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.
shifted the contract to functions that operate on reference based coordinates. The clipper should do the right thing with unmapped reads, but it needs more testing (Ryan is using it at the moment and says it works). Will write some unit tests.
* added functions to create synthetic reads for unit testing with reasonable default parameters
* added more functions to create synthetic reads based on cigar string + bases and quals.
bug: When performing multiple hard clip operations in a read that has indels, if the N+1 hardclip requests to clip inside an indel that has been removed by one of the (1..N) previous hardclips, the hard clipper would go out of bounds.
fix: dynamically adjust the boundaries according to the new hardclipped read length. (this maintains the current contract that hardclipping will never return a read starting or ending in indels).
-- Uses 8 threads to load BAM files and indices in parallel, decreasing costs to read thousands of BAM files by a significant amount
-- Added logger.info message noting progress and cost of reading low-level BAM data.
-- Now properly handles the case where a sample isn't present (no longer adds a null to the genotypes list)
-- Fix for logic failure where if the number of requested samples equals the number of known genotypes then all of the records were returned, which isn't correct when there are missing samples.
-- Unit tests added to handle these cases
Eric Banks
Khalid Shakir
Mauricio Carneiro
Mark DePristo
Ryan Poplin
Matt Hanna
Laurent Francioli