-- New resources argument used to prefix all data files (ref, rods, bams)
-- Work around for CommandLineProgram double add bug in Queue (KS knows about it)
-- New test mode to just run a tiny intervals (can be run single threaded on cmdline)
Another script (PhaseIndelRedoCombining.scala) does the combining of all pieces - not the best solution, but best for development/debugging to have two separate entities.
c) Experimental walker to assess GL concordance of two callsets - just accumulates squared error between each sample and site GL's and outputs at the end.
d) Another one-off to fill a callset of given GL's with greedy genotypes (genotype that maximizes PL) to have more meaningful metrics and QC of a given GL file.
Creating a single temporary directory per ant test run instead of a putting temp files across all runs in the same directory.
Updated various tests for above items and other small fixes.
fixed issue where a read starting with an insertion followed by a deletion would break, clipper can now safely clip the insertion and the deletion if that's the case.
note: test is turned off until contract changes to allow hanging insertions (left/right).
* fixed edge case when requested to hard clip beginning of a read that had hanging soft clipped bases on the left tail.
* fixed edge case when requested to hard clip end of a read that had hanging soft clipped bases on the right tail.
* fixed AlignmentStart of a clipped read that results in only hard clips and soft clips
note: added tests to all these beautiful cases...
This change and my previous change have dropped runtime when dynamically merging 2k BAM files from 72.6min/1M reads to 46.8sec/1M reads.
Note that many of these changes are stopgaps -- the real problem is the way ReadWalkers interface with Picard, and I'll have to work with
Tim&Co to produce a more maintainable patch.
-- Serial version can be re-enabled with a static boolean, if we decide to return to the serial version
-- Comparison of serial and parallel reader with cached and uncached files:
Initialization time: serial with 500 fully cached BAMs: 8.20 seconds
Initialization time: serial with 500 uncached BAMs : 197.02 seconds
Initialization time: parallel with 500 fully cached BAMs: 30.12 seconds
Initialization time: parallel with 500 uncached BAMs : 75.47 seconds
* expanded the systematic cigar string space test framework Roger wrote to all tests
* moved utility functions into Utils and ReadUtils
* cleaned up unused classes
caught a bug in the hard clipper where it does not account for hard clipping softclipped bases in the resulting cigar string, if there is already a hard clipped base immediately after it.
* updated unit test for hardClipSoftClippedBases with corresponding test-case.
Christopher Hartl
Mauricio Carneiro
Guillermo del Angel
Mark DePristo
Laurent Francioli
Eric Banks
Matt Hanna
Ryan Poplin
Khalid Shakir