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comparison PsiCLASS-1.0.2/samtools-0.1.19/Makefile @ 0:903fc43d6227 draft default tip

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author lsong10
date Fri, 26 Mar 2021 16:52:45 +0000
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-1:000000000000 0:903fc43d6227
1 CC= gcc
2 CFLAGS= -g -Wall -O2
3 #LDFLAGS= -Wl,-rpath,\$$ORIGIN/../lib
4 DFLAGS= -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0
5 KNETFILE_O= knetfile.o
6 LOBJS= bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o \
7 bam_pileup.o bam_lpileup.o bam_md.o razf.o faidx.o bedidx.o \
8 $(KNETFILE_O) bam_sort.o sam_header.o bam_reheader.o kprobaln.o bam_cat.o
9 AOBJS= bam_tview.o bam_plcmd.o sam_view.o \
10 bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o \
11 bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o \
12 cut_target.o phase.o bam2depth.o padding.o bedcov.o bamshuf.o \
13 bam_tview_curses.o bam_tview_html.o
14 PROG= samtools
15 INCLUDES= -I.
16 SUBDIRS= . bcftools misc
17 LIBPATH=
18 LIBCURSES= # -lXCurses
19
20 .SUFFIXES:.c .o
21 .PHONY: all lib
22
23 .c.o:
24 $(CC) -c $(CFLAGS) $(DFLAGS) $(INCLUDES) $< -o $@
25
26 all-recur lib-recur clean-recur cleanlocal-recur install-recur:
27 @target=`echo $@ | sed s/-recur//`; \
28 wdir=`pwd`; \
29 list='$(SUBDIRS)'; for subdir in $$list; do \
30 cd $$subdir; \
31 $(MAKE) CC="$(CC)" DFLAGS="$(DFLAGS)" CFLAGS="$(CFLAGS)" \
32 INCLUDES="$(INCLUDES)" LIBPATH="$(LIBPATH)" $$target || exit 1; \
33 cd $$wdir; \
34 done;
35
36 all:$(PROG)
37
38 .PHONY:all lib clean cleanlocal
39 .PHONY:all-recur lib-recur clean-recur cleanlocal-recur install-recur
40
41 lib:libbam.a
42
43 libbam.a:$(LOBJS)
44 $(AR) -csru $@ $(LOBJS)
45
46 samtools:lib-recur $(AOBJS)
47 $(CC) $(CFLAGS) -o $@ $(AOBJS) $(LDFLAGS) libbam.a -Lbcftools -lbcf $(LIBPATH) $(LIBCURSES) -lm -lz -lpthread
48
49 razip:razip.o razf.o $(KNETFILE_O)
50 $(CC) $(CFLAGS) -o $@ $^ -lz
51
52 bgzip:bgzip.o bgzf.o $(KNETFILE_O)
53 $(CC) $(CFLAGS) -o $@ $^ -lz -lpthread
54
55 bgzf.o:bgzf.c bgzf.h
56 $(CC) -c $(CFLAGS) $(DFLAGS) -DBGZF_CACHE $(INCLUDES) bgzf.c -o $@
57
58 razip.o:razf.h
59 bam.o:bam.h razf.h bam_endian.h kstring.h sam_header.h
60 sam.o:sam.h bam.h
61 bam_import.o:bam.h kseq.h khash.h razf.h
62 bam_pileup.o:bam.h razf.h ksort.h
63 bam_plcmd.o:bam.h faidx.h bcftools/bcf.h bam2bcf.h
64 bam_index.o:bam.h khash.h ksort.h razf.h bam_endian.h
65 bam_lpileup.o:bam.h ksort.h
66 bam_tview.o:bam.h faidx.h bam_tview.h
67 bam_tview_curses.o:bam.h faidx.h bam_tview.h
68 bam_tview_html.o:bam.h faidx.h bam_tview.h
69 bam_sort.o:bam.h ksort.h razf.h
70 bam_md.o:bam.h faidx.h
71 sam_header.o:sam_header.h khash.h
72 bcf.o:bcftools/bcf.h
73 bam2bcf.o:bam2bcf.h errmod.h bcftools/bcf.h
74 bam2bcf_indel.o:bam2bcf.h
75 errmod.o:errmod.h
76 phase.o:bam.h khash.h ksort.h
77 bamtk.o:bam.h
78
79 faidx.o:faidx.h razf.h khash.h
80 faidx_main.o:faidx.h razf.h
81
82
83 libbam.1.dylib-local:$(LOBJS)
84 libtool -dynamic $(LOBJS) -o libbam.1.dylib -lc -lz
85
86 libbam.so.1-local:$(LOBJS)
87 $(CC) -shared -Wl,-soname,libbam.so -o libbam.so.1 $(LOBJS) -lc -lz
88
89 dylib:
90 @$(MAKE) cleanlocal; \
91 case `uname` in \
92 Linux) $(MAKE) CFLAGS="$(CFLAGS) -fPIC" libbam.so.1-local;; \
93 Darwin) $(MAKE) CFLAGS="$(CFLAGS) -fPIC" libbam.1.dylib-local;; \
94 *) echo 'Unknown OS';; \
95 esac
96
97
98 cleanlocal:
99 rm -fr gmon.out *.o a.out *.exe *.dSYM razip bgzip $(PROG) *~ *.a *.so.* *.so *.dylib
100
101 clean:cleanlocal-recur