pairs from chromap results in seg fault

[olekto]

Hi,
what kind of pairs format have you run PretextMap on? When I try running it on a pairs file from https://github.com/haowenz/chromap, I get a seg fault.

I don't understand what's going on. The content looks like this:

#chromsize: scaffold_1494 13653
#chromsize: scaffold_1496 13619
#chromsize: scaffold_1497 13524
#chromsize: scaffold_1499 13000
#chromsize: scaffold_1500 13000
#chromsize: scaffold_1508 11662
#columns: readID chrom1 pos1 chrom2 pos2 strand1 strand2 pair_type
A00943:441:HCFLNDSX3:1:1256:19244:10238 scaffold_1      61      scaffold_1      50603551        +       -       UU
A00943:441:HCFLNDSX3:1:1314:13286:20306 scaffold_1      67      scaffold_1      518     +       +       UU
A00943:441:HCFLNDSX3:1:2227:30083:30608 scaffold_1      67      scaffold_1      560     +       -       UU
A00943:441:HCFLNDSX3:1:1519:12762:2049  scaffold_1      72      scaffold_1      792     +       -       UU
A00943:441:HCFLNDSX3:1:1126:5177:7388   scaffold_1      97      scaffold_1      566     +       -       UU

So it doesn't follow the format exactly, but only column 1-7 are defined as far as I can see from the format specification. Do you know what goes wrong here?

Thank you.

Sincerely,
Ole

[yumisims]

@muffato I am not able to assign this issue to myself.

[jacquelinemattos]

Hi,
Any news on this? I'm having the same problem here. Thanks!

[yumisims]

Hi, Any news on this? I'm having the same problem here. Thanks!

Hello, thank you for your message. We are looking into this issue and will update the code shortly.

[yumisims]

@olekto and @jacquelinemattos Could you please try the latest release (v0.2.3)? This should resolve the issue. If the problem persists, please share the pairs file with us and we will be happy to take a look. Thank you.