https://sourceforge.net/p/picard/activity/Recent activity for picardenThu, 24 Sep 2015 00:57:03 -0000https://sourceforge.net/p/picard/wiki/Main_Page/Main_PageGeraldine A Van der AuweraThu, 24 Sep 2015 00:57:03 -0000https://sourceforge.net/p/picard/wiki/Main_Page/https://sourceforge.nethttp%3A//sourceforge.net/projects/picard/files/picard-tools/1.119/README.txt/downloadpicardMon, 25 Aug 2014 20:19:05 -0000http://sourceforge.net/projects/picard/files/picard-tools/1.119/README.txt/downloadhttps://sourceforge.nethttp%3A//sourceforge.net/projects/picard/files/picard-tools/1.119/picard-tools-1.119.zip/downloadpicardMon, 25 Aug 2014 20:19:05 -0000http://sourceforge.net/projects/picard/files/picard-tools/1.119/picard-tools-1.119.zip/downloadhttps://sourceforge.nethttp%3A//sourceforge.net/projects/picard/files/picard-tools/1.118/README.txt/downloadpicardMon, 28 Jul 2014 15:31:05 -0000http://sourceforge.net/projects/picard/files/picard-tools/1.118/README.txt/downloadhttps://sourceforge.nethttp%3A//sourceforge.net/projects/picard/files/picard-tools/1.118/picard-tools-1.118.zip/downloadpicardMon, 28 Jul 2014 15:31:05 -0000http://sourceforge.net/projects/picard/files/picard-tools/1.118/picard-tools-1.118.zip/downloadhttps://sourceforge.net/p/picard/wiki/Main_Page/Main_PageAlec WysokerMon, 28 Jul 2014 15:18:53 -0000https://sourceforge.net/p/picard/wiki/Main_Page/https://sourceforge.nethttp%3A//sourceforge.net/projects/picard/files/picard-tools/1.117/README.txt/downloadpicardMon, 14 Jul 2014 17:06:05 -0000http://sourceforge.net/projects/picard/files/picard-tools/1.117/README.txt/downloadhttps://sourceforge.nethttp%3A//sourceforge.net/projects/picard/files/picard-tools/1.117/picard-tools-1.117.zip/downloadpicardMon, 14 Jul 2014 17:06:05 -0000http://sourceforge.net/projects/picard/files/picard-tools/1.117/picard-tools-1.117.zip/downloadhttps://sourceforge.net/p/picard/wiki/Main_Page/Main_PageAlec WysokerMon, 30 Jun 2014 15:18:05 -0000https://sourceforge.net/p/picard/wiki/Main_Page/https://sourceforge.net/p/picard/wiki/Alec WysokerMon, 30 Jun 2014 15:10:20 -0000https://sourceforge.net/p/picard/wiki/https://sourceforge.nethttp%3A//sourceforge.net/projects/picard/files/picard-tools/1.115/picard-tools-1.115.zip/downloadpicardMon, 16 Jun 2014 14:32:04 -0000http://sourceforge.net/projects/picard/files/picard-tools/1.115/picard-tools-1.115.zip/downloadhttps://sourceforge.nethttp%3A//sourceforge.net/projects/picard/files/picard-tools/1.115/README.txt/downloadpicardMon, 16 Jun 2014 14:32:04 -0000http://sourceforge.net/projects/picard/files/picard-tools/1.115/README.txt/downloadhttps://sourceforge.nethttp%3A//sourceforge.net/projects/picard/files/picard-tools/1.114/README.txt/downloadpicardTue, 20 May 2014 13:57:06 -0000http://sourceforge.net/projects/picard/files/picard-tools/1.114/README.txt/downloadhttps://sourceforge.nethttp%3A//sourceforge.net/projects/picard/files/picard-tools/1.114/picard-tools-1.114.zip/downloadpicardTue, 20 May 2014 13:57:06 -0000http://sourceforge.net/projects/picard/files/picard-tools/1.114/picard-tools-1.114.zip/downloadhttps://sourceforge.nethttp%3A//sourceforge.net/projects/picard/files/sam-jdk/1.113/sam-1.113.jar/downloadpicardMon, 05 May 2014 14:50:06 -0000http://sourceforge.net/projects/picard/files/sam-jdk/1.113/sam-1.113.jar/downloadhttps://sourceforge.nethttp%3A//sourceforge.net/projects/picard/files/picard-tools/1.113/README.txt/downloadpicardMon, 05 May 2014 14:50:06 -0000http://sourceforge.net/projects/picard/files/picard-tools/1.113/README.txt/downloadhttps://sourceforge.nethttp%3A//sourceforge.net/projects/picard/files/picard-tools/1.113/picard-tools-1.113.zip/downloadpicardMon, 05 May 2014 14:50:06 -0000http://sourceforge.net/projects/picard/files/picard-tools/1.113/picard-tools-1.113.zip/downloadhttps://sourceforge.net/p/picard/code/1962/Release 1.113Alec WysokerMon, 05 May 2014 14:22:16 -0000https://sourceforge.net/p/picard/code/1962/https://sourceforge.net/p/picard/code/1961/Adapt to changed error message