Merge pull request #66 from Miaolingfeng/master

Upgrade cgmaptools from py2 to py3
guoweilong · Dec 22, 2023 · afa6e40 · afa6e40
2 parents 9e6617d + 0c80cba
commit afa6e40
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Showing 115 changed files with 1,031 additions and 711 deletions.
diff --git a/cgmaptools b/cgmaptools
@@ -6,6 +6,7 @@
     Copyright (C) Weilong Guo & Ping Zhu
     Contact: Weilong Guo <[email protected]>
              Ping Zhu <[email protected]>
+             Lingfeng Miao <[email protected]>
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal
@@ -44,8 +45,8 @@ import subprocess
 argv_len = len(sys.argv)
 
 def PrintVersion() :
-   print("Version:  0.1.2")
-   print("Updated on: Dec. 14th, 2018")
+   print("Version:  0.1.3")
+   print("Updated on: May. 14th, 2022")
 #
 
 if (argv_len) == 1  or sys.argv[1] in ["-h", "-H", "--help"]:
@@ -92,6 +93,7 @@ if (argv_len) == 1  or sys.argv[1] in ["-h", "-H", "--help"]:
    print("Authors:")
    print("  GUO, Weilong; [email protected];  http://guoweilong.github.io")
    print("  ZHU, Ping; [email protected]; http://perry-zhu.github.io")
+   print("  Miao, Lingfeng; [email protected]; http://miaolingfeng.github.io")
    print("")
 else :
    code1 = sys.argv[1]

diff --git a/include/samtools-0.1.18/bam.o b/include/samtools-0.1.18/bam.o
diff --git a/include/samtools-0.1.18/bam_aux.o b/include/samtools-0.1.18/bam_aux.o
diff --git a/include/samtools-0.1.18/bam_cat.o b/include/samtools-0.1.18/bam_cat.o
diff --git a/include/samtools-0.1.18/bam_import.o b/include/samtools-0.1.18/bam_import.o
diff --git a/include/samtools-0.1.18/bam_index.o b/include/samtools-0.1.18/bam_index.o
diff --git a/include/samtools-0.1.18/bam_lpileup.o b/include/samtools-0.1.18/bam_lpileup.o
diff --git a/include/samtools-0.1.18/bam_md.o b/include/samtools-0.1.18/bam_md.o
diff --git a/include/samtools-0.1.18/bam_pileup.o b/include/samtools-0.1.18/bam_pileup.o
diff --git a/include/samtools-0.1.18/bam_reheader.o b/include/samtools-0.1.18/bam_reheader.o
diff --git a/include/samtools-0.1.18/bam_sort.o b/include/samtools-0.1.18/bam_sort.o
diff --git a/include/samtools-0.1.18/bcftools/bcf.o b/include/samtools-0.1.18/bcftools/bcf.o
diff --git a/include/samtools-0.1.18/bcftools/bcf2qcall.o b/include/samtools-0.1.18/bcftools/bcf2qcall.o
diff --git a/include/samtools-0.1.18/bcftools/bcfutils.o b/include/samtools-0.1.18/bcftools/bcfutils.o
diff --git a/include/samtools-0.1.18/bcftools/em.o b/include/samtools-0.1.18/bcftools/em.o
diff --git a/include/samtools-0.1.18/bcftools/fet.o b/include/samtools-0.1.18/bcftools/fet.o
diff --git a/include/samtools-0.1.18/bcftools/index.o b/include/samtools-0.1.18/bcftools/index.o
diff --git a/include/samtools-0.1.18/bcftools/kfunc.o b/include/samtools-0.1.18/bcftools/kfunc.o
diff --git a/include/samtools-0.1.18/bcftools/kmin.o b/include/samtools-0.1.18/bcftools/kmin.o
diff --git a/include/samtools-0.1.18/bcftools/libbcf.a b/include/samtools-0.1.18/bcftools/libbcf.a
diff --git a/include/samtools-0.1.18/bcftools/mut.o b/include/samtools-0.1.18/bcftools/mut.o
diff --git a/include/samtools-0.1.18/bcftools/prob1.o b/include/samtools-0.1.18/bcftools/prob1.o
diff --git a/include/samtools-0.1.18/bcftools/vcf.o b/include/samtools-0.1.18/bcftools/vcf.o
diff --git a/include/samtools-0.1.18/bedidx.o b/include/samtools-0.1.18/bedidx.o
diff --git a/include/samtools-0.1.18/bgzf.o b/include/samtools-0.1.18/bgzf.o
diff --git a/include/samtools-0.1.18/faidx.o b/include/samtools-0.1.18/faidx.o
diff --git a/include/samtools-0.1.18/knetfile.o b/include/samtools-0.1.18/knetfile.o
diff --git a/include/samtools-0.1.18/kprobaln.o b/include/samtools-0.1.18/kprobaln.o
diff --git a/include/samtools-0.1.18/kstring.o b/include/samtools-0.1.18/kstring.o
diff --git a/include/samtools-0.1.18/libbam.a b/include/samtools-0.1.18/libbam.a
diff --git a/include/samtools-0.1.18/razf.o b/include/samtools-0.1.18/razf.o
diff --git a/include/samtools-0.1.18/sam.o b/include/samtools-0.1.18/sam.o
diff --git a/include/samtools-0.1.18/sam_header.o b/include/samtools-0.1.18/sam_header.o
diff --git a/include/zlib-1.2.8/Makefile b/include/zlib-1.2.8/Makefile
@@ -18,34 +18,34 @@
 
