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Merge pull request #2 from samtools/develop
Merge upstream changes
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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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