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Check that paired reads have the same QNAME 

This detects desynchronised input files, which occasionally happens
due to user error or system failure.

Checking the names just after printing them has no real performance
implications because the strings are already in cache.  (It might
be better to check while reading the input, but that would be more
complicated in the two-input-files case.)
This commit is contained in:
John Marshall 2013-06-14 13:57:22 +01:00
parent 7ec8b5c9e7
commit 20dc9dd41a
2 changed files with 3 additions and 0 deletions
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2
bwamem_pair.c
View File

@ -301,6 +301,7 @@ int mem_sam_pe(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t *pac, co
h[1] = mem_reg2aln(opt, bns, pac, s[1].l_seq, s[1].seq, &a[1].a[z[1]]); h[1].mapq = q_se[1]; h[1].flag |= 0x80 | extra_flag;
mem_aln2sam(bns, &str, &s[0], 1, &h[0], 0, &h[1]); s[0].sam = strdup(str.s); str.l = 0;
mem_aln2sam(bns, &str, &s[1], 1, &h[1], 0, &h[0]); s[1].sam = str.s;
if (strcmp(s[0].name, s[1].name) != 0) err_fatal(__func__, "paired reads have different names: \"%s\", \"%s\"\n", s[0].name, s[1].name);
free(h[0].cigar); free(h[1].cigar);
} else goto no_pairing;
return n;
@ -319,6 +320,7 @@ no_pairing:
}
mem_reg2sam_se(opt, bns, pac, &s[0], &a[0], 0x41|extra_flag, &h[1]);
mem_reg2sam_se(opt, bns, pac, &s[1], &a[1], 0x81|extra_flag, &h[0]);
if (strcmp(s[0].name, s[1].name) != 0) err_fatal(__func__, "paired reads have different names: \"%s\", \"%s\"\n", s[0].name, s[1].name);
free(h[0].cigar); free(h[1].cigar);
return n;
}

1
bwape.c
View File

@ -706,6 +706,7 @@ void bwa_sai2sam_pe_core(const char *prefix, char *const fn_sa[2], char *const f
}
bwa_print_sam1(bns, p[0], p[1], opt.mode, opt.max_top2);
bwa_print_sam1(bns, p[1], p[0], opt.mode, opt.max_top2);
if (strcmp(p[0]->name, p[1]->name) != 0) err_fatal(__func__, "paired reads have different names: \"%s\", \"%s\"\n", p[0]->name, p[1]->name);
}
fprintf(stderr, "%.2f sec\n", (float)(clock() - t) / CLOCKS_PER_SEC); t = clock();