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Crash when QUAL = . #16

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fabbyrob opened this issue Feb 6, 2012 · 2 comments
Closed

Crash when QUAL = . #16

fabbyrob opened this issue Feb 6, 2012 · 2 comments

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@fabbyrob
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fabbyrob commented Feb 6, 2012

I have some sites in my data that have no quality, because no reads mapped there. For example:

scaffold_1 1330 . T . . . Dels=0.01;MQ=6.79;MQ0=0 GT ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./.
scaffold_1 1331 . C . . . Dels=0.01;MQ=6.70;MQ0=0 GT ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./.
scaffold_1 1332 . G . . . Dels=0.00;MQ=6.70;MQ0=0 GT ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./.
scaffold_1 1333 . A . . . Dels=0.00;MQ=6.58;MQ0=0 GT ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./.

The parser breaks on line 444. I've modified my version to give a 0 quality to these records, as a quick fix:

    qual = 0 if row[5] == '.' else (float(row[5]) if '.' in row[5] else int(row[5]))
@jamescasbon
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I think that's fixed in trunk. Which version is this? I should cut a new release.

@fabbyrob
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fabbyrob commented Feb 6, 2012

My HISTORY.md file says release 0.1, so it may very well be fixed in the new version.

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