[ADAM-1061] Clean up attributes regex and denormalized fields #1080

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fnothaft commented Jul 17, 2016

Resolves #1061 and #483.

@fnothaft fnothaft added this to the 0.20.0 milestone Jul 17, 2016

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Tacked on one more commit (f8aeaf8) that cleans up the SAMRecordConverter class, which had not gotten cleaned up previously.

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fnothaft commented Jul 17, 2016

Tacked on one more commit (f8aeaf8) that cleans up the SAMRecordConverter class, which had not gotten cleaned up previously.

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+ * ADAM, we have promoted some of these fields to "primary" fields, so that we
+ * can more efficiently access them. These include the MD tag, which describes
+ * substitutions against the reference; the OQ tag, which describes the
+ * original read base qualities; and the OP and OC tag, which describe the

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OP and OC tagOP and OC tags

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OP and OC tagOP and OC tags

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LGTM

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heuermh commented Jul 18, 2016

LGTM

@heuermh heuermh modified the milestone: 0.20.0 Jul 18, 2016

@heuermh heuermh changed the title from Clean up attributes regex and denormalized fields to [ADAM-1061] Clean up attributes regex and denormalized fields Jul 18, 2016

fnothaft added some commits Jul 17, 2016

[ADAM-1061] Fix attribute regex bug.
We had a bug in `org.bdgenomics.adam.util.AttributeUtils` where the regex for
splitting out the formatting string for array attributes was applied to all
attributes. In an array attribute (SAM "B" tags), the type of the array elements
is encoded before the attribute values, and is split off by commas. E.g.,
"B:i,1,2,3". If the attribute is a string (SAM "Z" tags), commas are allowed.
To resolve this, I split this regex into two regexes. We only apply the
regex for splitting out the array type if we are working on an array
attribute. This resolves #1061.
[ADAM-483] Properly handle denormalized OP, OC, OQ fields.
Properly splits the denormalized fields out of the attribute line. Adds better
test coverage to SAMRecordConverterSuite. Oddly enough, the other side of the
conversion (AlignmentRecordConverterSuite) had coverage. Resolves #483.
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Rebased and addressed review comment.

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fnothaft commented Jul 18, 2016

Rebased and addressed review comment.

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@heuermh heuermh merged commit 06d0fd2 into bigdatagenomics:master Jul 19, 2016

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Thank you, @fnothaft!

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heuermh commented Jul 19, 2016

Thank you, @fnothaft!

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