be removed once we start + # requiring Autoconf 2.70 or later. + case $CONFIG_FILES in #( + *\'*) : + eval set x "$CONFIG_FILES" ;; #( + *) : + set x $CONFIG_FILES ;; #( + *) : + ;; +esac shift - for mf + # Used to flag and report bootstrapping failures. + am_rc=0 + for am_mf do # Strip MF so we end up with the name of the file. - mf=`echo "$mf" | sed -e 's/:.*$//'` - # Check whether this is an Automake generated Makefile or not. - # We used to match only the files named 'Makefile.in', but - # some people rename them; so instead we look at the file content. - # Grep'ing the first line is not enough: some people post-process - # each Makefile.in and add a new line on top of each file to say so. - # Grep'ing the whole file is not good either: AIX grep has a line + am_mf=`$as_echo "$am_mf" | sed -e 's/:.*$//'` + # Check whether this is an Automake generated Makefile which includes + # dependency-tracking related rules and includes. + # Grep'ing the whole file directly is not great: AIX grep has a line # limit of 2048, but all sed's we know have understand at least 4000. - if sed -n 's,^#.*generated by automake.*,X,p' "$mf" | grep X >/dev/null 2>&1; then - dirpart=`$as_dirname -- "$mf" || -$as_expr X"$mf" : 'X\(.*[^/]\)//*[^/][^/]*/*$' \| \ - X"$mf" : 'X\(//\)[^/]' \| \ - X"$mf" : 'X\(//\)$' \| \ - X"$mf" : 'X\(/\)' \| . 2>/dev/null || -$as_echo X"$mf" | + sed -n 's,^am--depfiles:.*,X,p' "$am_mf" | grep X >/dev/null 2>&1 \ + || continue + am_dirpart=`$as_dirname -- "$am_mf" || +$as_expr X"$am_mf" : 'X\(.*[^/]\)//*[^/][^/]*/*$' \| \ + X"$am_mf" : 'X\(//\)[^/]' \| \ + X"$am_mf" : 'X\(//\)$' \| \ + X"$am_mf" : 'X\(/\)' \| . 2>/dev/null || +$as_echo X"$am_mf" | sed '/^X\(.*[^/]\)\/\/*[^/][^/]*\/*$/{ s//\1/ q @@ -6258,53 +6264,48 @@ $as_echo X"$mf" | q } s/.*/./; q'` - else - continue - fi - # Extract the definition of DEPDIR, am__include, and am__quote - # from the Makefile without running 'make'. - DEPDIR=`sed -n 's/^DEPDIR = //p' < "$mf"` - test -z "$DEPDIR" && continue - am__include=`sed -n 's/^am__include = //p' < "$mf"` - test -z "$am__include" && continue - am__quote=`sed -n 's/^am__quote = //p' < "$mf"` - # Find all dependency output files, they are included files with - # $(DEPDIR) in their names. 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"Something went wrong bootstrapping makefile fragments + for automatic dependency tracking. Try re-running configure with the + '--disable-dependency-tracking' option to at least be able to build + the package (albeit without support for automatic dependency tracking). +See \`config.log' for more details" "$LINENO" 5; } + fi + { am_dirpart=; unset am_dirpart;} + { am_filepart=; unset am_filepart;} + { am_mf=; unset am_mf;} + { am_rc=; unset am_rc;} + rm -f conftest-deps.mk } ;; diff --git a/configure.ac b/configure.ac index 90d3a79..ec6e01f 100644 --- a/configure.ac +++ b/configure.ac @@ -45,7 +45,7 @@ AC_SUBST(AM_CXXFLAGS, "-g -Wall -Wextra $fail_on_warning -Wno-unknown-pragmas -s ##AC_SUBST(CXXFLAGS, "-O3") ##AC_SUBST(CFLAGS, "-O3") ##AC_SUBST(CPPFLAGS, "$CPPFLAGS $boost_include") -AC_SUBST(LDFLAGS, "$LDFLAGS -pthread -std=c++11") +AC_SUBST(LDFLAGS, "$LDFLAGS -pthread -std=c++11 -lbz2 -llzma") # We always need to specify to link to certain libraries ##AC_SUBST(LIBS, "$LIBS") # libboost_regex.a libboost_filesystem.a libboost_system.a") diff --git a/src/SGA/Algorithm/Makefile.in b/src/SGA/Algorithm/Makefile.in index 5ed2ce9..221fd9b 100644 --- a/src/SGA/Algorithm/Makefile.in +++ b/src/SGA/Algorithm/Makefile.in @@ -1,7 +1,7 @@ -# Makefile.in generated by automake 1.15 from Makefile.am. +# Makefile.in generated by automake 1.16.1 from Makefile.am. # @configure_input@ -# Copyright (C) 1994-2014 Free Software Foundation, Inc. +# Copyright (C) 1994-2018 Free Software Foundation, Inc. # This Makefile.in is free software; the Free Software Foundation # gives unlimited permission to copy and/or distribute it, @@ -125,7 +125,12 @@ am__v_at_0 = @ am__v_at_1 = DEFAULT_INCLUDES = -I.@am__isrc@ -I$(top_builddir) depcomp = $(SHELL) $(top_srcdir)/depcomp -am__depfiles_maybe = depfiles +am__maybe_remake_depfiles = depfiles +am__depfiles_remade = ./$(DEPDIR)/libalgorithm_a-OverlapAlgorithm.Po \ + ./$(DEPDIR)/libalgorithm_a-OverlapBlock.Po \ + ./$(DEPDIR)/libalgorithm_a-OverlapTools.Po \ + ./$(DEPDIR)/libalgorithm_a-SearchHistory.Po \ + ./$(DEPDIR)/libalgorithm_a-SearchSeed.Po am__mv = mv -f AM_V_lt = $(am__v_lt_@AM_V@) am__v_lt_ = $(am__v_lt_@AM_DEFAULT_V@) @@ -315,8 +320,8 @@ Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status *config.status*) \ cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh;; \ *) \ - echo ' cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__depfiles_maybe)'; \ - cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__depfiles_maybe);; \ + echo ' cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__maybe_remake_depfiles)'; \ + cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__maybe_remake_depfiles);; \ esac; $(top_builddir)/config.status: $(top_srcdir)/configure $(CONFIG_STATUS_DEPENDENCIES) @@ -342,11 +347,17 @@ mostlyclean-compile: distclean-compile: -rm -f *.tab.c -@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libalgorithm_a-OverlapAlgorithm.Po@am__quote@ -@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libalgorithm_a-OverlapBlock.Po@am__quote@ -@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libalgorithm_a-OverlapTools.Po@am__quote@ -@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libalgorithm_a-SearchHistory.Po@am__quote@ -@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libalgorithm_a-SearchSeed.Po@am__quote@ +@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libalgorithm_a-OverlapAlgorithm.Po@am__quote@ # am--include-marker +@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libalgorithm_a-OverlapBlock.Po@am__quote@ # am--include-marker +@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libalgorithm_a-OverlapTools.Po@am__quote@ # am--include-marker +@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libalgorithm_a-SearchHistory.Po@am__quote@ # am--include-marker +@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libalgorithm_a-SearchSeed.Po@am__quote@ # am--include-marker + +$(am__depfiles_remade): + @$(MKDIR_P) $(@D) + @echo '# dummy' >$@-t && $(am__mv) $@-t $@ + +am--depfiles: $(am__depfiles_remade) .cpp.o: @am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXXCOMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ $< @@ -484,7 +495,10 @@ cscopelist-am: $(am__tagged_files) distclean-tags: -rm -f TAGS ID GTAGS GRTAGS GSYMS GPATH tags -distdir: $(DISTFILES) +distdir: $(BUILT_SOURCES) + $(MAKE) $(AM_MAKEFLAGS) distdir-am + +distdir-am: $(DISTFILES) @srcdirstrip=`echo "$(srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \ topsrcdirstrip=`echo "$(top_srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \ list='$(DISTFILES)'; \ @@ -553,7 +567,11 @@ clean: clean-am clean-am: clean-generic clean-noinstLIBRARIES mostlyclean-am distclean: distclean-am - -rm -rf ./$(DEPDIR) + -rm -f ./$(DEPDIR)/libalgorithm_a-OverlapAlgorithm.Po + -rm -f ./$(DEPDIR)/libalgorithm_a-OverlapBlock.Po + -rm -f ./$(DEPDIR)/libalgorithm_a-OverlapTools.Po + -rm -f ./$(DEPDIR)/libalgorithm_a-SearchHistory.Po + -rm -f ./$(DEPDIR)/libalgorithm_a-SearchSeed.Po -rm -f Makefile distclean-am: clean-am distclean-compile distclean-generic \ distclean-tags @@ -599,7 +617,11 @@ install-ps-am: installcheck-am: maintainer-clean: maintainer-clean-am - -rm -rf ./$(DEPDIR) + -rm -f ./$(DEPDIR)/libalgorithm_a-OverlapAlgorithm.Po + -rm -f ./$(DEPDIR)/libalgorithm_a-OverlapBlock.Po + -rm -f ./$(DEPDIR)/libalgorithm_a-OverlapTools.Po + -rm -f ./$(DEPDIR)/libalgorithm_a-SearchHistory.Po + -rm -f ./$(DEPDIR)/libalgorithm_a-SearchSeed.Po -rm -f Makefile maintainer-clean-am: distclean-am maintainer-clean-generic @@ -619,18 +641,18 @@ uninstall-am: .MAKE: install-am install-strip -.PHONY: CTAGS GTAGS TAGS all all-am check check-am clean clean-generic \ - clean-noinstLIBRARIES cscopelist-am ctags ctags-am distclean \ - distclean-compile distclean-generic distclean-tags distdir dvi \ - dvi-am html html-am info info-am install install-am \ - install-data install-data-am install-dvi install-dvi-am \ - install-exec install-exec-am install-html install-html-am \ - install-info install-info-am install-man install-pdf \ - install-pdf-am install-ps install-ps-am install-strip \ - installcheck installcheck-am installdirs maintainer-clean \ - maintainer-clean-generic mostlyclean mostlyclean-compile \ - mostlyclean-generic pdf pdf-am ps ps-am tags tags-am uninstall \ - uninstall-am +.PHONY: CTAGS GTAGS TAGS all all-am am--depfiles check check-am clean \ + clean-generic clean-noinstLIBRARIES cscopelist-am ctags \ + ctags-am distclean distclean-compile distclean-generic \ + distclean-tags distdir dvi dvi-am html html-am info info-am \ + install install-am install-data install-data-am install-dvi \ + install-dvi-am install-exec install-exec-am install-html \ + install-html-am install-info install-info-am install-man \ + install-pdf install-pdf-am install-ps install-ps-am \ + install-strip installcheck installcheck-am installdirs \ + maintainer-clean maintainer-clean-generic mostlyclean \ + mostlyclean-compile mostlyclean-generic pdf pdf-am ps ps-am \ + tags tags-am uninstall uninstall-am .PRECIOUS: Makefile diff --git a/src/SGA/Bigraph/Makefile.in b/src/SGA/Bigraph/Makefile.in index e2ddb63..5b8e5a6 100644 --- a/src/SGA/Bigraph/Makefile.in +++ b/src/SGA/Bigraph/Makefile.in @@ -1,7 +1,7 @@ -# Makefile.in generated by automake 1.15 from Makefile.am. +# Makefile.in generated by automake 1.16.1 from Makefile.am. # @configure_input@ -# Copyright (C) 1994-2014 Free Software Foundation, Inc. +# Copyright (C) 1994-2018 Free Software Foundation, Inc. # This Makefile.in is free software; the Free Software Foundation # gives unlimited permission to copy and/or distribute it, @@ -123,7 +123,11 @@ am__v_at_0 = @ am__v_at_1 = DEFAULT_INCLUDES = -I.@am__isrc@ -I$(top_builddir) depcomp = $(SHELL) $(top_srcdir)/depcomp -am__depfiles_maybe = depfiles +am__maybe_remake_depfiles = depfiles +am__depfiles_remade = ./$(DEPDIR)/libbigraph_a-Bigraph.Po \ + ./$(DEPDIR)/libbigraph_a-Edge.Po \ + ./$(DEPDIR)/libbigraph_a-EdgeDesc.Po \ + ./$(DEPDIR)/libbigraph_a-Vertex.Po am__mv = mv -f AM_V_lt = $(am__v_lt_@AM_V@) am__v_lt_ = $(am__v_lt_@AM_DEFAULT_V@) @@ -310,8 +314,8 @@ Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status *config.status*) \ cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh;; \ *) \ - echo ' cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__depfiles_maybe)'; \ - cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__depfiles_maybe);; \ + echo ' cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__maybe_remake_depfiles)'; \ + cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__maybe_remake_depfiles);; \ esac; $(top_builddir)/config.status: $(top_srcdir)/configure $(CONFIG_STATUS_DEPENDENCIES) @@ -337,10 +341,16 @@ mostlyclean-compile: distclean-compile: -rm -f *.tab.c -@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libbigraph_a-Bigraph.Po@am__quote@ -@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libbigraph_a-Edge.Po@am__quote@ -@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libbigraph_a-EdgeDesc.Po@am__quote@ -@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libbigraph_a-Vertex.Po@am__quote@ +@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libbigraph_a-Bigraph.Po@am__quote@ # am--include-marker +@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libbigraph_a-Edge.Po@am__quote@ # am--include-marker +@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libbigraph_a-EdgeDesc.Po@am__quote@ # am--include-marker +@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libbigraph_a-Vertex.Po@am__quote@ # am--include-marker + +$(am__depfiles_remade): + @$(MKDIR_P) $(@D) + @echo '# dummy' >$@-t && $(am__mv) $@-t $@ + +am--depfiles: $(am__depfiles_remade) .cpp.o: @am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXXCOMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ $< @@ -464,7 +474,10 @@ cscopelist-am: $(am__tagged_files) distclean-tags: -rm -f TAGS ID GTAGS GRTAGS GSYMS GPATH tags -distdir: $(DISTFILES) +distdir: $(BUILT_SOURCES) + $(MAKE) $(AM_MAKEFLAGS) distdir-am + +distdir-am: $(DISTFILES) @srcdirstrip=`echo "$(srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \ topsrcdirstrip=`echo "$(top_srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \ list='$(DISTFILES)'; \ @@ -533,7 +546,10 @@ clean: clean-am clean-am: clean-generic clean-noinstLIBRARIES mostlyclean-am distclean: distclean-am - -rm -rf ./$(DEPDIR) + -rm -f ./$(DEPDIR)/libbigraph_a-Bigraph.Po + -rm -f ./$(DEPDIR)/libbigraph_a-Edge.Po + -rm -f ./$(DEPDIR)/libbigraph_a-EdgeDesc.Po + -rm -f ./$(DEPDIR)/libbigraph_a-Vertex.Po -rm -f Makefile distclean-am: clean-am distclean-compile distclean-generic \ distclean-tags @@ -579,7 +595,10 @@ install-ps-am: installcheck-am: maintainer-clean: maintainer-clean-am - -rm -rf ./$(DEPDIR) + -rm -f ./$(DEPDIR)/libbigraph_a-Bigraph.Po + -rm -f ./$(DEPDIR)/libbigraph_a-Edge.Po + -rm -f ./$(DEPDIR)/libbigraph_a-EdgeDesc.Po + -rm -f ./$(DEPDIR)/libbigraph_a-Vertex.Po -rm -f Makefile maintainer-clean-am: distclean-am maintainer-clean-generic @@ -599,18 +618,18 @@ uninstall-am: .MAKE: install-am install-strip -.PHONY: CTAGS GTAGS TAGS all all-am check check-am clean clean-generic \ - clean-noinstLIBRARIES cscopelist-am ctags ctags-am distclean \ - distclean-compile distclean-generic distclean-tags distdir dvi \ - dvi-am html html-am info info-am install install-am \ - install-data install-data-am install-dvi install-dvi-am \ - install-exec install-exec-am install-html install-html-am \ - install-info install-info-am install-man install-pdf \ - install-pdf-am install-ps install-ps-am install-strip \ - installcheck installcheck-am installdirs maintainer-clean \ - maintainer-clean-generic mostlyclean mostlyclean-compile \ - mostlyclean-generic pdf pdf-am ps ps-am tags tags-am uninstall \ - uninstall-am +.PHONY: CTAGS GTAGS TAGS all all-am am--depfiles check check-am clean \ + clean-generic clean-noinstLIBRARIES cscopelist-am ctags \ + ctags-am distclean distclean-compile distclean-generic \ + distclean-tags distdir dvi dvi-am html html-am info info-am \ + install install-am install-data install-data-am install-dvi \ + install-dvi-am install-exec install-exec-am install-html \ + install-html-am install-info install-info-am install-man \ + install-pdf install-pdf-am install-ps install-ps-am \ + install-strip installcheck installcheck-am installdirs \ + maintainer-clean maintainer-clean-generic mostlyclean \ + mostlyclean-compile mostlyclean-generic pdf pdf-am ps ps-am \ + tags tags-am uninstall uninstall-am .PRECIOUS: Makefile diff --git a/src/SGA/SGA/Makefile.in b/src/SGA/SGA/Makefile.in index bd4d671..52c2e59 100644 --- a/src/SGA/SGA/Makefile.in +++ b/src/SGA/SGA/Makefile.in @@ -1,7 +1,7 @@ -# Makefile.in generated by automake 1.15 from Makefile.am. +# Makefile.in generated by automake 1.16.1 from Makefile.am. # @configure_input@ -# Copyright (C) 1994-2014 Free Software Foundation, Inc. +# Copyright (C) 1994-2018 Free Software Foundation, Inc. # This Makefile.in is free software; the Free Software Foundation # gives unlimited permission to copy and/or distribute it, @@ -121,7 +121,8 @@ am__v_at_0 = @ am__v_at_1 = DEFAULT_INCLUDES = -I.@am__isrc@ -I$(top_builddir) depcomp = $(SHELL) $(top_srcdir)/depcomp -am__depfiles_maybe = depfiles +am__maybe_remake_depfiles = depfiles +am__depfiles_remade = ./$(DEPDIR)/libsga_a-OverlapCommon.Po am__mv = mv -f AM_V_lt = $(am__v_lt_@AM_V@) am__v_lt_ = $(am__v_lt_@AM_DEFAULT_V@) @@ -309,8 +310,8 @@ Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status *config.status*) \ cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh;; \ *) \ - echo ' cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__depfiles_maybe)'; \ - cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__depfiles_maybe);; \ + echo ' cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__maybe_remake_depfiles)'; \ + cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__maybe_remake_depfiles);; \ esac; $(top_builddir)/config.status: $(top_srcdir)/configure $(CONFIG_STATUS_DEPENDENCIES) @@ -336,7 +337,13 @@ mostlyclean-compile: distclean-compile: -rm -f *.tab.c -@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libsga_a-OverlapCommon.Po@am__quote@ +@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libsga_a-OverlapCommon.Po@am__quote@ # am--include-marker + +$(am__depfiles_remade): + @$(MKDIR_P) $(@D) + @echo '# dummy' >$@-t && $(am__mv) $@-t $@ + +am--depfiles: $(am__depfiles_remade) .cpp.o: @am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXXCOMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ $< @@ -418,7 +425,10 @@ cscopelist-am: $(am__tagged_files) distclean-tags: -rm -f TAGS ID GTAGS GRTAGS GSYMS GPATH tags -distdir: $(DISTFILES) +distdir: $(BUILT_SOURCES) + $(MAKE) $(AM_MAKEFLAGS) distdir-am + +distdir-am: $(DISTFILES) @srcdirstrip=`echo "$(srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \ topsrcdirstrip=`echo "$(top_srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \ list='$(DISTFILES)'; \ @@ -487,7 +497,7 @@ clean: clean-am clean-am: clean-generic clean-noinstLIBRARIES mostlyclean-am distclean: distclean-am - -rm -rf ./$(DEPDIR) + -rm -f ./$(DEPDIR)/libsga_a-OverlapCommon.Po -rm -f Makefile distclean-am: clean-am distclean-compile distclean-generic \ distclean-tags @@ -533,7 +543,7 @@ install-ps-am: installcheck-am: maintainer-clean: maintainer-clean-am - -rm -rf ./$(DEPDIR) + -rm -f ./$(DEPDIR)/libsga_a-OverlapCommon.Po -rm -f Makefile maintainer-clean-am: distclean-am maintainer-clean-generic @@ -553,18 +563,18 @@ uninstall-am: .MAKE: install-am install-strip -.PHONY: CTAGS GTAGS TAGS all all-am check check-am clean clean-generic \ - clean-noinstLIBRARIES cscopelist-am ctags ctags-am distclean \ - distclean-compile distclean-generic distclean-tags distdir dvi \ - dvi-am html html-am info info-am install install-am \ - install-data install-data-am install-dvi install-dvi-am \ - install-exec install-exec-am install-html install-html-am \ - install-info install-info-am install-man install-pdf \ - install-pdf-am install-ps install-ps-am install-strip \ - installcheck installcheck-am installdirs maintainer-clean \ - maintainer-clean-generic mostlyclean mostlyclean-compile \ - mostlyclean-generic pdf pdf-am ps ps-am tags tags-am uninstall \ - uninstall-am +.PHONY: CTAGS GTAGS TAGS all all-am am--depfiles check check-am clean \ + clean-generic clean-noinstLIBRARIES cscopelist-am ctags \ + ctags-am distclean distclean-compile distclean-generic \ + distclean-tags distdir dvi dvi-am html html-am info info-am \ + install install-am install-data install-data-am install-dvi \ + install-dvi-am install-exec install-exec-am install-html \ + install-html-am install-info install-info-am install-man \ + install-pdf install-pdf-am install-ps install-ps-am \ + install-strip installcheck installcheck-am installdirs \ + maintainer-clean maintainer-clean-generic mostlyclean \ + mostlyclean-compile mostlyclean-generic pdf pdf-am ps ps-am \ + tags tags-am uninstall uninstall-am .PRECIOUS: Makefile diff --git a/src/SGA/SQG/Makefile.in b/src/SGA/SQG/Makefile.in index d7ed758..f2ecc8f 100644 --- a/src/SGA/SQG/Makefile.in +++ b/src/SGA/SQG/Makefile.in @@ -1,7 +1,7 @@ -# Makefile.in generated by automake 1.15 from Makefile.am. +# Makefile.in generated by automake 1.16.1 from Makefile.am. # @configure_input@ -# Copyright (C) 1994-2014 Free Software Foundation, Inc. +# Copyright (C) 1994-2018 Free Software Foundation, Inc. # This Makefile.in is free software; the Free Software Foundation # gives unlimited permission to copy and/or distribute it, @@ -121,7 +121,9 @@ am__v_at_0 = @ am__v_at_1 = DEFAULT_INCLUDES = -I.@am__isrc@ -I$(top_builddir) depcomp = $(SHELL) $(top_srcdir)/depcomp -am__depfiles_maybe = depfiles +am__maybe_remake_depfiles = depfiles +am__depfiles_remade = ./$(DEPDIR)/libsqg_a-ASQG.Po \ + ./$(DEPDIR)/libsqg_a-SQG.Po am__mv = mv -f AM_V_lt = $(am__v_lt_@AM_V@) am__v_lt_ = $(am__v_lt_@AM_DEFAULT_V@) @@ -305,8 +307,8 @@ Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status *config.status*) \ cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh;; \ *) \ - echo ' cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__depfiles_maybe)'; \ - cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__depfiles_maybe);; \ + echo ' cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__maybe_remake_depfiles)'; \ + cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__maybe_remake_depfiles);; \ esac; $(top_builddir)/config.status: $(top_srcdir)/configure $(CONFIG_STATUS_DEPENDENCIES) @@ -332,8 +334,14 @@ mostlyclean-compile: distclean-compile: -rm -f *.tab.c -@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libsqg_a-ASQG.Po@am__quote@ -@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libsqg_a-SQG.Po@am__quote@ +@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libsqg_a-ASQG.Po@am__quote@ # am--include-marker +@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libsqg_a-SQG.Po@am__quote@ # am--include-marker + +$(am__depfiles_remade): + @$(MKDIR_P) $(@D) + @echo '# dummy' >$@-t && $(am__mv) $@-t $@ + +am--depfiles: $(am__depfiles_remade) .cpp.o: @am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXXCOMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ $< @@ -429,7 +437,10 @@ cscopelist-am: $(am__tagged_files) distclean-tags: -rm -f TAGS ID GTAGS GRTAGS GSYMS GPATH tags -distdir: $(DISTFILES) +distdir: $(BUILT_SOURCES) + $(MAKE) $(AM_MAKEFLAGS) distdir-am + +distdir-am: $(DISTFILES) @srcdirstrip=`echo "$(srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \ topsrcdirstrip=`echo "$(top_srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \ list='$(DISTFILES)'; \ @@ -498,7 +509,8 @@ clean: clean-am clean-am: clean-generic clean-noinstLIBRARIES mostlyclean-am distclean: distclean-am - -rm -rf ./$(DEPDIR) + -rm -f ./$(DEPDIR)/libsqg_a-ASQG.Po + -rm -f ./$(DEPDIR)/libsqg_a-SQG.Po -rm -f Makefile distclean-am: clean-am distclean-compile distclean-generic \ distclean-tags @@ -544,7 +556,8 @@ install-ps-am: installcheck-am: maintainer-clean: maintainer-clean-am - -rm -rf ./$(DEPDIR) + -rm -f ./$(DEPDIR)/libsqg_a-ASQG.Po + -rm -f ./$(DEPDIR)/libsqg_a-SQG.Po -rm -f Makefile maintainer-clean-am: distclean-am maintainer-clean-generic @@ -564,18 +577,18 @@ uninstall-am: .MAKE: install-am install-strip -.PHONY: CTAGS GTAGS TAGS all all-am check check-am clean clean-generic \ - clean-noinstLIBRARIES cscopelist-am ctags ctags-am distclean \ - distclean-compile distclean-generic distclean-tags distdir dvi \ - dvi-am html html-am info info-am install install-am \ - install-data install-data-am install-dvi install-dvi-am \ - install-exec install-exec-am install-html install-html-am \ - install-info install-info-am install-man install-pdf \ - install-pdf-am install-ps install-ps-am install-strip \ - installcheck installcheck-am installdirs maintainer-clean \ - maintainer-clean-generic mostlyclean mostlyclean-compile \ - mostlyclean-generic pdf pdf-am ps ps-am tags tags-am uninstall \ - uninstall-am +.PHONY: CTAGS GTAGS TAGS all all-am am--depfiles check check-am clean \ + clean-generic clean-noinstLIBRARIES cscopelist-am ctags \ + ctags-am distclean distclean-compile distclean-generic \ + distclean-tags distdir dvi dvi-am html html-am info info-am \ + install install-am install-data install-data-am install-dvi \ + install-dvi-am install-exec install-exec-am install-html \ + install-html-am install-info install-info-am install-man \ + install-pdf install-pdf-am install-ps install-ps-am \ + install-strip installcheck installcheck-am installdirs \ + maintainer-clean maintainer-clean-generic mostlyclean \ + mostlyclean-compile mostlyclean-generic pdf pdf-am ps ps-am \ + tags tags-am uninstall uninstall-am .PRECIOUS: Makefile diff --git a/src/SGA/StringGraph/Makefile.in b/src/SGA/StringGraph/Makefile.in index a1d0d79..7115126 100644 --- a/src/SGA/StringGraph/Makefile.in +++ b/src/SGA/StringGraph/Makefile.in @@ -1,7 +1,7 @@ -# Makefile.in generated by automake 1.15 from Makefile.am. +# Makefile.in generated by automake 1.16.1 from Makefile.am. # @configure_input@ -# Copyright (C) 1994-2014 Free Software Foundation, Inc. +# Copyright (C) 1994-2018 Free Software Foundation, Inc. # This Makefile.in is free software; the Free Software Foundation # gives unlimited permission to copy and/or distribute it, @@ -127,7 +127,15 @@ am__v_at_0 = @ am__v_at_1 = DEFAULT_INCLUDES = -I.