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fix BAM/SAM header setting when writing on cluster #691

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merged 1 commit into from Jun 2, 2015

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ryan-williams commented Jun 1, 2015

fixes #676

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test failure should be fixed. Jenkins, retest this please?

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ryan-williams commented Jun 1, 2015

test failure should be fixed. Jenkins, retest this please?

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Jenkins, retest this please

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ryan-williams commented Jun 1, 2015

Jenkins, retest this please

@fnothaft fnothaft added this to the 0.17.0 milestone Jun 1, 2015

@@ -68,7 +68,7 @@ class IlluminaOptics(val tile: Long, val x: Long, val y: Long) {}
class RichAlignmentRecord(val record: AlignmentRecord) {
lazy val referenceLength: Int = RichAlignmentRecord.referenceLengthFromCigar(record.getCigar.toString)
lazy val referenceLength: Int = RichAlignmentRecord.referenceLengthFromCigar(record.getCigar)

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Thanks for getting these; we've got several redundant toStrings hanging around from the pre-bdg-formats/36 merged.

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Thanks for getting these; we've got several redundant toStrings hanging around from the pre-bdg-formats/36 merged.

fix BAM/SAM header setting when writing on cluster
  fixes #676

- formatting / unnecessary `.toString` nits

- one more header fix

- whitespace nits
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rebased and squashed

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ryan-williams commented Jun 1, 2015

rebased and squashed

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Jenkins, retest this please.

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fnothaft commented Jun 2, 2015

Jenkins, retest this please.

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Another head-scratcher:

FATAL: Could not checkout null with start point 8bb41727766ea4ca8c51379f77036be0ca64701e
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ryan-williams commented Jun 2, 2015

Another head-scratcher:

FATAL: Could not checkout null with start point 8bb41727766ea4ca8c51379f77036be0ca64701e
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Jenkins, retest this please.

@ryan-williams that's a known issue in the Jenkins Github Pull Request Builder plugin. It occasionally fails to check out the PR after a force push to the branch.

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fnothaft commented Jun 2, 2015

Jenkins, retest this please.

@ryan-williams that's a known issue in the Jenkins Github Pull Request Builder plugin. It occasionally fails to check out the PR after a force push to the branch.

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ah, good to know! I'll try to hold off the force-push-squash until after I've gotten a green build in the future.

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ryan-williams commented Jun 2, 2015

ah, good to know! I'll try to hold off the force-push-squash until after I've gotten a green build in the future.

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Jenkins, retest this please.

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fnothaft commented Jun 2, 2015

Jenkins, retest this please.

fnothaft added a commit that referenced this pull request Jun 2, 2015

Merge pull request #691 from ryan-williams/sam-cluster
fix BAM/SAM header setting when writing on cluster

@fnothaft fnothaft merged commit 2b5c8e9 into bigdatagenomics:master Jun 2, 2015

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Merged! Thanks @ryan-williams!

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fnothaft commented Jun 2, 2015

Merged! Thanks @ryan-williams!

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nice! thank you, @fnothaft!

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ryan-williams commented Jun 2, 2015

nice! thank you, @fnothaft!

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