8000 invalid 2 field records introduced after inversion patching · Issue #263 · waveygang/wfmash · GitHub
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invalid 2 field records introduced after inversion patching #263

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ASLeonard opened this issue Aug 9, 2024 · 3 comments
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invalid 2 field records introduced after inversion patching #263

ASLeonard opened this issue Aug 9, 2024 · 3 comments

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@ASLeonard
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I was rerunning alignments with the new version, and something seems to incorrectly be triggering a newline during the record writing, producing an alignment record of just "pt:Z:true iv:Z:false".

This happens rarely (3 chromosomes out of 29, and 2/1/3 times for those chromosomes), but kills seqwish with an error related to an invalid line.

[seqwish::alignments] 8.006 processing alignments
terminate called after throwing an instance of 'std::invalid_argument'
  what():  stoull
Aborted

Every time the errored lines have "pt:Z:true iv:Z:false", but there are other lines with "pt:Z:true iv:Z:false" that are valid (i.e. have 18 fields per alignment). There was also no obvious pattern about the preceding line that would trigger this (but that may irrelevant due to multithreading order).

This is with commit 13882fe. The input file is 306 Mb, so can share that if needed to debug this.

Best,
Alex
@ekg
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ekg commented Aug 9, 2024 via email

@ASLeonard
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I retested one of the failing chromosomes with 087ada0 from #264 and the output correctly had records with only 16/18 fields, so the error seems to be fixed.

@ekg
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ekg commented Aug 19, 2024

Thanks for checking this! I can merge #264 and close this issue.

@ekg ekg closed this as completed Aug 19, 2024
@ASLeonard ASLeonard mentioned this issue Sep 24, 2024
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