BIO-DIKU / SeqScan

Pattern matching in biological sequences
GNU General Public License v2.0
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Bug in group unit #102

Closed maasha closed 8 years ago

maasha commented 8 years ago
maasha@edna:~/install/src/SeqScan/benchmark$ time -p seqscan -m 10 -P pat_group/seqscan_aa.pat -V data/Aurpu2p4.faa
seqscan_123.2.23

seqscan -m 10 -P pat_group/seqscan_aa.pat -V data/Aurpu2p4.faa

Options:
  help:           false
  pattern:
  pattern_file:   pat_group/seqscan_aa.pat
  complement:     forward
  direction:      forward
  start:          0
  end:            0
  threads:        1
  score_encoding: Phred33
  score_min:      25
  ambiguate:      false
  match_type:     10
  match_file:
  output:
  overlap:        false
  filter:
  version:        false
  verbose:        true

Patterns:
  [DEN]{20}
Assertion failed: (pos!=max_pos), function Initialize, file /Users/maasha/install/src/SeqScan/src/pu/group_unit.cc, line 37.
Abort trap: 6
real 0.28
user 0.02
sys 0.00
RasmusFonseca commented 8 years ago

Where is pat_group/seqscan_aa.pat?

maasha commented 8 years ago

I have:

maasha@edna:~/install/src/SeqScan/benchmark/pat_group$ cat seqscan_aa.pat [DEN]{20} maasha@edna:~/install/src/SeqScan/benchmark/pat_group$ git status On branch group-benchmark Changes not staged for commit: (use "git add ..." to update what will be committed) (use "git checkout -- ..." to discard changes in working directory)

modified: seqscan_aa.pat modified: ../pat_group_neg/seqscan_aa.pat

no changes added to commit (use "git add" and/or "git commit -a")

On Sun, Mar 20, 2016 at 7:51 PM, Rasmus Fonseca notifications@github.com wrote:

Where is pat_group/seqscan_aa.pat?

— You are receiving this because you authored the thread. Reply to this email directly or view it on GitHub https://github.com/BIO-DIKU/SeqScan/issues/102#issuecomment-198987805

RasmusFonseca commented 8 years ago

On branch group-benchmark

Got it.

RasmusFonseca commented 8 years ago

Bug was in repeatunit. Fixed in branch group-benchmark