Parsing errors when using run_calls.pl
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#6 Parsing errors when using run_calls.pl
Hey, thanks for writing this. It seems to work pretty well.
run_calls.pl seemed to run clean as in your manual/docs once for me. After that it seems to crash out with some minor bugs. There is an illegal line that gets output by VCFFile.pm if there are undefined lines (not sure how they got in there) that causes errors in downstream processing. The script also crashes out if one of the kmers gives no snps, in one place due to a file not getting made (it's ok for later scripts if it's empty) and in another due to a logical error that assumes there is >= 1 variant. I tracked them down and am attaching a patch that fixes things for me and now it runs through without problems so far.
I hope the patch does the right thing and doesn't contaminate results that come out, but they seem like minor bugs that won't affect anything seriously.
Thanks again.
Patch for parse errors, uninitialized values, and zero variant scenarios when using run_calls.pl
Hi! So Sorry for not replying, sourceforge is meant to email me when bugs get raised, but it didn't, and so I didn't know about this. Thanks for the patch, I'll take a look. Some of the things you mention are definitely bugs which I think I have fixed since then. THANKs for this!