Geraldine A Van der Auwera modified a wiki page

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picard released /picard-tools/1.119/README.txt

picard released /picard-tools/1.119/picard-tools-1.119.zip

picard released /picard-tools/1.118/README.txt

picard released /picard-tools/1.118/picard-tools-1.118.zip

Alec Wysoker modified a wiki page

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picard released /picard-tools/1.117/README.txt

picard released /picard-tools/1.117/picard-tools-1.117.zip

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picard released /picard-tools/1.115/picard-tools-1.115.zip

picard released /picard-tools/1.115/README.txt

picard released /picard-tools/1.114/README.txt

picard released /picard-tools/1.114/picard-tools-1.114.zip

picard released /sam-jdk/1.113/sam-1.113.jar

picard released /picard-tools/1.113/README.txt

picard released /picard-tools/1.113/picard-tools-1.113.zip

Alec Wysoker committed [r1962]

Release 1.113

Alec Wysoker committed [r1961]

Adapt to changed error message from SVN about n...

Alec Wysoker committed [r1960]

Release 1.113

Nils Homer committed [r1959]

Adding .gitignore files to empty directories an...

Brad Taylor committed [r1958]

Added a DiskBackedQueue and began alterations t...

jcarey committed [r1957]

Removed debugging message from BlockCompressedI...

jcarey committed [r1956]

Fix failing check dir tests

jcarey committed [r1955]

Fix for CheckIlluminaDirectory when the number ...

jcarey committed [r1954]

[r1953] (HEAD) by jacarey

jcarey committed [r1953]

Merge trunk to branch jc_file_util_refactor

jcarey committed [r1952]

Reverting previous merge

jcarey committed [r1951]

Merged changes from the jc_file_util_refactor b...

Jeff Gentry committed [r1950]

Provide capability to reheader BAM files, along...

Brad Taylor committed [r1949]

replaced boolean wrappedRecord with a record->b...

Nils Homer committed [r1948]

optimizing the to mark queue to reduce memory

Nils Homer committed [r1947]

adding a mark duplicates with mate cigar versio...

Tim Fennell committed [r1946]

Added a simple toString to AbstractSAMHeaderRec...

Brad Taylor committed [r1945]

replaced alignmentStartSortedCounts with a bool...

Joe committed [r1944]

Moving WgsMetrics into CollectWgsMetrics (and m...

Joel Thibault committed [r1943]

Make two methods public so Hadoop-BAM can use them

Joe committed [r1942]

PFB-600 Separating the WGS metrics class from i...

Nils Homer committed [r1941]

Removing unnecessary IoUtil imports

Nils Homer committed [r1940]

adding a reference fasta to the Defaults to fac...

Nils Homer committed [r1939]

Further optimizing how we update the alignment ...

jcarey committed [r1938]

Multi-tile parser changes.

Nils Homer committed [r1937]

Optimizing the subtractCount function by groupi...

Nils Homer committed [r1936]

Unmapped reads could contribute to determing th...

Joel Thibault committed [r1935]

Require a reference dictionary for Tribble inde...

Nils Homer committed [r1934]

do not check for OQ when we are not reverting OQs

Tim Fennell committed [r1933]

First version of CollectWgsMetrics a program th...

Tim Fennell committed [r1932]

Changes to SamLocusIterator to a) check the map...

Tim Fennell committed [r1931]

Addition of a simple SamRecordFilter that filte...

picard released /sam-jdk/1.112/sam-1.112.jar

picard released /picard-tools/1.112/README.txt

picard released /picard-tools/1.112/picard-tools-1.112.zip

Alec Wysoker committed [r1930]

Release 1.112

Alec Wysoker committed [r1929]

Release 1.112

Joe committed [r1928]

Fixing unit tests for CheckIlluminaDirectories

Joe committed [r1927]

Faker now produces the correct length faked fil...

Brad Taylor committed [r1926]

Fixed multiple bugs in the MarkDuplicatesWithMa...

Joel Thibault committed [r1925]

Deprecate VariantContextWriterFactory

Joel Thibault committed [r1924]

Create Tabix indices for block-compressed VCFs

Joe committed [r1923]

PO-326 Removing checking PL values

jcarey committed [r1922]

Code clean up and optimization of SequenceUtil....

"mmcowan" committed [r1921]

Various de-wildcarding of imports.

Joel Thibault committed [r1920]

Move BLOCK_COMPRESSED_EXTENSIONS to Tribble so ...

Joe committed [r1919]

Adding support for gzipped and block gzipped fi...

Brad Taylor committed [r1918]

Moved output directory creation to constructor....

jcarey committed [r1917]

assert file structure for bcl only on uncompres...

jcarey committed [r1916]

Fix tile filtering for multi tile bcl files.

jcarey committed [r1915]

Initial pass on making sure we are cleaning up/...

Joe committed [r1914]

PO-326 Updating test data to include the platfo...

Alec Wysoker committed [r1913]

Make public.

jcarey committed [r1912]

Fixed BCLReader tests and added back support fo...

Joe committed [r1911]

PO-326 Validating the PL attribute in SAMFileVa...

Joe committed [r1910]

PO-326 Validating the PL attribute in SAMFileVa...

Joe committed [r1909]

Adding the name of the file to the error string...

jcarey committed [r1908]

Added better Bcl parsing. Reader test is still ...

Joe committed [r1907]

Writing the proper size to faked-out BCL files

Yossi committed [r1906]

fixed imports the point to the correct SamPairU...

jcarey committed [r1905]

Basic refactor of per tile and per cycle per ti...

jcarey committed [r1904]

Pulled subclasses out of IlluminaFileUtil.

jcarey committed [r1903]

Remove extraneous test data files.

droazen committed [r1902]

Add ability to remap sample names for single-sa...

picard released /sam-jdk/1.111/sam-1.111.jar

picard released /picard-tools/1.111/picard-tools-1.111.zip

picard released /picard-tools/1.111/README.txt

Alec Wysoker committed [r1901]

Release 1.111

Alec Wysoker committed [r1900]

Release 1.111

Nils Homer committed [r1899]

setting ADD_MATE_CIGAR to default to true in Fi...

Brad Taylor committed [r1898]

Fixed two bugs related to subtracting alignment...

Brad Taylor committed [r1897]

Fixed two bugs related to subtracting alignment...

Joel Thibault committed [r1896]

New VariantContextWriterBuilder class and tests

Nils Homer committed [r1895]

Sync the nh_mark_duplicates branch with /trunk ...

Eric Banks committed [r1894]

Added support for VCFv4.2 Version tags in heade...

jcarey committed [r1893]

Removed support for Qseq, Cif and Cnf file form...

jcarey committed [r1892]

Adding a new branch for the Illumina file util ...

jcarey committed [r1891]

Merged nh_mate_cigar_refactoring r1775:r1889 in...

jcarey committed [r1890]

Revert modified function arguments.

jcarey committed [r1889]

Reassign the file util when checking symlinks s...

jcarey committed [r1888]

Set ADD_MATE_CIGAR to false by default.

Brad Taylor committed [r1887]

Moved DuplicationMetrics back out of markduplic...

Nils Homer committed [r1886]

Adding a utility RemoveSamAttributes that will ...