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mcshanemcshane
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print the version in main command help including git hash if available; print command line and version to vcf header on output
1 parent eba479f commit 2cd7f22

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6 files changed

+55
-13
lines changed

6 files changed

+55
-13
lines changed

‎.gitignore

+3
Original file line numberDiff line numberDiff line change
@@ -19,3 +19,6 @@ utils
1919
*.exe
2020
*.out
2121
*.app
22+
23+
# Version file
24+
/version.h

‎makefile

+17-3
Original file line numberDiff line numberDiff line change
@@ -5,6 +5,20 @@ HTSLIB = $(HTSDIR)/libhts.a
55

66
all: pbwt
77

8+
PBWT_COMMIT_HASH = ""
9+
ifneq "$(wildcard .git)" ""
10+
PBWT_COMMIT_HASH = $(shell git describe --always --long --dirty | sed 's/^[0-9\.]*-*//')
11+
version.h: $(if $(wildcard version.h),$(if $(findstring "$(PBWT_COMMIT_HASH)",$(shell cat version.h)),,force))
12+
endif
13+
version.h:
14+
echo '#define PBWT_COMMIT_HASH "$(PBWT_COMMIT_HASH)"' > $@
15+
16+
force:
17+
18+
.c.o:
19+
gcc -c $(CFLAGS) $(DFLAGS) $(INCLUDES) $< -o $@
20+
21+
822
test:
923
./test/test.pl
1024

@@ -16,7 +30,7 @@ pbwt: $(PBWT_OBJS) utils
1630
autozygExtract: autozygExtract.o
1731
gcc $(CFLAGS) -o autozygExtract autozygExtract.o utils.o $(HTSLIB) -lpthread -lz -lm
1832

19-
pbwtMain.o: pbwtMain.c pbwt.h utils.h
33+
pbwtMain.o: pbwtMain.c version.h pbwt.h utils.h
2034
gcc $(CFLAGS) -c pbwtMain.c
2135

2236
pbwtCore.o: pbwtCore.c pbwt.h utils.h
@@ -72,7 +86,7 @@ utils.o: utils.c utils.h
7286
gcc $(CFLAGS) -c utils.c
7387

7488
clean:
75-
rm -f *.o pbwt *~
89+
rm -f *.o pbwt *~ version.h
7690

77-
.PHONY: all test clean
91+
.PHONY: all test clean force
7892

‎pbwt.h

+4-1
Original file line numberDiff line numberDiff line change
@@ -23,7 +23,10 @@
2323

2424
#include "utils.h"
2525

26-
static int pbwtMajorVersion = 3, pbwtMinorVersion = 0 ;
26+
const static int pbwtMajorVersion = 3, pbwtMinorVersion = 0 ;
27+
28+
const char *pbwtCommitHash(void);
29+
const char *pbwtHtslibVersionString(void);
2730

2831
/* data types */
2932

‎pbwtHtslib.c

+12-2
Original file line numberDiff line numberDiff line change
@@ -16,6 +16,11 @@
1616
#include <htslib/synced_bcf_reader.h>
1717
#include <htslib/faidx.h>
1818

19+
const char *pbwtHtslibVersionString(void)
20+
{
21+
return hts_version();
22+
}
23+
1924
static void readVcfSamples (PBWT *p, bcf_hdr_t *hr)
2025
{
2126
int i, k ;
@@ -228,8 +233,13 @@ void pbwtWriteVcf (PBWT *p, char *filename, char *referenceFasta, char *mode)
228233
bcf_hdr_printf(bcfHeader, "##contig=<ID=%s,length=%d>", p->chrom, 0x7fffffff); // MAX_CSI_COOR
229234
}
230235
kstring_t str = {0,0,0} ;
231-
ksprintf(&str, "##pbwtVersion=%d.%d+htslib-%s",
232-
pbwtMajorVersion, pbwtMinorVersion, hts_version()) ;
236+
if (strcmp(pbwtCommitHash(),"")!=0)
237+
ksprintf(&str, "##pbwtVersion=%d.%d-%s+htslib-%s", pbwtMajorVersion, pbwtMinorVersion, pbwtCommitHash(), pbwtHtslibVersionString()) ;
238+
else
239+
ksprintf(&str, "##pbwtVersion=%d.%d+htslib-%s", pbwtMajorVersion, pbwtMinorVersion, pbwtHtslibVersionString()) ;
240+
bcf_hdr_append(bcfHeader, str.s) ;
241+
str.l = 0;
242+
ksprintf(&str, "##pbwtCommand=pbwt %s", commandLine) ;
233243
bcf_hdr_append(bcfHeader, str.s) ;
234244
free(str.s) ;
235245
bcf_hdr_append(bcfHeader, "##INFO=<ID=AC,Number=A,Type=Integer,Description=\"Allele count in genotypes\">") ;

‎pbwtMain.c

+13-1
Original file line numberDiff line numberDiff line change
@@ -22,6 +22,7 @@
2222
*/
2323

2424
#include "pbwt.h"
25+
#include "version.h"
2526

2627
/*********************************************************/
2728

@@ -166,6 +167,11 @@ static void recordCommandLine (int argc, char *argv[])
166167
#define FOPEN(name,mode) if (!strcmp (argv[1], "-")) fp = !strcmp(mode,"r") ? stdin : stdout ; else if (!(fp = fopen (argv[1],mode))) die ("failed to open %s file", name, argv[1])
167168
#define FCLOSE if (strcmp(argv[1], "-")) fclose(fp)
168169

170+
const char *pbwtCommitHash(void)
171+
{
172+
return PBWT_COMMIT_HASH ;
173+
}
174+
169175
int main (int argc, char *argv[])
170176
{
171177
FILE *fp ;
@@ -179,7 +185,13 @@ int main (int argc, char *argv[])
179185
recordCommandLine (argc, argv) ;
180186

181187
if (!argc) /* print help */
182-
{ fprintf (stderr, "Usage: pbwt [ -<command> [options]* ]+\n") ;
188+
{ fprintf (stderr, "Program: pbwt\n") ;
189+
if (strcmp(pbwtCommitHash(),"")!=0)
190+
fprintf (stderr, "Version: %d.%d-%s (using htslib %s)\n", pbwtMajorVersion, pbwtMinorVersion, pbwtCommitHash(), pbwtHtslibVersionString()) ;
191+
else
192+
fprintf (stderr, "Version: %d.%d (using htslib %s)\n", pbwtMajorVersion, pbwtMinorVersion, pbwtHtslibVersionString()) ;
193+
fprintf (stderr, "Contact: Richard Durbin [[email protected]]\n") ;
194+
fprintf (stderr, "Usage: pbwt [ -<command> [options]* ]+\n") ;
183195
fprintf (stderr, "Commands:\n") ;
184196
fprintf (stderr, " -check do various checks\n") ;
185197
fprintf (stderr, " -stats print stats depending on commands; writes to stdout\n") ;

