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Added filenames to "Unmatched SAI magic" message #20

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Added filenames to "Unmatched SAI magic" message #20

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23 changes: 11 additions & 12 deletions bwape.c
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Original file line number Diff line number Diff line change
Expand Up @@ -643,22 +643,21 @@ void bwa_sai2sam_pe_core(const char *prefix, char *const fn_sa[2], char *const f
for (i = 1; i != 256; ++i) g_log_n[i] = (int)(4.343 * log(i) + 0.5);
bns = bns_restore(prefix);
srand48(bns->seed);
fp_sa[0] = xopen(fn_sa[0], "r");
fp_sa[1] = xopen(fn_sa[1], "r");
g_hash = kh_init(b128);
last_ii.avg = -1.0;

err_fread_noeof(magic[0], 1, 4, fp_sa[0]);
err_fread_noeof(magic[1], 1, 4, fp_sa[1]);
if (strncmp(magic[0], SAI_MAGIC, 4) != 0 || strncmp(magic[1], SAI_MAGIC, 4) != 0) {
fprintf(stderr, "[E::%s] Unmatched SAI magic. Please re-run `aln' with the same version of bwa.\n", __func__);
exit(1);
for (i=0; i<2; i++) {
fp_sa[i] = xopen(fn_sa[i], "r");
err_fread_noeof(magic[i], 1, 4, fp_sa[i]);
if (strncmp(magic[i], SAI_MAGIC, 4) != 0) {
fprintf(stderr, "[E::%s] Unmatched SAI magic in file \"%s\". Please re-run `aln' with the same version of bwa.\n", __func__, fn_sa[i]);
exit(1);
}
err_fread_noeof(&opt, sizeof(gap_opt_t), 1, fp_sa[i]);
ks[i] = bwa_open_reads(opt.mode, fn_fa[i]);
if(!i)
opt0 = opt;
}
err_fread_noeof(&opt, sizeof(gap_opt_t), 1, fp_sa[0]);
ks[0] = bwa_open_reads(opt.mode, fn_fa[0]);
opt0 = opt;
err_fread_noeof(&opt, sizeof(gap_opt_t), 1, fp_sa[1]); // overwritten!
ks[1] = bwa_open_reads(opt.mode, fn_fa[1]);
{ // for Illumina alignment only
if (popt->is_preload) {
strcpy(str, prefix); strcat(str, ".bwt"); bwt = bwt_restore_bwt(str);
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2 changes: 1 addition & 1 deletion bwase.c
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Original file line number Diff line number Diff line change
Expand Up @@ -525,7 +525,7 @@ void bwa_sai2sam_se_core(const char *prefix, const char *fn_sa, const char *fn_f
m_aln = 0;
err_fread_noeof(magic, 1, 4, fp_sa);
if (strncmp(magic, SAI_MAGIC, 4) != 0) {
fprintf(stderr, "[E::%s] Unmatched SAI magic. Please re-run `aln' with the same version of bwa.\n", __func__);
fprintf(stderr, "[E::%s] Unmatched SAI magic in file \"%s\". Please re-run `aln' with the same version of bwa.\n", __func__, fn_sa);
exit(1);
}
err_fread_noeof(&opt, sizeof(gap_opt_t), 1, fp_sa);
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