Picard release 1.129
23 February 2015
- Enable file source for Bam Index creation.
- Separate out the actual work for FastqToSam so an outside caller can
directly pass in FastqReaders
- A recent change to the command line parsing causes problems with scala
based CLPs. In cases where the new system fails, fall back to the original
system
- Allow tools to work with GA4GH resources specified via urls. This first
batch includes AddOrReplaceReadGroups, MarkDuplicates and ViewSam.
HTSJDK changes
- removing SAMRecord.setAlignmentEnd it throws unsupported operation
exception
- adding getResourceDescription() to SamReader
- fixed issue 155: CRAMFileWriter injects slice refMD5 now; added slice
refMD5 check into CRAMIterator, for now only error message is show.
- Made ReadTag.buf ThreadLocal. Fixes
https://github.com/samtools/htsjdk/issues/153
In addition to the following changes to the htsjdk we are now publishing
our releases to sonatype so they should be available at maven central
within a few minutes of each major release.
-J
------------------------------------------------------------------------------
Download BIRT iHub F-Type - The Free Enterprise-Grade BIRT Server
from Actuate! Instantly Supercharge Your Business Reports and Dashboards
with Interactivity, Sharing, Native Excel Exports, App Integration & more
Get technology previously reserved for billion-dollar corporations, FREE
http://pubads.g.doubleclick.net/gampad/clk?id=190641631&iu=/4140/ostg.clktrk
_______________________________________________
Samtools-help mailing list
Samtools-help@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/samtools-help
