Changed loadIndexedBam to use hadoop-bam InputFormat #1036
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Test PASSed. |
| @@ -41,4 +42,19 @@ trait Interval { | |||
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| def width: Long = end - start | |||
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| * Need to implement getStart function from Locatable. (1-based start position. closed) | |||
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Mixing 0- and 1- based coordinate systems in the same class gives me the hives. Can we hide this as an implementation detail in an adapter somewhere in the i/o code?
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I don't think we can hide it, but we could mark it as @deprecated to hint that it is only for use with legacy codebases?
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I guess I don't see where it is used, so I'm not sure what suggestion to make. Will have to dig a bit.
And is this the Interval that will need to go into bdg-utils to support IntervalRDD? Then there's no way I want to mix htsjdk stuff in.
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No, this allows us to supply ReferenceRegions to the Hadoop-BAM indexed input format code without going through an intermediate class.
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Actually, think I may have misread.
And is this the Interval that will need to go into bdg-utils to support IntervalRDD? Then there's no way I want to mix htsjdk stuff in.
@akmorrow13 @erictu, can you all comment?
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Actually, I get what you're saying now, @heuermh. I will refactor this out.
fnothaft
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oh how I like to see code being removed :)
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Indeed; it is uniquely satisfying!
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LGTM |
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+1 |
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Rebased and ready to merge! |
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Oops, didn't let Jenkins have a final say before merging. Builds & tests ok for me locally. Thank you, @fnothaft @andrewmchen! |
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Test FAILed. Build result: FAILURE[...truncated 24 lines...]Triggering ADAM-prb ? 2.6.0,2.10,1.6.1,centosTriggering ADAM-prb ? 2.3.0,2.10,1.6.1,centosTriggering ADAM-prb ? 2.3.0,2.10,1.5.2,centosTriggering ADAM-prb ? 2.6.0,2.10,1.4.1,centosTriggering ADAM-prb ? 2.3.0,2.11,1.5.2,centosTriggering ADAM-prb ? 2.6.0,2.11,1.4.1,centosTriggering ADAM-prb ? 2.3.0,2.11,1.6.1,centosTriggering ADAM-prb ? 2.3.0,2.11,1.4.1,centosTriggering ADAM-prb ? 2.3.0,2.10,1.4.1,centosADAM-prb ? 2.6.0,2.11,1.6.1,centos completed with result FAILUREADAM-prb ? 2.6.0,2.11,1.3.1,centos completed with result FAILUREADAM-prb ? 2.3.0,2.10,1.3.1,centos completed with result FAILUREADAM-prb ? 2.6.0,2.10,1.3.1,centos completed with result FAILUREADAM-prb ? 2.3.0,2.11,1.3.1,centos completed with result FAILUREADAM-prb ? 2.6.0,2.10,1.6.1,centos completed with result FAILUREADAM-prb ? 2.3.0,2.10,1.6.1,centos completed with result FAILUREADAM-prb ? 2.3.0,2.10,1.5.2,centos completed with result FAILUREADAM-prb ? 2.6.0,2.10,1.4.1,centos completed with result FAILUREADAM-prb ? 2.3.0,2.11,1.5.2,centos completed with result FAILUREADAM-prb ? 2.6.0,2.11,1.4.1,centos completed with result FAILUREADAM-prb ? 2.3.0,2.11,1.6.1,centos completed with result FAILUREADAM-prb ? 2.3.0,2.11,1.4.1,centos completed with result FAILUREADAM-prb ? 2.3.0,2.10,1.4.1,centos completed with result FAILURENotifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'Test FAILed. |
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Looks like the @AmplabJenkins failures were just the git |
A bit of cleanup on top of @andrewmchen's work in #953.