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Merge pull request #84 from jblachly/readgroupfix 

Forbid literal TAB control characters in @RG line
This commit is contained in:
Heng Li 2017-07-30 18:56:39 -04:00 committed by GitHub
parent 24a8d66481 8cc02badd9
commit 1eee77ad93
1 changed files with 5 additions and 1 deletions
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6
bwa.c
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@ -424,10 +424,14 @@ char *bwa_set_rg(const char *s)
if (bwa_verbose >= 1) fprintf(stderr, "[E::%s] the read group line is not started with @RG\n", __func__);
goto err_set_rg;
}
if (strstr(s, "\t") != NULL) {
if (bwa_verbose >= 1) fprintf(stderr, "[E::%s] the read group line contained literal <tab> characters -- replace with escaped tabs: \\t\n", __func__);
goto err_set_rg;
}
rg_line = strdup(s);
bwa_escape(rg_line);
if ((p = strstr(rg_line, "\tID:")) == 0) {
if (bwa_verbose >= 1) fprintf(stderr, "[E::%s] no ID at the read group line\n", __func__);
if (bwa_verbose >= 1) fprintf(stderr, "[E::%s] no ID within the read group line\n", __func__);
goto err_set_rg;
}
p += 4;