prophyle / prophex

ProPhex – an exact k-mer index using Burrows-Wheeler Transform
MIT License
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bwt2fa: Segmentation fault: 11 #21

Open karel-brinda opened 6 years ago

karel-brinda commented 6 years ago
$ "/Users/karel/github/my/prophex/prophex" bwt2fa index.fa index.fa
[prophex:bwt2fa] Loaded bwa index from index.fa
Segmentation fault: 11
$ lldb -- "/Users/karel/github/my/prophex/prophex" bwt2fa index.fa index.fa
(lldb) target create "/Users/karel/github/my/prophex/prophex"
Current executable set to '/Users/karel/github/my/prophex/prophex' (x86_64).
(lldb) settings set -- target.run-args  "bwt2fa" "index.fa" "index.fa"
(lldb) run
Process 40906 launched: '/Users/karel/github/my/prophex/prophex' (x86_64)
[prophex:bwt2fa] Loaded bwa index from index.fa
prophex was compiled with optimization - stepping may behave oddly; variables may not be available.
Process 40906 stopped
* thread #1, queue = 'com.apple.main-thread', stop reason = EXC_BAD_ACCESS (code=EXC_I386_GPFLT)
    frame #0: 0x0000000100024b6d prophex`bwt2fa(prefix=<unavailable>, output_filename="index.fa") at prophex_build.c:130 [opt]
   127      bwtint_t progress_output_step = (bwt->seq_len + 9) / 10;
   128      while (i < bwt->seq_len) {
   129          bwtint_t new_pos = bwt_pos - (bwt_pos > bwt->primary);
-> 130          new_pos = bwt_B0(bwt, new_pos);
   131          seq[bwt->seq_len - i - 1] = "ACGT"[new_pos];
   132          new_pos = bwt->L2[new_pos] + bwt_occ(bwt, bwt_pos, new_pos);
   133          bwt_pos = bwt_pos == bwt->primary ? 0 : new_pos;
Target 0: (prophex) stopped.
(lldb)