Merge branch 'master' of github.com:WangGenomicsLab/SeqMule

jchenpku · Feb 13, 2015 · 5a7c4c0 · 5a7c4c0
2 parents 1045ef7 + 055de3b
commit 5a7c4c0
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Showing 2 changed files with 7 additions and 6 deletions.
diff --git a/bin/secondary/pipeline b/bin/secondary/pipeline
@@ -18,6 +18,7 @@ use Pod::Usage qw/pod2usage/;
 use Getopt::Long qw/GetOptions/;
 use File::Copy qw/copy move/;
 use File::Basename qw/basename dirname/;
+use File::Glob ':bsd_glob';
 use Cwd qw/abs_path realpath/;
 use SeqMule::Utils;
 use SeqMule::Parallel;
@@ -2222,8 +2223,8 @@ sub procFQ
 {
     $fq_toggle=1 if $fq1;
     $paired=1 if ($fq1 && $fq2);
-    @fq1_list=split /,/,$fq1 if $fq1; @fq1_list= map { abs_path glob $_ } @fq1_list;
-    @fq2_list=split /,/,$fq2 if $fq2; @fq2_list= map { abs_path glob $_ } @fq2_list;
+    @fq1_list=split /,/,$fq1 if $fq1; @fq1_list= map { abs_path bsd_glob $_ } @fq1_list;
+    @fq2_list=split /,/,$fq2 if $fq2; @fq2_list= map { abs_path bsd_glob $_ } @fq2_list;
     if ( grep { $_ !~ /\.(fq|fastq|fastq\.gz|fq\.gz)$/i } (@fq1_list,@fq2_list) )
     {
 	die "ERROR: All FASTQ files must have suffix .fq.gz .fastq.gz .fq or .fastq\n";
@@ -2385,7 +2386,7 @@ sub procBAM
 {
     my $samtools=&getExe(&SeqMule::Utils::getProgramExe("samtools"));
     @bam_list=split /,/,$bam if $bam; 
-    @bam_list= map { abs_path glob $_ } @bam_list;
+    @bam_list= map { abs_path bsd_glob $_ } @bam_list;
     if (grep { $_ !~ /\.bam$/i } @bam_list)
     {
 	die "ERROR: All BAM files must have suffix .bam\n";

diff --git a/bin/secondary/test_suite b/bin/secondary/test_suite
@@ -10,9 +10,9 @@ my $ncpu=4;
 my $mem="6g"; #request larger mem for GATK
 my $jmem="2500m";
 my $gatknt=4;
-my $exe="/home/yunfeiguo/projects/SeqMule_dev/bin/seqmule";
+my $exe="/home/yunfeiguo/projects/SeqMule/bin/seqmule";
 my $test_folder="/home/yunfeiguo/projects/data/test";
-my $config_folder="/home/yunfeiguo/projects/SeqMule_dev/misc/predefined_config";
+my $config_folder="/home/yunfeiguo/projects/SeqMule/misc/predefined_config";
 #for no merge, no ms
 my $first_fq="part.1.fastq";
 my $second_fq="part.2.fastq";
@@ -85,7 +85,7 @@ for my $q("","-quick")
 		push @cmd, "cd $test_folder";
 
 		#&exec(@cmd) if grep{$count==$_} (84,86,88,90,92,96,98);
-		&exec(@cmd) if $count>=1 and $count<=15;
+		&exec(@cmd) if $count>=0 and $count<=0;
 		$count++;
 	}
     }