 CC=gcc
 
-CFLAGS=-O3  -DHAVE_HIDDEN
+CFLAGS=-O3  -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN
 #CFLAGS=-O -DMAX_WBITS=14 -DMAX_MEM_LEVEL=7
 #CFLAGS=-g -DDEBUG
 #CFLAGS=-O3 -Wall -Wwrite-strings -Wpointer-arith -Wconversion \
 #           -Wstrict-prototypes -Wmissing-prototypes
 
-SFLAGS=-O3  -fPIC -DHAVE_HIDDEN
+SFLAGS=-O3  -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN
 LDFLAGS= 
 TEST_LDFLAGS=-L. libz.a
-LDSHARED=gcc -dynamiclib -install_name ${exec_prefix}/lib/libz.1.dylib -compatibility_version 1 -current_version 1.2.8
+LDSHARED=gcc -shared -Wl,-soname,libz.so.1,--version-script,zlib.map
 CPP=gcc -E
 
 STATICLIB=libz.a
-SHAREDLIB=libz.dylib
-SHAREDLIBV=libz.1.2.8.dylib
-SHAREDLIBM=libz.1.dylib
+SHAREDLIB=libz.so
+SHAREDLIBV=libz.so.1.2.8
+SHAREDLIBM=libz.so.1
 LIBS=$(STATICLIB) $(SHAREDLIBV)
 
-AR=libtool
-ARFLAGS=-o
+AR=ar
+ARFLAGS=rc
 RANLIB=ranlib
 LDCONFIG=ldconfig
 LDSHAREDLIBC=-lc
 TAR=tar
 SHELL=/bin/sh
 EXE=
 
-prefix =/Users/weilongguo/Documents/program/cgmaptools/src/zlib-1.2.8
+prefix =/data2/user2/miaolf/bin/cgmaptools_for_python3/include/zlib-1.2.8
 exec_prefix =${prefix}
 libdir =${exec_prefix}/lib
 sharedlibdir =${libdir}
@@ -70,7 +70,7 @@ OBJS = $(OBJC) $(OBJA)
 
 PIC_OBJS = $(PIC_OBJC) $(PIC_OBJA)
 
-all: static shared
+all: static shared all64
 
 static: example$(EXE) minigzip$(EXE)
 
@@ -80,7 +80,7 @@ all64: example64$(EXE) minigzip64$(EXE)
 
 check: test
 
-test: all teststatic testshared
+test: all teststatic testshared test64
 
 teststatic: static
 	@TMPST=tmpst_$$; \

diff --git a/include/zlib-1.2.8/adler32.lo b/include/zlib-1.2.8/adler32.lo
diff --git a/include/zlib-1.2.8/adler32.o b/include/zlib-1.2.8/adler32.o
diff --git a/include/zlib-1.2.8/compress.lo b/include/zlib-1.2.8/compress.lo
diff --git a/include/zlib-1.2.8/compress.o b/include/zlib-1.2.8/compress.o