-- Removed versions getAttribriteAsX(key) that except on not having the value.
-- Removed version that getAttributeAsXNoException(key)
-- The only available assessors are now getAttributeAsX(key, default).
-- This single accessors properly handle their argument types, so if the value is a double it is returned directly for getAttributeAsDouble(), or if it's a string it's converted to a double. If the key isn't found, default is returned.
-- Don't create an empty LinkedHashSet() for PASS fields. Just return Collections.emptySet() instead.
-- For filter fields with actual values, returns an unmodifiableSet instead of one that can be changed
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
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
-- Useful if you want to have a parameter like MAX_RECORDS that wants the walker to stop after some number of map calls without having to resort to the old System.exit() call directly.
Reads that were not hard clipped for the variable site no longer show up in output file
Walker now uses unclippedStart of Read to determine position in the sliding Window
It is time to bring the ReadClipper class to the main repo. Read Clipper has tested functionality for soft and hard clipping reads. I will prepare thorough documentation for it as it will be very useful for the assembler and the GATK in general.
b) More R-friendly VariantsToTable printing of AC in case of multiple alt alleles
c) Rename FixPLOrderingWalker to FixGenotypesWalker and rewrote: no longer need older code, replaced with code to replace genotypes with all-zero PL's with a no-call.
Mark DePristo
Eric Banks
Mauricio Carneiro
Ryan Poplin
Guillermo del Angel
Khalid Shakir
Roger Zurawicki