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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,7 +1,7 @@ | ||
| /* bam_sample.c -- group data by sample. | ||
| Copyright (C) 2010, 2011 Broad Institute. | ||
| Copyright (C) 2013, 2016 Genome Research Ltd. | ||
| Copyright (C) 2013, 2016-2018 Genome Research Ltd. | ||
| Author: Heng Li <[email protected]>, Petr Danecek <[email protected]> | ||
|
|
@@ -167,10 +167,14 @@ int bam_smpl_add_bam(bam_smpl_t *bsmpl, char *bam_hdr, const char *fname) | |
| void *bam_smpls = khash_str2int_init(); | ||
| int first_smpl = -1, nskipped = 0; | ||
| const char *p = bam_hdr, *q, *r; | ||
| while ((q = strstr(p, "@RG")) != 0) | ||
| while (p != NULL && (q = strstr(p, "@RG")) != 0) | ||
| { | ||
| char *eol = strchr(q + 3, '\n'); | ||
| if (q > bam_hdr && *(q - 1) != '\n') { // @RG must be at start of line | ||
| p = eol; | ||
| continue; | ||
| } | ||
| p = q + 3; | ||
| r = q = 0; | ||
| if ((q = strstr(p, "\tID:")) != 0) q += 4; | ||
| if ((r = strstr(p, "\tSM:")) != 0) r += 4; | ||
| if (r && q) | ||
|
|
@@ -220,7 +224,7 @@ int bam_smpl_add_bam(bam_smpl_t *bsmpl, char *bam_hdr, const char *fname) | |
| } | ||
| else | ||
| break; | ||
| p = q > r ? q : r; | ||
| p = eol; | ||
| } | ||
| int nsmpls = khash_str2int_size(bam_smpls); | ||
| khash_str2int_destroy_free(bam_smpls); | ||
|
|
@@ -234,6 +238,7 @@ int bam_smpl_add_bam(bam_smpl_t *bsmpl, char *bam_hdr, const char *fname) | |
| { | ||
| // no suitable read group is available in this bam: ignore the whole file. | ||
| free(file->fname); | ||
| if ( file->rg2idx ) khash_str2int_destroy_free(file->rg2idx); | ||
| bsmpl->nfiles--; | ||
| return -1; | ||
| } | ||
|
|
||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
|
|
@@ -23,13 +23,14 @@ | |
| # DEALINGS IN THE SOFTWARE. | ||
|
|
||
| dnl Process this file with autoconf to produce a configure script | ||
| AC_INIT([BCFtools], m4_esyscmd_s([make print-version]), | ||
| AC_INIT([BCFtools], m4_esyscmd_s([./version.sh 2>/dev/null]), | ||
| [[email protected]], [], [http://www.htslib.org/]) | ||
| AC_PREREQ([2.63]) dnl This version introduced 4-argument AC_CHECK_HEADER | ||
| AC_CONFIG_SRCDIR([main.c]) | ||
| AC_CONFIG_HEADERS([config.h]) | ||
|
|
||
| m4_include([m4/ax_with_htslib.m4]) | ||
| m4_include([m4/hts_prog_cc_warnings.m4]) | ||
|
|
||
| dnl Copyright notice to be copied into the generated configure script | ||
| AC_COPYRIGHT([Portions copyright (C) 2015,2017 Genome Research Ltd. | ||
|
|
@@ -39,6 +40,12 @@ redistribute it. There is NO WARRANTY, to the extent permitted by law.]) | |
|
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| AC_PROG_CC | ||
|
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||
| dnl Turn on compiler warnings, if possible | ||
| HTS_PROG_CC_WARNINGS | ||
| dnl Flags to treat warnings as errors. These need to be applied to CFLAGS | ||
| dnl later as they can interfere with some of the tests (notably AC_SEARCH_LIBS) | ||
| HTS_PROG_CC_WERROR(hts_late_cflags) | ||
|
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| AC_SYS_LARGEFILE | ||
|
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| AC_ARG_ENABLE([bcftools-plugins], | ||
|
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@@ -214,10 +221,11 @@ AS_IF([test "$enable_perl_filters" != "no" ], [dnl | |
| PERL_LIBS="`perl -MExtUtils::Embed -e ldopts`" | ||
| AC_SUBST([PERL_CCOPTS]) | ||
| AC_SUBST([PERL_LIBS]) | ||
| USE_GPL=1 | ||
| AC_SUBST([USE_GPL]) | ||
| ]) | ||
|
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||
| dnl Apply value from HTS_PROG_CC_WERROR (if set) | ||
| AS_IF([test "x$hts_late_cflags" != x],[CFLAGS="$CFLAGS $hts_late_cflags"]) | ||
|
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| AC_CONFIG_FILES([config.mk]) | ||
| AC_OUTPUT | ||
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