/htsjdk

Added support for an empty NM tag in SA tag fields using '*' character #693

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merged 1 commit into from Sep 15, 2016

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@jamesemery @coveralls @yfarjoun @lbergelson
@jamesemery
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jamesemery commented Aug 31, 2016

Description

Previously when encountered with a '*' in the last field of an SA tag for getOtherCannonicalAlignments() method would throw an exception. It will now gracefully allow for an empty NM field in the new field.

Checklist

  • Code compiles correctly
  • New tests covering changes and new functionality
  • All tests passing
  • Extended the README / documentation, if necessary
  • Is not backward compatible (breaks binary or source compatibility)
@jamesemery jamesemery Added support for an empty NM tag in SA tag fields using '*' character

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continuous-integration/travis-ci/pr — The Travis CI build passed
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coverage/coveralls — Coverage increased (+0.001%) to 68.922%
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720a729
@coveralls

coveralls commented Aug 31, 2016

Coverage Status

Coverage increased (+0.001%) to 68.922% when pulling 720a729 on jamesemery:je_SATagEmptyNMSupprot into c3d5a88 on samtools:master.

yfarjoun was assigned by droazen Sep 13, 2016

@yfarjoun
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yfarjoun commented Sep 14, 2016

👍 thanks @jamesemery

@lbergelson lbergelson merged commit 0e6edc7 into samtools:master Sep 15, 2016
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continuous-integration/travis-ci/pr The Travis CI build passed
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coverage/coveralls Coverage increased (+0.001%) to 68.922%
Details
@lbergelson
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lbergelson commented Sep 15, 2016

this may effect broadinstitute/gatk#2133
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