std::out_of_range when mapping reads

[ghar1821]

Using flexiplex v0.97 or v1.0:

# with 0.97
./flexiplex \
    -l CGATTGACTA \
    -r TGCTAATGCG \
    -b 60 \
    -u 0 \
    -f 6 \
    -e 3 \
    -n test \
    -k $basedir/data/test.ref.txt \
    -p 6 \
    test_37.fasta

# with 1.0
./flexiplex 
    -x CGATTGACTA \
    -b ???????????????????????????????????????????????????????????? \
    -u "" \
    -x TGCTAATGCG \
    -f 6 \
    -e 3 \
    -n test \
    -k test.ref.txt \
    -p 4 \
    test_37.fasta

I ran into an error:

v0.97:

terminate called after throwing an instance of 'std::out_of_range'
  what():  basic_string::substr
run_flexiplex.sh: line 5:  6881 Aborted                 (core dumped)

v1.0:

terminate called after throwing an instance of 'std::out_of_range'
    what():  basic_string::substr
  .command.sh: line 3: 52008 Aborted                 (core dumped)

The content of test_37.fasta file is:

>Cell_fake
ACTAGAGCTTTAAAGGTAACGTTCGAGGGAGGTTTGGAAGTTGCGTTGCACGATACATGG
GTTCTGCTAATGCGTACTGACTAGGCTAGCAAAAGAAAAGGGGGGACTGGAAGGGCTAAT
TCACTCCCAACGAAGACAAGATCTGCTTTT

Not quite sure what the problem is. When grepping the left and right flank, it can find the right flank but not the left. Could this be the problem?

[olliecheng]

Hi, thanks for reporting this! It seems like there is a partial match at the start of the string, which then had an offset applied. This resulted in an attempt to find substrings from index -1, which is out of bounds. Should be fixed now in #30, can you try that now? Thanks!

[ghar1821]

I think it's fixed now (tested it on a small data). I'll test it on the bigger one now. Should still be fine. Tyvm for the speedy fix!

[olliecheng]

Perfect, let me know when you've tried it on the bigger set to see if it works - if so, I'll merge 😁

[ghar1821]

@olliecheng just tested on the bigger set. it's working :)