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[ADAM-785] Add support for all numeric array (TYPE=B) tags, fixes #785 #809

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@jfeala
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jfeala commented Aug 26, 2015

Please review carefully, I'm a Scala beginner! Advice welcome for better, more Scala-ish patterns

  • Extends Attribute model and AttributeUtils.convertSAMTagAndValue to cover the 7 numeric array types [cCsSiIf] described in SAM spec
  • Updates tests to use TextTagCodec used natively by samtools parser
  • Adds a small SAM file with all tag types and tests with loadAlignments
Jake Feala
Add support for all numeric array (TYPE=B) tags
- Extends `Attribute` model and `AttributeUtils.convertSAMTagAndValue` to cover the 7 numeric array types [cCsSiIf] described in SAM spec
- Updates tests to use `TextTagCodec` used natively by samtools parser
- Adds a small SAM file with all tag types and tests with loadAlignments
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Test PASSed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins/job/ADAM-prb/886/
Test PASSed.

AmplabJenkins commented Aug 26, 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/886/
Test PASSed.

@@ -0,0 +1,9 @@
@HD VN:1.4 SO:coordinate
@SQ SN:1 LN:1000
StandardTags 0 1 1 255 10M * 0 0 ACACACACAC ********** NM:i:0 MD:Z:10 XS:A:-

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fnothaft Aug 26, 2015

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Nice read names ;)

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fnothaft Aug 26, 2015

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Nice read names ;)

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Generally looks good to me, other than the small nit above. Thanks for the contribution @jfeala!

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fnothaft commented Aug 26, 2015

Generally looks good to me, other than the small nit above. Thanks for the contribution @jfeala!

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Looks good to me, too. Thanks for the contribution, Jake. Appreciated.

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massie commented Aug 27, 2015

Looks good to me, too. Thanks for the contribution, Jake. Appreciated.

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jfeala Aug 27, 2015

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Thanks, guys. @fnothaft I updated that line, thanks for the suggestion.

Let me know if you want me to squash the extra commit before merge

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jfeala commented Aug 27, 2015

Thanks, guys. @fnothaft I updated that line, thanks for the suggestion.

Let me know if you want me to squash the extra commit before merge

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Test PASSed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins/job/ADAM-prb/891/
Test PASSed.

AmplabJenkins commented Aug 27, 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/891/
Test PASSed.

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Ping for anyone else who wants to review; if no one else wants to review, I will merge this noon PST tomorrow.

@jfeala no worries on squashing; I can take care of that when merging.

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fnothaft commented Aug 28, 2015

Ping for anyone else who wants to review; if no one else wants to review, I will merge this noon PST tomorrow.

@jfeala no worries on squashing; I can take care of that when merging.

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👍

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massie commented Aug 28, 2015

👍

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massie Sep 9, 2015

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Thanks, @jfeala !

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massie commented Sep 9, 2015

Thanks, @jfeala !

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Merged manually after rebase.

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massie commented Sep 9, 2015

Merged manually after rebase.

@massie massie closed this Sep 9, 2015

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