@am__isrc@ -I$(top_builddir) depcomp = $(SHELL) $(top_srcdir)/depcomp -am__depfiles_maybe = depfiles +am__maybe_remake_depfiles = depfiles +am__depfiles_remade = \ + ./$(DEPDIR)/libstringgraph_a-CompleteOverlapSet.Po \ + ./$(DEPDIR)/libstringgraph_a-RemovalAlgorithm.Po \ + ./$(DEPDIR)/libstringgraph_a-SGAlgorithms.Po \ + ./$(DEPDIR)/libstringgraph_a-SGSearch.Po \ + ./$(DEPDIR)/libstringgraph_a-SGUtil.Po \ + ./$(DEPDIR)/libstringgraph_a-SGVisitors.Po \ + ./$(DEPDIR)/libstringgraph_a-SGWalk.Po am__mv = mv -f AM_V_lt = $(am__v_lt_@AM_V@) am__v_lt_ = $(am__v_lt_@AM_DEFAULT_V@) @@ -320,8 +328,8 @@ Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status *config.status*) \ cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh;; \ *) \ - echo ' cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__depfiles_maybe)'; \ - cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__depfiles_maybe);; \ + echo ' cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__maybe_remake_depfiles)'; \ + cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__maybe_remake_depfiles);; \ esac; $(top_builddir)/config.status: $(top_srcdir)/configure $(CONFIG_STATUS_DEPENDENCIES) @@ -347,13 +355,19 @@ mostlyclean-compile: distclean-compile: -rm -f *.tab.c -@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libstringgraph_a-CompleteOverlapSet.Po@am__quote@ -@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libstringgraph_a-RemovalAlgorithm.Po@am__quote@ -@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libstringgraph_a-SGAlgorithms.Po@am__quote@ -@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libstringgraph_a-SGSearch.Po@am__quote@ -@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libstringgraph_a-SGUtil.Po@am__quote@ -@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libstringgraph_a-SGVisitors.Po@am__quote@ -@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libstringgraph_a-SGWalk.Po@am__quote@ +@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libstringgraph_a-CompleteOverlapSet.Po@am__quote@ # am--include-marker +@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libstringgraph_a-RemovalAlgorithm.Po@am__quote@ # am--include-marker +@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libstringgraph_a-SGAlgorithms.Po@am__quote@ # am--include-marker +@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libstringgraph_a-SGSearch.Po@am__quote@ # am--include-marker +@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libstringgraph_a-SGUtil.Po@am__quote@ # am--include-marker +@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libstringgraph_a-SGVisitors.Po@am__quote@ # am--include-marker +@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libstringgraph_a-SGWalk.Po@am__quote@ # am--include-marker + +$(am__depfiles_remade): + @$(MKDIR_P) $(@D) + @echo '# dummy' >$@-t && $(am__mv) $@-t $@ + +am--depfiles: $(am__depfiles_remade) .cpp.o: @am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXXCOMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ $< @@ -519,7 +533,10 @@ cscopelist-am: $(am__tagged_files) distclean-tags: -rm -f TAGS ID GTAGS GRTAGS GSYMS GPATH tags -distdir: $(DISTFILES) +distdir: $(BUILT_SOURCES) + $(MAKE) $(AM_MAKEFLAGS) distdir-am + +distdir-am: $(DISTFILES) @srcdirstrip=`echo "$(srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \ topsrcdirstrip=`echo "$(top_srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \ list='$(DISTFILES)'; \ @@ -588,7 +605,13 @@ clean: clean-am clean-am: clean-generic clean-noinstLIBRARIES mostlyclean-am distclean: distclean-am - -rm -rf ./$(DEPDIR) + -rm -f ./$(DEPDIR)/libstringgraph_a-CompleteOverlapSet.Po + -rm -f ./$(DEPDIR)/libstringgraph_a-RemovalAlgorithm.Po + -rm -f ./$(DEPDIR)/libstringgraph_a-SGAlgorithms.Po + -rm -f ./$(DEPDIR)/libstringgraph_a-SGSearch.Po + -rm -f ./$(DEPDIR)/libstringgraph_a-SGUtil.Po + -rm -f ./$(DEPDIR)/libstringgraph_a-SGVisitors.Po + -rm -f ./$(DEPDIR)/libstringgraph_a-SGWalk.Po -rm -f Makefile distclean-am: clean-am distclean-compile distclean-generic \ distclean-tags @@ -634,7 +657,13 @@ install-ps-am: installcheck-am: maintainer-clean: maintainer-clean-am - -rm -rf ./$(DEPDIR) + -rm -f ./$(DEPDIR)/libstringgraph_a-CompleteOverlapSet.Po + -rm -f ./$(DEPDIR)/libstringgraph_a-RemovalAlgorithm.Po + -rm -f ./$(DEPDIR)/libstringgraph_a-SGAlgorithms.Po + -rm -f ./$(DEPDIR)/libstringgraph_a-SGSearch.Po + -rm -f ./$(DEPDIR)/libstringgraph_a-SGUtil.Po + -rm -f ./$(DEPDIR)/libstringgraph_a-SGVisitors.Po + -rm -f ./$(DEPDIR)/libstringgraph_a-SGWalk.Po -rm -f Makefile maintainer-clean-am: distclean-am maintainer-clean-generic @@ -654,18 +683,18 @@ uninstall-am: .MAKE: install-am install-strip -.PHONY: CTAGS GTAGS TAGS all all-am check check-am clean clean-generic \ - clean-noinstLIBRARIES cscopelist-am ctags ctags-am distclean \ - distclean-compile distclean-generic distclean-tags distdir dvi \ - dvi-am html html-am info info-am install install-am \ - install-data install-data-am install-dvi install-dvi-am \ - install-exec install-exec-am install-html install-html-am \ - install-info install-info-am install-man install-pdf \ - install-pdf-am install-ps install-ps-am install-strip \ - installcheck installcheck-am installdirs maintainer-clean \ - maintainer-clean-generic mostlyclean mostlyclean-compile \ - mostlyclean-generic pdf pdf-am ps ps-am tags tags-am uninstall \ - uninstall-am +.PHONY: CTAGS GTAGS TAGS all all-am am--depfiles check check-am clean \ + clean-generic clean-noinstLIBRARIES cscopelist-am ctags \ + ctags-am distclean distclean-compile distclean-generic \ + distclean-tags distdir dvi dvi-am html html-am info info-am \ + install install-am install-data install-data-am install-dvi \ + install-dvi-am install-exec install-exec-am install-html \ + install-html-am install-info install-info-am install-man \ + install-pdf install-pdf-am install-ps install-ps-am \ + install-strip installcheck installcheck-am installdirs \ + maintainer-clean maintainer-clean-generic mostlyclean \ + mostlyclean-compile mostlyclean-generic pdf pdf-am ps ps-am \ + tags tags-am uninstall uninstall-am .PRECIOUS: Makefile diff --git a/src/SGA/SuffixTools/Makefile.in b/src/SGA/SuffixTools/Makefile.in index 8a35534..0833596 100644 --- a/src/SGA/SuffixTools/Makefile.in +++ b/src/SGA/SuffixTools/Makefile.in @@ -1,7 +1,7 @@ -# Makefile.in generated by automake 1.15 from Makefile.am. +# Makefile.in generated by automake 1.16.1 from Makefile.am. # @configure_input@ -# Copyright (C) 1994-2014 Free Software Foundation, Inc. +# Copyright (C) 1994-2018 Free Software Foundation, Inc. # This Makefile.in is free software; the Free Software Foundation # gives unlimited permission to copy and/or distribute it, @@ -141,7 +141,26 @@ am__v_at_0 = @ am__v_at_1 = DEFAULT_INCLUDES = -I.@am__isrc@ -I$(top_builddir) depcomp = $(SHELL) $(top_srcdir)/depcomp -am__depfiles_maybe = depfiles +am__maybe_remake_depfiles = depfiles +am__depfiles_remade = ./$(DEPDIR)/libsuffixtools_a-BWTAlgorithms.Po \ + ./$(DEPDIR)/libsuffixtools_a-BWTIntervalCache.Po \ + ./$(DEPDIR)/libsuffixtools_a-BWTReader.Po \ + ./$(DEPDIR)/libsuffixtools_a-BWTReaderAscii.Po \ + ./$(DEPDIR)/libsuffixtools_a-BWTReaderBinary.Po \ + ./$(DEPDIR)/libsuffixtools_a-BWTWriter.Po \ + ./$(DEPDIR)/libsuffixtools_a-BWTWriterAscii.Po \ + ./$(DEPDIR)/libsuffixtools_a-BWTWriterBinary.Po \ + ./$(DEPDIR)/libsuffixtools_a-InverseSuffixArray.Po \ + ./$(DEPDIR)/libsuffixtools_a-Occurrence.Po \ + ./$(DEPDIR)/libsuffixtools_a-RLBWT.Po \ + ./$(DEPDIR)/libsuffixtools_a-SACAInducedCopying.Po \ + ./$(DEPDIR)/libsuffixtools_a-SAReader.Po \ + ./$(DEPDIR)/libsuffixtools_a-SAWriter.Po \ + ./$(DEPDIR)/libsuffixtools_a-SBWT.Po \ + ./$(DEPDIR)/libsuffixtools_a-STCommon.Po \ + ./$(DEPDIR)/libsuffixtools_a-SampledSuffixArray.Po \ + ./$(DEPDIR)/libsuffixtools_a-SuffixArray.Po \ + ./$(DEPDIR)/libsuffixtools_a-SuffixCompare.Po am__mv = mv -f AM_V_lt = $(am__v_lt_@AM_V@) am__v_lt_ = $(am__v_lt_@AM_DEFAULT_V@) @@ -351,8 +370,8 @@ Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status *config.status*) \ cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh;; \ *) \ - echo ' cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__depfiles_maybe)'; \ - cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__depfiles_maybe);; \ + echo ' cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__maybe_remake_depfiles)'; \ + cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__maybe_remake_depfiles);; \ esac; $(top_builddir)/config.status: $(top_srcdir)/configure $(CONFIG_STATUS_DEPENDENCIES) @@ -378,25 +397,31 @@ mostlyclean-compile: distclean-compile: -rm -f *.tab.c -@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libsuffixtools_a-BWTAlgorithms.Po@am__quote@ -@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libsuffixtools_a-BWTIntervalCache.Po@am__quote@ -@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libsuffixtools_a-BWTReader.Po@am__quote@ -@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libsuffixtools_a-BWTReaderAscii.Po@am__quote@ -@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libsuffixtools_a-BWTReaderBinary.Po@am__quote@ -@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libsuffixtools_a-BWTWriter.Po@am__quote@ -@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libsuffixtools_a-BWTWriterAscii.Po@am__quote@ -@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libsuffixtools_a-BWTWriterBinary.Po@am__quote@ -@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libsuffixtools_a-InverseSuffixArray.Po@am__quote@ -@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libsuffixtools_a-Occurrence.Po@am__quote@ -@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libsuffixtools_a-RLBWT.Po@am__quote@ -@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libsuffixtools_a-SACAInducedCopying.Po@am__quote@ -@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libsuffixtools_a-SAReader.Po@am__quote@ -@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libsuffixtools_a-SAWriter.Po@am__quote@ -@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libsuffixtools_a-SBWT.Po@am__quote@ -@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libsuffixtools_a-STCommon.Po@am__quote@ -@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libsuffixtools_a-SampledSuffixArray.Po@am__quote@ -@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libsuffixtools_a-SuffixArray.Po@am__quote@ -@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libsuffixtools_a-SuffixCompare.Po@am__quote@ +@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libsuffixtools_a-BWTAlgorithms.Po@am__quote@ # am--include-marker +@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libsuffixtools_a-BWTIntervalCache.Po@am__quote@ # am--include-marker +@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libsuffixtools_a-BWTReader.Po@am__quote@ # am--include-marker +@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libsuffixtools_a-BWTReaderAscii.Po@am__quote@ # am--include-marker +@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libsuffixtools_a-BWTReaderBinary.Po@am__quote@ # am--include-marker +@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libsuffixtools_a-BWTWriter.Po@am__quote@ # am--include-marker +@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libsuffixtools_a-BWTWriterAscii.Po@am__quote@ # am--include-marker +@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libsuffixtools_a-BWTWriterBinary.Po@am__quote@ # am--include-marker +@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libsuffixtools_a-InverseSuffixArray.Po@am__quote@ # am--include-marker +@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libsuffixtools_a-Occurrence.Po@am__quote@ # am--include-marker +@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libsuffixtools_a-RLBWT.Po@am__quote@ # am--include-marker +@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libsuffixtools_a-SACAInducedCopying.Po@am__quote@ # am--include-marker +@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libsuffixtools_a-SAReader.Po@am__quote@ # am--include-marker +@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libsuffixtools_a-SAWriter.Po@am__quote@ # am--include-marker +@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libsuffixtools_a-SBWT.Po@am__quote@ # am--include-marker +@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libsuffixtools_a-STCommon.Po@am__quote@ # am--include-marker +@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libsuffixtools_a-SampledSuffixArray.Po@am__quote@ # am--include-marker +@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libsuffixtools_a-SuffixArray.Po@am__quote@ # am--include-marker +@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libsuffixtools_a-SuffixCompare.Po@am__quote@ # am--include-marker + +$(am__depfiles_remade): + @$(MKDIR_P) $(@D) + @echo '# dummy' >$@-t && $(am__mv) $@-t $@ + +am--depfiles: $(am__depfiles_remade) .cpp.o: @am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXXCOMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ $< @@ -730,7 +755,10 @@ cscopelist-am: $(am__tagged_files) distclean-tags: -rm -f TAGS ID GTAGS GRTAGS GSYMS GPATH tags -distdir: $(DISTFILES) +distdir: $(BUILT_SOURCES) + $(MAKE) $(AM_MAKEFLAGS) distdir-am + +distdir-am: $(DISTFILES) @srcdirstrip=`echo "$(srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \ topsrcdirstrip=`echo "$(top_srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \ list='$(DISTFILES)'; \ @@ -799,7 +827,25 @@ clean: clean-am clean-am: clean-generic clean-noinstLIBRARIES mostlyclean-am distclean: distclean-am - -rm -rf ./$(DEPDIR) + -rm -f ./$(DEPDIR)/libsuffixtools_a-BWTAlgorithms.Po + -rm -f ./$(DEPDIR)/libsuffixtools_a-BWTIntervalCache.Po + -rm -f ./$(DEPDIR)/libsuffixtools_a-BWTReader.Po + -rm -f ./$(DEPDIR)/libsuffixtools_a-BWTReaderAscii.Po + -rm -f ./$(DEPDIR)/libsuffixtools_a-BWTReaderBinary.Po + -rm -f ./$(DEPDIR)/libsuffixtools_a-BWTWriter.Po + -rm -f ./$(DEPDIR)/libsuffixtools_a-BWTWriterAscii.Po + -rm -f ./$(DEPDIR)/libsuffixtools_a-BWTWriterBinary.Po + -rm -f ./$(DEPDIR)/libsuffixtools_a-InverseSuffixArray.Po + -rm -f ./$(DEPDIR)/libsuffixtools_a-Occurrence.Po + -rm -f ./$(DEPDIR)/libsuffixtools_a-RLBWT.Po + -rm -f ./$(DEPDIR)/libsuffixtools_a-SACAInducedCopying.Po + -rm -f ./$(DEPDIR)/libsuffixtools_a-SAReader.Po + -rm -f ./$(DEPDIR)/libsuffixtools_a-SAWriter.Po + -rm -f ./$(DEPDIR)/libsuffixtools_a-SBWT.Po + -rm -f ./$(DEPDIR)/libsuffixtools_a-STCommon.Po + -rm -f ./$(DEPDIR)/libsuffixtools_a-SampledSuffixArray.Po + -rm -f ./$(DEPDIR)/libsuffixtools_a-SuffixArray.Po + -rm -f ./$(DEPDIR)/libsuffixtools_a-SuffixCompare.Po -rm -f Makefile distclean-am: clean-am distclean-compile distclean-generic \ distclean-tags @@ -845,7 +891,25 @@ install-ps-am: installcheck-am: maintainer-clean: maintainer-clean-am - -rm -rf ./$(DEPDIR) + -rm -f ./$(DEPDIR)/libsuffixtools_a-BWTAlgorithms.Po + -rm -f ./$(DEPDIR)/libsuffixtools_a-BWTIntervalCache.Po + -rm -f ./$(DEPDIR)/libsuffixtools_a-BWTReader.Po + -rm -f ./$(DEPDIR)/libsuffixtools_a-BWTReaderAscii.Po + -rm -f ./$(DEPDIR)/libsuffixtools_a-BWTReaderBinary.Po + -rm -f ./$(DEPDIR)/libsuffixtools_a-BWTWriter.Po + -rm -f ./$(DEPDIR)/libsuffixtools_a-BWTWriterAscii.Po + -rm -f ./$(DEPDIR)/libsuffixtools_a-BWTWriterBinary.Po + -rm -f ./$(DEPDIR)/libsuffixtools_a-InverseSuffixArray.Po + -rm -f ./$(DEPDIR)/libsuffixtools_a-Occurrence.Po + -rm -f ./$(DEPDIR)/libsuffixtools_a-RLBWT.Po + -rm -f ./$(DEPDIR)/libsuffixtools_a-SACAInducedCopying.Po + -rm -f ./$(DEPDIR)/libsuffixtools_a-SAReader.Po + -rm -f ./$(DEPDIR)/libsuffixtools_a-SAWriter.Po + -rm -f ./$(DEPDIR)/libsuffixtools_a-SBWT.Po + -rm -f ./$(DEPDIR)/libsuffixtools_a-STCommon.Po + -rm -f ./$(DEPDIR)/libsuffixtools_a-SampledSuffixArray.Po + -rm -f ./$(DEPDIR)/libsuffixtools_a-SuffixArray.Po + -rm -f ./$(DEPDIR)/libsuffixtools_a-SuffixCompare.Po -rm -f Makefile maintainer-clean-am: distclean-am maintainer-clean-generic @@ -865,18 +929,18 @@ uninstall-am: .MAKE: install-am install-strip -.PHONY: CTAGS GTAGS TAGS all all-am check check-am clean clean-generic \ - clean-noinstLIBRARIES cscopelist-am ctags ctags-am distclean \ - distclean-compile distclean-generic distclean-tags distdir dvi \ - dvi-am html html-am info info-am install install-am \ - install-data install-data-am install-dvi install-dvi-am \ - install-exec install-exec-am install-html install-html-am \ - install-info install-info-am install-man install-pdf \ - install-pdf-am install-ps install-ps-am install-strip \ - installcheck installcheck-am installdirs maintainer-clean \ - maintainer-clean-generic mostlyclean mostlyclean-compile \ - mostlyclean-generic pdf pdf-am ps ps-am tags tags-am uninstall \ - uninstall-am +.PHONY: CTAGS GTAGS TAGS all all-am am--depfiles check check-am clean \ + clean-generic clean-noinstLIBRARIES cscopelist-am ctags \ + ctags-am distclean distclean-compile distclean-generic \ + distclean-tags distdir dvi dvi-am html html-am info info-am \ + install install-am install-data install-data-am install-dvi \ + install-dvi-am install-exec install-exec-am install-html \ + install-html-am install-info install-info-am install-man \ + install-pdf install-pdf-am install-ps install-ps-am \ + install-strip installcheck installcheck-am installdirs \ + maintainer-clean maintainer-clean-generic mostlyclean \ + mostlyclean-compile mostlyclean-generic pdf pdf-am ps ps-am \ + tags tags-am uninstall uninstall-am .PRECIOUS: Makefile diff --git a/src/SGA/Util/Makefile.in b/src/SGA/Util/Makefile.in index 70b67fa..a5cae70 100644 --- a/src/SGA/Util/Makefile.in +++ b/src/SGA/Util/Makefile.in @@ -1,7 +1,7 @@ -# Makefile.in generated by automake 1.15 from Makefile.am. +# Makefile.in generated by automake 1.16.1 from Makefile.am. # @configure_input@ -# Copyright (C) 1994-2014 Free Software Foundation, Inc. +# Copyright (C) 1994-2018 Free Software Foundation, Inc. # This Makefile.in is free software; the Free Software Foundation # gives unlimited permission to copy and/or distribute it, @@ -133,7 +133,28 @@ am__v_at_0 = @ am__v_at_1 = DEFAULT_INCLUDES = -I.@am__isrc@ -I$(top_builddir) depcomp = $(SHELL) $(top_srcdir)/depcomp -am__depfiles_maybe = depfiles +am__maybe_remake_depfiles = depfiles +am__depfiles_remade = ./$(DEPDIR)/libutil_a-Alphabet.Po \ + ./$(DEPDIR)/libutil_a-BitChar.Po \ + ./$(DEPDIR)/libutil_a-ClusterReader.Po \ + ./$(DEPDIR)/libutil_a-Contig.Po \ + ./$(DEPDIR)/libutil_a-CorrectionThresholds.Po \ + ./$(DEPDIR)/libutil_a-DNAString.Po \ + ./$(DEPDIR)/libutil_a-Interval.Po \ + ./$(DEPDIR)/libutil_a-Match.Po \ + ./$(DEPDIR)/libutil_a-MultiOverlap.Po \ + ./$(DEPDIR)/libutil_a-Pileup.Po \ + ./$(DEPDIR)/libutil_a-PrimerScreen.Po \ + ./$(DEPDIR)/libutil_a-Quality.Po \ + ./$(DEPDIR)/libutil_a-QualityTable.Po \ + ./$(DEPDIR)/libutil_a-QualityVector.Po \ + ./$(DEPDIR)/libutil_a-ReadInfoTable.Po \ + ./$(DEPDIR)/libutil_a-ReadTable.Po \ + ./$(DEPDIR)/libutil_a-SeqCoord.Po \ + ./$(DEPDIR)/libutil_a-SeqReader.Po \ + ./$(DEPDIR)/libutil_a-Util.Po \ + ./$(DEPDIR)/libutil_a-gzstream.Po \ + ./$(DEPDIR)/libutil_a-stdaln.Po am__mv = mv -f AM_V_lt = $(am__v_lt_@AM_V@) am__v_lt_ = $(am__v_lt_@AM_DEFAULT_V@) @@ -317,8 +338,8 @@ Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status *config.status*) \ cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh;; \ *) \ - echo ' cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__depfiles_maybe)'; \ - cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__depfiles_maybe);; \ + echo ' cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__maybe_remake_depfiles)'; \ + cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__maybe_remake_depfiles);; \ esac; $(top_builddir)/config.status: $(top_srcdir)/configure $(CONFIG_STATUS_DEPENDENCIES) @@ -344,27 +365,33 @@ mostlyclean-compile: distclean-compile: -rm -f *.tab.c -@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libutil_a-Alphabet.Po@am__quote@ -@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libutil_a-BitChar.Po@am__quote@ -@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libutil_a-ClusterReader.Po@am__quote@ -@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libutil_a-Contig.Po@am__quote@ -@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libutil_a-CorrectionThresholds.Po@am__quote@ -@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libutil_a-DNAString.Po@am__quote@ -@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libutil_a-Interval.Po@am__quote@ -@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libutil_a-Match.Po@am__quote@ -@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libutil_a-MultiOverlap.Po@am__quote@ -@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libutil_a-Pileup.Po@am__quote@ -@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libutil_a-PrimerScreen.Po@am__quote@ -@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libutil_a-Quality.Po@am__quote@ -@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libutil_a-QualityTable.Po@am__quote@ -@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libutil_a-QualityVector.Po@am__quote@ -@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libutil_a-ReadInfoTable.Po@am__quote@ -@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libutil_a-ReadTable.Po@am__quote@ -@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libutil_a-SeqCoord.Po@am__quote@ -@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libutil_a-SeqReader.Po@am__quote@ -@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libutil_a-Util.Po@am__quote@ -@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libutil_a-gzstream.Po@am__quote@ -@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libutil_a-stdaln.Po@am__quote@ +@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libutil_a-Alphabet.Po@am__quote@ # am--include-marker +@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libutil_a-BitChar.Po@am__quote@ # am--include-marker +@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libutil_a-ClusterReader.Po@am__quote@ # am--include-marker +@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libutil_a-Contig.Po@am__quote@ # am--include-marker +@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libutil_a-CorrectionThresholds.Po@am__quote@ # am--include-marker +@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libutil_a-DNAString.Po@am__quote@ # am--include-marker +@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libutil_a-Interval.Po@am__quote@ # am--include-marker +@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libutil_a-Match.Po@am__quote@ # am--include-marker +@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libutil_a-MultiOverlap.Po@am__quote@ # am--include-marker +@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libutil_a-Pileup.Po@am__quote@ # am--include-marker +@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libutil_a-PrimerScreen.Po@am__quote@ # am--include-marker +@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libutil_a-Quality.Po@am__quote@ # am--include-marker +@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libutil_a-QualityTable.Po@am__quote@ # am--include-marker +@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libutil_a-QualityVector.Po@am__quote@ # am--include-marker +@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libutil_a-ReadInfoTable.Po@am__quote@ # am--include-marker +@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libutil_a-ReadTable.Po@am__quote@ # am--include-marker +@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libutil_a-SeqCoord.Po@am__quote@ # am--include-marker +@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libutil_a-SeqReader.Po@am__quote@ # am--include-marker +@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libutil_a-Util.Po@am__quote@ # am--include-marker +@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libutil_a-gzstream.Po@am__quote@ # am--include-marker +@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libutil_a-stdaln.Po@am__quote@ # am--include-marker + +$(am__depfiles_remade): + @$(MKDIR_P) $(@D) + @echo '# dummy' >$@-t && $(am__mv) $@-t $@ + +am--depfiles: $(am__depfiles_remade) .C.o: @am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXXCOMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ $< @@ -754,7 +781,10 @@ cscopelist-am: $(am__tagged_files) distclean-tags: -rm -f TAGS ID GTAGS GRTAGS GSYMS GPATH tags -distdir: $(DISTFILES) +distdir: $(BUILT_SOURCES) + $(MAKE) $(AM_MAKEFLAGS) distdir-am + +distdir-am: $(DISTFILES) @srcdirstrip=`echo "$(srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \ topsrcdirstrip=`echo "$(top_srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \ list='$(DISTFILES)'; \ @@ -823,7 +853,27 @@ clean: clean-am clean-am: clean-generic clean-noinstLIBRARIES mostlyclean-am distclean: distclean-am - -rm -rf ./$(DEPDIR) + -rm -f ./$(DEPDIR)/libutil_a-Alphabet.Po + -rm -f ./$(DEPDIR)/libutil_a-BitChar.Po + -rm -f ./$(DEPDIR)/libutil_a-ClusterReader.Po + -rm -f ./$(DEPDIR)/libutil_a-Contig.Po + -rm -f ./$(DEPDIR)/libutil_a-CorrectionThresholds.Po + -rm -f ./$(DEPDIR)/libutil_a-DNAString.Po + -rm -f ./$(DEPDIR)/libutil_a-Interval.Po + -rm -f ./$(DEPDIR)/libutil_a-Match.Po + -rm -f ./$(DEPDIR)/libutil_a-MultiOverlap.Po + -rm -f ./$(DEPDIR)/libutil_a-Pileup.Po + -rm -f ./$(DEPDIR)/libutil_a-PrimerScreen.Po + -rm -f ./$(DEPDIR)/libutil_a-Quality.Po + -rm -f ./$(DEPDIR)/libutil_a-QualityTable.Po + -rm -f ./$(DEPDIR)/libutil_a-QualityVector.Po + -rm -f ./$(DEPDIR)/libutil_a-ReadInfoTable.Po + -rm -f ./$(DEPDIR)/libutil_a-ReadTable.Po + -rm -f ./$(DEPDIR)/libutil_a-SeqCoord.Po + -rm -f ./$(DEPDIR)/libutil_a-SeqReader.Po + -rm -f ./$(DEPDIR)/libutil_a-Util.Po + -rm -f ./$(DEPDIR)/libutil_a-gzstream.Po + -rm -f ./$(DEPDIR)/libutil_a-stdaln.Po -rm -f Makefile distclean-am: clean-am distclean-compile distclean-generic \ distclean-tags @@ -869,7 +919,27 @@ install-ps-am: installcheck-am: maintainer-clean: maintainer-clean-am - -rm -rf ./$(DEPDIR) + -rm -f ./$(DEPDIR)/libutil_a-Alphabet.Po + -rm -f ./$(DEPDIR)/libutil_a-BitChar.Po + -rm -f ./$(DEPDIR)/libutil_a-ClusterReader.Po + -rm -f ./$(DEPDIR)/libutil_a-Contig.Po + -rm -f ./$(DEPDIR)/libutil_a-CorrectionThresholds.Po + -rm -f ./$(DEPDIR)/libutil_a-DNAString.Po + -rm -f ./$(DEPDIR)/libutil_a-Interval.Po + -rm -f ./$(DEPDIR)/libutil_a-Match.Po + -rm -f ./$(DEPDIR)/libutil_a-MultiOverlap.Po + -rm -f ./$(DEPDIR)/libutil_a-Pileup.Po + -rm -f ./$(DEPDIR)/libutil_a-PrimerScreen.Po + -rm -f ./$(DEPDIR)/libutil_a-Quality.Po + -rm -f ./$(DEPDIR)/libutil_a-QualityTable.Po + -rm -f ./$(DEPDIR)/libutil_a-QualityVector.Po + -rm -f ./$(DEPDIR)/libutil_a-ReadInfoTable.Po + -rm -f ./$(DEPDIR)/libutil_a-ReadTable.Po + -rm -f ./$(DEPDIR)/libutil_a-SeqCoord.Po + -rm -f ./$(DEPDIR)/libutil_a-SeqReader.Po + -rm -f ./$(DEPDIR)/libutil_a-Util.Po + -rm -f ./$(DEPDIR)/libutil_a-gzstream.Po + -rm -f ./$(DEPDIR)/libutil_a-stdaln.Po -rm -f Makefile maintainer-clean-am: distclean-am maintainer-clean-generic @@ -889,18 +959,18 @@ uninstall-am: .MAKE: install-am install-strip -.PHONY: CTAGS GTAGS TAGS all all-am check check-am clean clean-generic \ - clean-noinstLIBRARIES cscopelist-am ctags ctags-am distclean \ - distclean-compile distclean-generic distclean-tags distdir dvi \ - dvi-am html html-am info info-am install install-am \ - install-data install-data-am install-dvi install-dvi-am \ - install-exec install-exec-am install-html install-html-am \ - install-info install-info-am install-man install-pdf \ - install-pdf-am install-ps install-ps-am install-strip \ - installcheck installcheck-am installdirs maintainer-clean \ - maintainer-clean-generic mostlyclean mostlyclean-compile \ - mostlyclean-generic pdf pdf-am ps ps-am tags tags-am uninstall \ - uninstall-am +.PHONY: CTAGS GTAGS TAGS all all-am am--depfiles check check-am clean \ + clean-generic clean-noinstLIBRARIES cscopelist-am ctags \ + ctags-am distclean distclean-compile distclean-generic \ + distclean-tags distdir dvi dvi-am html html-am info info-am \ + install install-am install-data install-data-am install-dvi \ + install-dvi-am install-exec install-exec-am install-html \ + install-html-am install-info install-info-am install-man \ + install-pdf install-pdf-am install-ps install-ps-am \ + install-strip installcheck installcheck-am installdirs \ + maintainer-clean maintainer-clean-generic mostlyclean \ + mostlyclean-compile mostlyclean-generic pdf pdf-am ps ps-am \ + tags tags-am uninstall uninstall-am .PRECIOUS: Makefile diff --git a/src/svaba/Makefile.in b/src/svaba/Makefile.in index 6d20ef2..fddb7ea 100644 --- a/src/svaba/Makefile.in +++ b/src/svaba/Makefile.in @@ -1,7 +1,7 @@ -# Makefile.in generated by automake 1.15 from Makefile.am. +# Makefile.in generated by automake 1.16.1 from Makefile.am. # @configure_input@ -# Copyright (C) 1994-2014 Free Software Foundation, Inc. +# Copyright (C) 1994-2018 Free Software Foundation, Inc. # This Makefile.in is free software; the Free Software Foundation # gives unlimited permission to copy and/or distribute it, @@ -138,7 +138,24 @@ am__v_at_0 = @ am__v_at_1 = DEFAULT_INCLUDES = -I.@am__isrc@ -I$(top_builddir) depcomp = $(SHELL) $(top_srcdir)/depcomp -am__depfiles_maybe = depfiles +am__maybe_remake_depfiles = depfiles +am__depfiles_remade = ./$(DEPDIR)/svaba-AlignedContig.Po \ + ./$(DEPDIR)/svaba-AlignmentFragment.Po \ + ./$(DEPDIR)/svaba-BamStats.Po ./$(DEPDIR)/svaba-BreakPoint.Po \ + ./$(DEPDIR)/svaba-DBSnpFilter.Po \ + ./$(DEPDIR)/svaba-DiscordantCluster.Po \ + ./$(DEPDIR)/svaba-DiscordantRealigner.Po \ + ./$(DEPDIR)/svaba-Histogram.Po ./$(DEPDIR)/svaba-KmerFilter.Po \ + ./$(DEPDIR)/svaba-LearnBamParams.Po \ + ./$(DEPDIR)/svaba-PONFilter.Po ./$(DEPDIR)/svaba-STCoverage.Po \ + ./$(DEPDIR)/svaba-refilter.Po ./$(DEPDIR)/svaba-run_svaba.Po \ + ./$(DEPDIR)/svaba-svaba.Po ./$(DEPDIR)/svaba-svabaASQG.Po \ + ./$(DEPDIR)/svaba-svabaAssemble.Po \ + ./$(DEPDIR)/svaba-svabaAssemblerEngine.Po \ + ./$(DEPDIR)/svaba-svabaBamWalker.Po \ + ./$(DEPDIR)/svaba-svabaOverlapAlgorithm.Po \ + ./$(DEPDIR)/svaba-svabaRead.Po ./$(DEPDIR)/svaba-svabaUtils.Po \ + ./$(DEPDIR)/svaba-vcf.Po am__mv = mv -f AM_V_lt = $(am__v_lt_@AM_V@) am__v_lt_ = $(am__v_lt_@AM_DEFAULT_V@) @@ -332,8 +349,8 @@ Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status *config.status*) \ cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh;; \ *) \ - echo ' cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__depfiles_maybe)'; \ - cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__depfiles_maybe);; \ + echo ' cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__maybe_remake_depfiles)'; \ + cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__maybe_remake_depfiles);; \ esac; $(top_builddir)/config.status: $(top_srcdir)/configure $(CONFIG_STATUS_DEPENDENCIES) @@ -397,29 +414,35 @@ mostlyclean-compile: distclean-compile: -rm -f *.tab.c -@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/svaba-AlignedContig.Po@am__quote@ -@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/svaba-AlignmentFragment.Po@am__quote@ -@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/svaba-BamStats.Po@am__quote@ -@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/svaba-BreakPoint.Po@am__quote@ -@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/svaba-DBSnpFilter.Po@am__quote@ -@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/svaba-DiscordantCluster.Po@am__quote@ -@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/svaba-DiscordantRealigner.Po@am__quote@ -@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/svaba-Histogram.Po@am__quote@ -@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/svaba-KmerFilter.Po@am__quote@ -@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/svaba-LearnBamParams.Po@am__quote@ -@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/svaba-PONFilter.Po@am__quote@ -@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/svaba-STCoverage.Po@am__quote@ -@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/svaba-refilter.Po@am__quote@ -@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/svaba-run_svaba.Po@am__quote@ -@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/svaba-svaba.Po@am__quote@ -@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/svaba-svabaASQG.Po@am__quote@ -@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/svaba-svabaAssemble.Po@am__quote@ -@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/svaba-svabaAssemblerEngine.Po@am__quote@ -@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/svaba-svabaBamWalker.Po@am__quote@ -@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/svaba-svabaOverlapAlgorithm.Po@am__quote@ -@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/svaba-svabaRead.Po@am__quote@ -@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/svaba-svabaUtils.Po@am__quote@ -@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/svaba-vcf.Po@am__quote@ +@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/svaba-AlignedContig.Po@am__quote@ # am--include-marker +@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/svaba-AlignmentFragment.Po@am__quote@ # am--include-marker +@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/svaba-BamStats.Po@am__quote@ # am--include-marker +@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/svaba-BreakPoint.Po@am__quote@ # am--include-marker +@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/svaba-DBSnpFilter.Po@am__quote@ # am--include-marker +@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/svaba-DiscordantCluster.Po@am__quote@ # am--include-marker +@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/svaba-DiscordantRealigner.Po@am__quote@ # am--include-marker +@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/svaba-Histogram.Po@am__quote@ # am--include-marker +@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/svaba-KmerFilter.Po@am__quote@ # am--include-marker +@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/svaba-LearnBamParams.Po@am__quote@ # am--include-marker +@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/svaba-PONFilter.Po@am__quote@ # am--include-marker +@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/svaba-STCoverage.Po@am__quote@ # am--include-marker +@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/svaba-refilter.Po@am__quote@ # am--include-marker +@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/svaba-run_svaba.Po@am__quote@ # am--include-marker +@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/svaba-svaba.Po@am__quote@ # am--include-marker +@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/svaba-svabaASQG.Po@am__quote@ # am--include-marker +@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/svaba-svabaAssemble.Po@am__quote@ # am--include-marker +@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/svaba-svabaAssemblerEngine.Po@am__quote@ # am--include-marker +@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/svaba-svabaBamWalker.Po@am__quote@ # am--include-marker +@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/svaba-svabaOverlapAlgorithm.Po@am__quote@ # am--include-marker +@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/svaba-svabaRead.Po@am__quote@ # am--include-marker +@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/svaba-svabaUtils.Po@am__quote@ # am--include-marker +@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/svaba-vcf.Po@am__quote@ # am--include-marker + +$(am__depfiles_remade): + @$(MKDIR_P) $(@D) + @echo '# dummy' >$@-t && $(am__mv) $@-t $@ + +am--depfiles: $(am__depfiles_remade) .cpp.o: @am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXXCOMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ $< @@ -809,7 +832,10 @@ cscopelist-am: $(am__tagged_files) distclean-tags: -rm -f TAGS ID GTAGS GRTAGS GSYMS GPATH tags -distdir: $(DISTFILES) +distdir: $(BUILT_SOURCES) + $(MAKE) $(AM_MAKEFLAGS) distdir-am + +distdir-am: $(DISTFILES) @srcdirstrip=`echo "$(srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \ topsrcdirstrip=`echo "$(top_srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \ list='$(DISTFILES)'; \ @@ -880,7 +906,29 @@ clean: clean-am clean-am: clean-binPROGRAMS clean-generic mostlyclean-am distclean: distclean-am - -rm -rf ./$(DEPDIR) + -rm -f ./$(DEPDIR)/svaba-AlignedContig.Po + -rm -f ./$(DEPDIR)/svaba-AlignmentFragment.Po + -rm -f ./$(DEPDIR)/svaba-BamStats.Po + -rm -f ./$(DEPDIR)/svaba-BreakPoint.Po + -rm -f ./$(DEPDIR)/svaba-DBSnpFilter.Po + -rm -f ./$(DEPDIR)/svaba-DiscordantCluster.Po + -rm -f ./$(DEPDIR)/svaba-DiscordantRealigner.Po + -rm -f ./$(DEPDIR)/svaba-Histogram.Po + -rm -f ./$(DEPDIR)/svaba-KmerFilter.Po + -rm -f ./$(DEPDIR)/svaba-LearnBamParams.Po + -rm -f ./$(DEPDIR)/svaba-PONFilter.Po + -rm -f ./$(DEPDIR)/svaba-STCoverage.Po + -rm -f ./$(DEPDIR)/svaba-refilter.Po + -rm -f ./$(DEPDIR)/svaba-run_svaba.Po + -rm -f ./$(DEPDIR)/svaba-svaba.Po + -rm -f ./$(DEPDIR)/svaba-svabaASQG.Po + -rm -f ./$(DEPDIR)/svaba-svabaAssemble.Po + -rm -f ./$(DEPDIR)/svaba-svabaAssemblerEngine.Po + -rm -f ./$(DEPDIR)/svaba-svabaBamWalker.Po + -rm -f ./$(DEPDIR)/svaba-svabaOverlapAlgorithm.Po + -rm -f ./$(DEPDIR)/svaba-svabaRead.Po + -rm -f ./$(DEPDIR)/svaba-svabaUtils.Po + -rm -f ./$(DEPDIR)/svaba-vcf.Po -rm -f Makefile distclean-am: clean-am distclean-compile distclean-generic \ distclean-tags @@ -926,7 +974,29 @@ install-ps-am: installcheck-am: maintainer-clean: maintainer-clean-am - -rm -rf ./$(DEPDIR) + -rm -f ./$(DEPDIR)/svaba-AlignedContig.Po + -rm -f ./$(DEPDIR)/svaba-AlignmentFragment.Po + -rm -f ./$(DEPDIR)/svaba-BamStats.Po + -rm -f ./$(DEPDIR)/svaba-BreakPoint.Po + -rm -f ./$(DEPDIR)/svaba-DBSnpFilter.Po + -rm -f ./$(DEPDIR)/svaba-DiscordantCluster.Po + -rm -f ./$(DEPDIR)/svaba-DiscordantRealigner.Po + -rm -f ./$(DEPDIR)/svaba-Histogram.Po + -rm -f ./$(DEPDIR)/svaba-KmerFilter.Po + -rm -f ./$(DEPDIR)/svaba-LearnBamParams.Po + -rm -f ./$(DEPDIR)/svaba-PONFilter.Po + -rm -f ./$(DEPDIR)/svaba-STCoverage.Po + -rm -f ./$(DEPDIR)/svaba-refilter.Po + -rm -f ./$(DEPDIR)/svaba-run_svaba.Po + -rm -f ./$(DEPDIR)/svaba-svaba.Po + -rm -f ./$(DEPDIR)/svaba-svabaASQG.Po + -rm -f ./$(DEPDIR)/svaba-svabaAssemble.Po + -rm -f ./$(DEPDIR)/svaba-svabaAssemblerEngine.Po + -rm -f ./$(DEPDIR)/svaba-svabaBamWalker.Po + -rm -f ./$(DEPDIR)/svaba-svabaOverlapAlgorithm.Po + -rm -f ./$(DEPDIR)/svaba-svabaRead.Po + -rm -f ./$(DEPDIR)/svaba-svabaUtils.Po + -rm -f ./$(DEPDIR)/svaba-vcf.Po -rm -f Makefile maintainer-clean-am: distclean-am maintainer-clean-generic @@ -946,7 +1016,7 @@ uninstall-am: uninstall-binPROGRAMS .MAKE: install-am install-strip -.PHONY: CTAGS GTAGS TAGS all all-am check check-am clean \ +.PHONY: CTAGS GTAGS TAGS all all-am am--depfiles check check-am clean \ clean-binPROGRAMS clean-generic cscopelist-am ctags ctags-am \ distclean distclean-compile distclean-generic distclean-tags \ distdir dvi dvi-am html html-am info info-am install \ From e9a82f66a23c27c95c87c0d971979217c27b91a4 Mon Sep 17 00:00:00 2001 From: Jeremiah Wala Date: Fri, 1 Mar 2019 11:37:49 -0500 Subject: [PATCH 5/6] updated SeqLib module --- SeqLib | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/SeqLib b/SeqLib index af5dbb1..f7a89a1 160000 --- a/SeqLib +++ b/SeqLib @@ -1 +1 @@ -Subproject commit af5dbb16e71879d1e306c092b0794b6732f45696 +Subproject commit f7a89a127409a3f52fdf725fa74e5438c68e48fb From e91ab4bb22ef7f32082f59fd3e5ae2fa8aebdce4 Mon Sep 17 00:00:00 2001 From: Jeremiah Wala Date: Fri, 1 Mar 2019 11:55:36 -0500 Subject: [PATCH 6/6] added lzma and lbz2 flags to build --- configure | 2 +- configure.ac | 2 +- src/svaba/Makefile.am | 3 ++- src/svaba/Makefile.in | 3 ++- 4 files changed, 6 insertions(+), 4 deletions(-) diff --git a/configure b/configure index 81e9889..0d3af1f 100755 --- a/configure +++ b/configure @@ -4843,7 +4843,7 @@ AM_CXXFLAGS="-g -Wall -Wextra $fail_on_warning -Wno-unknown-pragmas -std=c++11 - ##AC_SUBST(CXXFLAGS, "-O3") ##AC_SUBST(CFLAGS, "-O3") ##AC_SUBST(CPPFLAGS, "$CPPFLAGS $boost_include") -LDFLAGS="$LDFLAGS -pthread -std=c++11 -lbz2 -llzma" +LDFLAGS="$LDFLAGS -pthread -std=c++11" # We always need to specify to link to certain libraries diff --git a/configure.ac b/configure.ac index ec6e01f..90d3a79 100644 --- a/configure.ac +++ b/configure.ac @@ -45,7 +45,7 @@ AC_SUBST(AM_CXXFLAGS, "-g -Wall -Wextra $fail_on_warning -Wno-unknown-pragmas -s ##AC_SUBST(CXXFLAGS, "-O3") ##AC_SUBST(CFLAGS, "-O3") ##AC_SUBST(CPPFLAGS, "$CPPFLAGS $boost_include") -AC_SUBST(LDFLAGS, "$LDFLAGS -pthread -std=c++11 -lbz2 -llzma") +AC_SUBST(LDFLAGS, "$LDFLAGS -pthread -std=c++11") # We always need to specify to link to certain libraries ##AC_SUBST(LIBS, "$LIBS") # libboost_regex.a libboost_filesystem.a libboost_system.a") diff --git a/src/svaba/Makefile.am b/src/svaba/Makefile.am index cbdc8ff..8a12f79 100644 --- a/src/svaba/Makefile.am +++ b/src/svaba/Makefile.am @@ -22,7 +22,8 @@ svaba_LDADD = \ $(top_builddir)/SeqLib/src/libseqlib.a \ $(top_builddir)/SeqLib/bwa/libbwa.a \ $(top_builddir)/SeqLib/htslib/libhts.a \ - $(top_builddir)/SeqLib/fermi-lite/libfml.a + $(top_builddir)/SeqLib/fermi-lite/libfml.a \ + -llzma -lbz2 -lz ##svaba_LDFLAGS = -pthread -std=c++11 diff --git a/src/svaba/Makefile.in b/src/svaba/Makefile.in index fddb7ea..52ab41e 100644 --- a/src/svaba/Makefile.in +++ b/src/svaba/Makefile.in @@ -318,7 +318,8 @@ svaba_LDADD = \ $(top_builddir)/SeqLib/src/libseqlib.a \ $(top_builddir)/SeqLib/bwa/libbwa.a \ $(top_builddir)/SeqLib/htslib/libhts.a \ - $(top_builddir)/SeqLib/fermi-lite/libfml.a + $(top_builddir)/SeqLib/fermi-lite/libfml.a \ + -llzma -lbz2 -lz svaba_SOURCES = run_svaba.cpp BreakPoint.cpp AlignedContig.cpp AlignmentFragment.cpp \ DiscordantCluster.cpp DBSnpFilter.cpp PONFilter.cpp \