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A few small conversion fixes #570

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merged 2 commits into from Feb 12, 2015

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fnothaft commented Feb 6, 2015

Resolves #479. Also adds a bit of logging to the legacy format converters.

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Test PASSed.
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Rebased.

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fnothaft commented Feb 11, 2015

Rebased.

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Test PASSed.
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// Position of the mate/next segment
val mateReference: Int = samRecord.getMateReferenceIndex
// Position of the mate/next segment
val mateReference: Int = samRecord.getMateReferenceIndex

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Is this indentation intentional? I'm surprised that Scalariform didn't complain.

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massie Feb 11, 2015

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Is this indentation intentional? I'm surprised that Scalariform didn't complain.

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fnothaft Feb 12, 2015

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The patch modifies the conditionals surrounding this code block, which leads to an indentation change for this stretch of code.

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fnothaft Feb 12, 2015

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The patch modifies the conditionals surrounding this code block, which leads to an indentation change for this stretch of code.

if (mateReference != SAMRecord.NO_ALIGNMENT_REFERENCE_INDEX) {
builder.setMateContig(SequenceRecord.toADAMContig(dict(samRecord.getMateReferenceName).get))
if (mateReference != SAMRecord.NO_ALIGNMENT_REFERENCE_INDEX) {
builder.setMateContig(SequenceRecord.toADAMContig(dict(samRecord.getMateReferenceName).get))

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massie Feb 11, 2015

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Same here.

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massie Feb 11, 2015

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Same here.

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Thanks, Frank!

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massie commented Feb 12, 2015

Thanks, Frank!

massie added a commit that referenced this pull request Feb 12, 2015

@massie massie merged commit a760b9d into bigdatagenomics:master Feb 12, 2015

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@simplelive simplelive referenced this pull request Apr 7, 2015

Closed

adam-submit VerifyError #642

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