New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Update to Hadoop-BAM 7.8.0 #1455

Closed
fnothaft opened this Issue Mar 23, 2017 · 1 comment

Comments

Projects
None yet
2 participants
@fnothaft
Member

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 https://github.com/heuermh/cannoli/pull/15).

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

@heuermh

This comment has been minimized.

Show comment
Hide comment
@heuermh

heuermh Mar 23, 2017

Member

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

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

And from loadAlignments

} else if (filePath.endsWith("contig.adam")) {
  log.info(s"Loading $filePath as Parquet of NucleotideContigFragment and converting to AlignmentRecords. Projection is ignored.")
  AlignmentRecordRDD.unaligned(loadParquetContigFragments(filePath).toReads)

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

Member

heuermh commented Mar 23, 2017

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

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

And from loadAlignments

} else if (filePath.endsWith("contig.adam")) {
  log.info(s"Loading $filePath as Parquet of NucleotideContigFragment and converting to AlignmentRecords. Projection is ignored.")
  AlignmentRecordRDD.unaligned(loadParquetContigFragments(filePath).toReads)

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

fnothaft added a commit to fnothaft/adam that referenced this issue Mar 27, 2017

[ADAM-1455] Upgrade to Hadoop-BAM 7.8.0 and htsjdk 2.9.1
Resolves #1455. Adds `org.bdgenomics.adam.rdd.read.RepairPartitions`, 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

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment