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Forbid literal TAB control characters in @RG line #84

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merged 1 commit into from
Jul 30, 2017
Merged

Forbid literal TAB control characters in @RG line #84

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6 changes: 5 additions & 1 deletion bwa.c
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Original file line number Diff line number Diff line change
Expand Up @@ -414,10 +414,14 @@ 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;
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