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Update to Hadoop-BAM 7.8.0 #1455

fnothaft opened this issue Mar 23, 2017 · 1 comment

Update to Hadoop-BAM 7.8.0 #1455

fnothaft opened this issue Mar 23, 2017 · 1 comment


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@fnothaft fnothaft commented Mar 23, 2017

Bumps to latest version of HTSJDK. Should tack on to #1440. Will need to update SAM/BAM/CRAM queryname sorted loading code. As part of that fix, we should consolidate the BAM->Fragments path into a loadBamAsFragments method, which will make it easier to use downstream (e.g., in

@fnothaft fnothaft added this to the 0.22.0 milestone Mar 23, 2017
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@heuermh heuermh commented Mar 23, 2017

While we're in there I'd suggest taking out

} else if (filePath.endsWith(".reads.adam")) {"Loading $filePath as ADAM AlignmentRecords and converting to Fragments.")

And from loadAlignments

} else if (filePath.endsWith("contig.adam")) {"Loading $filePath as Parquet of NucleotideContigFragment and converting to AlignmentRecords. Projection is ignored.")

Sorry, I'll create a new issue. See #1456.

fnothaft added a commit to fnothaft/adam that referenced this issue Mar 27, 2017
Resolves bigdatagenomics#1455. Adds ``, which
works around removed functionality from Hadoop-BAM for keeping read pairs from
a queryname sorted BAM file in a single partition.
@heuermh heuermh closed this in 4a74482 Mar 27, 2017
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