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Release 1.113
Adapt to changed error message from SVN about n...
Release 1.113
Adding .gitignore files to empty directories an...
Added a DiskBackedQueue and began alterations t...
Removed debugging message from BlockCompressedI...
Fix failing check dir tests
Fix for CheckIlluminaDirectory when the number ...
[r1953] (HEAD) by jacarey
Merge trunk to branch jc_file_util_refactor
Reverting previous merge
Merged changes from the jc_file_util_refactor b...
Provide capability to reheader BAM files, along...
replaced boolean wrappedRecord with a record->b...
optimizing the to mark queue to reduce memory
adding a mark duplicates with mate cigar versio...
Added a simple toString to AbstractSAMHeaderRec...
replaced alignmentStartSortedCounts with a bool...
Moving WgsMetrics into CollectWgsMetrics (and m...
Make two methods public so Hadoop-BAM can use them
PFB-600 Separating the WGS metrics class from i...
Removing unnecessary IoUtil imports
adding a reference fasta to the Defaults to fac...
Further optimizing how we update the alignment ...
Multi-tile parser changes.
Optimizing the subtractCount function by groupi...
Unmapped reads could contribute to determing th...
Require a reference dictionary for Tribble inde...
do not check for OQ when we are not reverting OQs
First version of CollectWgsMetrics a program th...
Changes to SamLocusIterator to a) check the map...
Addition of a simple SamRecordFilter that filte...
Release 1.112
Release 1.112
Fixing unit tests for CheckIlluminaDirectories
Faker now produces the correct length faked fil...
Fixed multiple bugs in the MarkDuplicatesWithMa...
Deprecate VariantContextWriterFactory
Create Tabix indices for block-compressed VCFs
PO-326 Removing checking PL values
Code clean up and optimization of SequenceUtil....
Various de-wildcarding of imports.
Move BLOCK_COMPRESSED_EXTENSIONS to Tribble so ...
Adding support for gzipped and block gzipped fi...
Moved output directory creation to constructor....
assert file structure for bcl only on uncompres...
Fix tile filtering for multi tile bcl files.
Initial pass on making sure we are cleaning up/...
PO-326 Updating test data to include the platfo...
Make public.
Fixed BCLReader tests and added back support fo...
PO-326 Validating the PL attribute in SAMFileVa...
PO-326 Validating the PL attribute in SAMFileVa...
Adding the name of the file to the error string...
Added better Bcl parsing. Reader test is still ...
Writing the proper size to faked-out BCL files
fixed imports the point to the correct SamPairU...
Basic refactor of per tile and per cycle per ti...
Pulled subclasses out of IlluminaFileUtil.
Remove extraneous test data files.
Add ability to remap sample names for single-sa...
Release 1.111
Release 1.111
setting ADD_MATE_CIGAR to default to true in Fi...
Fixed two bugs related to subtracting alignment...
Fixed two bugs related to subtracting alignment...
New VariantContextWriterBuilder class and tests
Sync the nh_mark_duplicates branch with /trunk ...
Added support for VCFv4.2 Version tags in heade...
Removed support for Qseq, Cif and Cnf file form...
Adding a new branch for the Illumina file util ...
Merged nh_mate_cigar_refactoring r1775:r1889 in...
Revert modified function arguments.
Reassign the file util when checking symlinks s...
Set ADD_MATE_CIGAR to false by default.
Moved DuplicationMetrics back out of markduplic...
Adding a utility RemoveSamAttributes that will ...