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Fix SAM Attribute parser for numeric array tags #782

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merged 1 commit into from Aug 20, 2015

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jfeala commented Aug 20, 2015

Page 6 of the SAMv1 specs allow for numeric array tags (TYPE="B"), with values matching:

[cCsSiIf](,[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?)+

This update of org.bdgenomics.adam.util.AttributeUtils.typedStringToValue skips the first character (a numeric type specifier) plus the leading comma, before trying to convert to a numeric array. This bug was breaking loadAlignments for BAM files generated by the STAR RNA-Seq aligner, which creates type "B" tags by default.

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AmplabJenkins Aug 20, 2015

Can one of the admins verify this patch?

AmplabJenkins commented Aug 20, 2015

Can one of the admins verify this patch?

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Jenkins, add to whitelist.

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fnothaft commented Aug 20, 2015

Jenkins, add to whitelist.

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AmplabJenkins Aug 20, 2015

Test PASSed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins/job/ADAM-prb/847/
Test PASSed.

AmplabJenkins commented Aug 20, 2015

Test PASSed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins/job/ADAM-prb/847/
Test PASSed.

@fnothaft fnothaft merged commit b64937c into bigdatagenomics:master Aug 20, 2015

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Thanks @jfeala! I have merged this manually.

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fnothaft commented Aug 20, 2015

Thanks @jfeala! I have merged this manually.

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