‎test/test.pl

+6-6
Original file line numberDiff line numberDiff line change
@@ -186,24 +186,24 @@ sub test_pbwt
186186
sub test_write_vcf
187187
{
188188
my ($opts,%args) = @_;
189-
test_cmd($opts,%args,cmd=>"$$opts{bin}/pbwt -read $$opts{tmp}/$args{in}.pbwt -readSites $$opts{tmp}/$args{in}.sites -writeVcf - 2>/dev/null | grep -v ^##pbwtVersion >$$opts{tmp}/$args{out}");
190-
test_cmd($opts,%args,cmd=>"$$opts{bin}/pbwt -read $$opts{tmp}/$args{in}.pbwt -readSites $$opts{tmp}/$args{in}.sites -writeVcfGz - 2>/dev/null | $$opts{bin}/pbwt -readVcfGT - -writeVcf - 2>/dev/null | grep -v ^##pbwtVersion >$$opts{tmp}/$args{out}");
191-
test_cmd($opts,%args,cmd=>"$$opts{bin}/pbwt -read $$opts{tmp}/$args{in}.pbwt -readSites $$opts{tmp}/$args{in}.sites -writeBcf - 2>/dev/null | $$opts{bin}/pbwt -readVcfGT - -writeVcf - 2>/dev/null | grep -v ^##pbwtVersion >$$opts{tmp}/$args{out}");
192-
test_cmd($opts,%args,cmd=>"$$opts{bin}/pbwt -read $$opts{tmp}/$args{in}.pbwt -readSites $$opts{tmp}/$args{in}.sites -writeBcfGz - 2>/dev/null | $$opts{bin}/pbwt -readVcfGT - -writeVcf - 2>/dev/null | grep -v ^##pbwtVersion >$$opts{tmp}/$args{out}");
189+
test_cmd($opts,%args,cmd=>"$$opts{bin}/pbwt -read $$opts{tmp}/$args{in}.pbwt -readSites $$opts{tmp}/$args{in}.sites -writeVcf - 2>/dev/null | grep -v ^##pbwt >$$opts{tmp}/$args{out}");
190+
test_cmd($opts,%args,cmd=>"$$opts{bin}/pbwt -read $$opts{tmp}/$args{in}.pbwt -readSites $$opts{tmp}/$args{in}.sites -writeVcfGz - 2>/dev/null | $$opts{bin}/pbwt -readVcfGT - -writeVcf - 2>/dev/null | grep -v ^##pbwt >$$opts{tmp}/$args{out}");
191+
test_cmd($opts,%args,cmd=>"$$opts{bin}/pbwt -read $$opts{tmp}/$args{in}.pbwt -readSites $$opts{tmp}/$args{in}.sites -writeBcf - 2>/dev/null | $$opts{bin}/pbwt -readVcfGT - -writeVcf - 2>/dev/null | grep -v ^##pbwt >$$opts{tmp}/$args{out}");
192+
test_cmd($opts,%args,cmd=>"$$opts{bin}/pbwt -read $$opts{tmp}/$args{in}.pbwt -readSites $$opts{tmp}/$args{in}.sites -writeBcfGz - 2>/dev/null | $$opts{bin}/pbwt -readVcfGT - -writeVcf - 2>/dev/null | grep -v ^##pbwt >$$opts{tmp}/$args{out}");
193193
}
194194

195195
sub test_read_vcf_gt
196196
{
197197
my ($opts,%args) = @_;
198-
test_cmd($opts,%args,cmd=>"$$opts{bin}/pbwt -readVcfGT $$opts{path}/read.vcf -writeVcf - 2>/dev/null | grep -v ^##pbwtVersion >$$opts{tmp}/$args{out}");
198+
test_cmd($opts,%args,cmd=>"$$opts{bin}/pbwt -readVcfGT $$opts{path}/read.vcf -writeVcf - 2>/dev/null | grep -v ^##pbwt >$$opts{tmp}/$args{out}");
199199
}
200200

201201
sub test_pbwt_reference_impute
202202
{
203203
my ($opts,%args) = @_;
204204
# create reference panel pbwt
205205
cmd("$$opts{bin}/pbwt -readVcfGT $$opts{path}/$args{ref}.vcf -writeAll $$opts{tmp}/$args{ref} 2>/dev/null");
206-
test_cmd($opts,%args,cmd=>"$$opts{bin}/pbwt -readVcfGT $$opts{path}/$args{in}.vcf -referenceImpute $$opts{tmp}/$args{ref} -writeVcf - 2>/dev/null | grep -v ^##pbwtVersion > $$opts{tmp}/$args{out}");
206+
test_cmd($opts,%args,cmd=>"$$opts{bin}/pbwt -readVcfGT $$opts{path}/$args{in}.vcf -referenceImpute $$opts{tmp}/$args{ref} -writeVcf - 2>/dev/null | grep -v ^##pbwt > $$opts{tmp}/$args{out}");
207207
}
208208

209209
sub test_merge

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