Found this neat little walker Kiran wrote stashed in the private tree. Very useful. Generalized it a bit, added GATKDocs and moved it to public. I might include it as a QC step on the pacbio processing pipeline.
* generalize it so it works with non pair ended reads.
* generalize it to work with no read group information
* getRefCoordSoftUnclippedEnd was not resetting the shift when hitting insertions. Fixed.
* getReadCoordinateForReferenceCoordinateBeforeAlignmentEnd was returning the wrong read coordinate position. Fixed.
The clipper could leave an insertion or deletion as the start or end of a read after hardclipping a read if the element adjacent to the clipping point was an indel. Fixed.
Read clipper now identifies and clips even if the requested coordinate is outside the alignment but the read contains soft clipped bases in that region.
* When hard clipping a read that had insertions in it, the insertion was being added to the cigar string's hard clip element. This way, the old UnclippedStart() was being modified and so was the calculation of the new AlignmentStart(). Fixed it by subtracting the number of insertions clipped from the total number of hard clipped bases.
* Walker was sending read instead of filtered read when deleting a read that contains only Q2 bases
* Sliding the window was causing reads that started on the new start position to be entirely clipped.
-- General purpose RScript executor in java (please use when invoking RScripts)
-- Removed groupName. This is now analysisName
-- Explicitly added capability to enable/disable individual QFunction
*Added the functions to turn a BLASR generated BAM file into a usable BAM file.
*Modified the bwa parameters according to test results from NA12878 pb2k dataset.
b) More useful AC,AF logging in VariantsToTable with multiallelic sites: instead of logging comma-separated values, log max value by default. Hidden, experimental argument -logACSum to log sum of ACs instead. This is due to extreme slowness of R in parsing strings to tokens and computing max/sum itself (~100x slower than gatk).
c) Added integrationtest for new SelectVariants commands
Instead of creating a bam list file, I dynamically create a scala list and pass as parameters. This way the intermediate bam files don't get deleted before they should.
Mauricio Carneiro
Mark DePristo
Eric Banks
Ryan Poplin
Guillermo del Angel