Activity for picard
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Geraldine A Van der Auwera modified a wiki page
Main_Page
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picard released /picard-tools/1.119/README.txt
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Alec Wysoker modified a wiki page
Main_Page
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Main_Page
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Release 1.113
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Adapt to changed error message from SVN about n...
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Release 1.113
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Nils Homer committed [r1959]
Adding .gitignore files to empty directories an...
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Brad Taylor committed [r1958]
Added a DiskBackedQueue and began alterations t...
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jcarey committed [r1957]
Removed debugging message from BlockCompressedI...
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Fix failing check dir tests
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Fix for CheckIlluminaDirectory when the number ...
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[r1953] (HEAD) by jacarey
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Merge trunk to branch jc_file_util_refactor
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Reverting previous merge
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Merged changes from the jc_file_util_refactor b...
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Jeff Gentry committed [r1950]
Provide capability to reheader BAM files, along...
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replaced boolean wrappedRecord with a record->b...
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optimizing the to mark queue to reduce memory
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adding a mark duplicates with mate cigar versio...
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Tim Fennell committed [r1946]
Added a simple toString to AbstractSAMHeaderRec...
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replaced alignmentStartSortedCounts with a bool...
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Joe committed [r1944]
Moving WgsMetrics into CollectWgsMetrics (and m...
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Joel Thibault committed [r1943]
Make two methods public so Hadoop-BAM can use them
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PFB-600 Separating the WGS metrics class from i...
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Removing unnecessary IoUtil imports
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adding a reference fasta to the Defaults to fac...
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Further optimizing how we update the alignment ...
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Multi-tile parser changes.
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Optimizing the subtractCount function by groupi...
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Unmapped reads could contribute to determing th...
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Require a reference dictionary for Tribble inde...
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do not check for OQ when we are not reverting OQs
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First version of CollectWgsMetrics a program th...
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Changes to SamLocusIterator to a) check the map...
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Addition of a simple SamRecordFilter that filte...
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Release 1.112
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Release 1.112
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Fixing unit tests for CheckIlluminaDirectories
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Faker now produces the correct length faked fil...
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Fixed multiple bugs in the MarkDuplicatesWithMa...
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Deprecate VariantContextWriterFactory
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Create Tabix indices for block-compressed VCFs
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PO-326 Removing checking PL values
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Code clean up and optimization of SequenceUtil....
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"mmcowan" committed [r1921]
Various de-wildcarding of imports.
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Move BLOCK_COMPRESSED_EXTENSIONS to Tribble so ...
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Adding support for gzipped and block gzipped fi...
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Moved output directory creation to constructor....
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assert file structure for bcl only on uncompres...
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Fix tile filtering for multi tile bcl files.
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Initial pass on making sure we are cleaning up/...
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PO-326 Updating test data to include the platfo...
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Make public.
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Fixed BCLReader tests and added back support fo...
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PO-326 Validating the PL attribute in SAMFileVa...
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PO-326 Validating the PL attribute in SAMFileVa...
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Adding the name of the file to the error string...
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Added better Bcl parsing. Reader test is still ...
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Writing the proper size to faked-out BCL files
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Yossi committed [r1906]
fixed imports the point to the correct SamPairU...
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Basic refactor of per tile and per cycle per ti...
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Pulled subclasses out of IlluminaFileUtil.
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Remove extraneous test data files.
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droazen committed [r1902]
Add ability to remap sample names for single-sa...
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Release 1.111
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Release 1.111
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setting ADD_MATE_CIGAR to default to true in Fi...
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Fixed two bugs related to subtracting alignment...
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Fixed two bugs related to subtracting alignment...
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New VariantContextWriterBuilder class and tests
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Sync the nh_mark_duplicates branch with /trunk ...
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Eric Banks committed [r1894]
Added support for VCFv4.2 Version tags in heade...
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Removed support for Qseq, Cif and Cnf file form...
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Adding a new branch for the Illumina file util ...
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Merged nh_mate_cigar_refactoring r1775:r1889 in...
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Revert modified function arguments.
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Reassign the file util when checking symlinks s...
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Set ADD_MATE_CIGAR to false by default.
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Moved DuplicationMetrics back out of markduplic...
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Adding a utility RemoveSamAttributes that will ...
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