from SVN about n...Alec WysokerMon, 05 May 2014 14:21:24 -0000https://sourceforge.net/p/picard/code/1961/https://sourceforge.net/p/picard/code/1960/Release 1.113Alec WysokerMon, 05 May 2014 14:11:47 -0000https://sourceforge.net/p/picard/code/1960/https://sourceforge.net/p/picard/code/1959/Adding .gitignore files to empty directories an...Nils HomerSat, 03 May 2014 14:30:55 -0000https://sourceforge.net/p/picard/code/1959/https://sourceforge.net/p/picard/code/1958/Added a DiskBackedQueue and began alterations t...Brad TaylorFri, 02 May 2014 21:10:09 -0000https://sourceforge.net/p/picard/code/1958/https://sourceforge.net/p/picard/code/1957/Removed debugging message from BlockCompressedI...jcareyThu, 01 May 2014 13:09:42 -0000https://sourceforge.net/p/picard/code/1957/https://sourceforge.net/p/picard/code/1956/Fix failing check dir testsjcareyWed, 30 Apr 2014 00:37:23 -0000https://sourceforge.net/p/picard/code/1956/https://sourceforge.net/p/picard/code/1955/Fix for CheckIlluminaDirectory when the number ...jcareyTue, 29 Apr 2014 23:18:20 -0000https://sourceforge.net/p/picard/code/1955/https://sourceforge.net/p/picard/code/1954/[r1953] (HEAD) by jacareyjcareyTue, 29 Apr 2014 16:09:24 -0000https://sourceforge.net/p/picard/code/1954/https://sourceforge.net/p/picard/code/1953/Merge trunk to branch jc_file_util_refactorjcareyTue, 29 Apr 2014 15:06:41 -0000https://sourceforge.net/p/picard/code/1953/https://sourceforge.net/p/picard/code/1952/Reverting previous mergejcareyTue, 29 Apr 2014 15:04:52 -0000https://sourceforge.net/p/picard/code/1952/https://sourceforge.net/p/picard/code/1951/Merged changes from the jc_file_util_refactor b...jcareyTue, 29 Apr 2014 13:51:27 -0000https://sourceforge.net/p/picard/code/1951/https://sourceforge.net/p/picard/code/1950/Provide capability to reheader BAM files, along...Jeff GentryMon, 28 Apr 2014 21:41:51 -0000https://sourceforge.net/p/picard/code/1950/https://sourceforge.net/p/picard/code/1949/replaced boolean wrappedRecord with a record->b...Brad TaylorMon, 28 Apr 2014 14:12:11 -0000https://sourceforge.net/p/picard/code/1949/https://sourceforge.net/p/picard/code/1948/optimizing the to mark queue to reduce memoryNils HomerMon, 28 Apr 2014 12:26:36 -0000https://sourceforge.net/p/picard/code/1948/https://sourceforge.net/p/picard/code/1947/adding a mark duplicates with mate cigar versio...Nils HomerMon, 28 Apr 2014 12:23:34 -0000https://sourceforge.net/p/picard/code/1947/https://sourceforge.net/p/picard/code/1946/Added a simple toString to AbstractSAMHeaderRec...Tim FennellSun, 27 Apr 2014 10:57:40 -0000https://sourceforge.net/p/picard/code/1946/https://sourceforge.net/p/picard/code/1945/replaced alignmentStartSortedCounts with a bool...Brad TaylorFri, 25 Apr 2014 19:25:38 -0000https://sourceforge.net/p/picard/code/1945/https://sourceforge.net/p/picard/code/1944/Moving WgsMetrics into CollectWgsMetrics (and m...JoeFri, 25 Apr 2014 18:10:30 -0000https://sourceforge.net/p/picard/code/1944/https://sourceforge.net/p/picard/code/1943/Make two methods public so Hadoop-BAM can use themJoel ThibaultFri, 25 Apr 2014 15:16:14 -0000https://sourceforge.net/p/picard/code/1943/https://sourceforge.net/p/picard/code/1942/PFB-600 Separating the WGS metrics class from i...JoeThu, 24 Apr 2014 20:59:50 -0000https://sourceforge.net/p/picard/code/1942/https://sourceforge.net/p/picard/code/1941/Removing unnecessary IoUtil importsNils HomerWed, 23 Apr 2014 19:42:52 -0000https://sourceforge.net/p/picard/code/1941/https://sourceforge.net/p/picard/code/1940/adding a reference fasta to the Defaults to fac...Nils HomerWed, 23 Apr 2014 19:41:49 -0000https://sourceforge.net/p/picard/code/1940/https://sourceforge.net/p/picard/code/1939/Further optimizing how we update the alignment ...Nils HomerWed, 23 Apr 2014 13:31:06 -0000https://sourceforge.net/p/picard/code/1939/https://sourceforge.net/p/picard/code/1938/Multi-tile parser changes.jcareyWed, 23 Apr 2014 12:47:06 -0000https://sourceforge.net/p/picard/code/1938/https://sourceforge.net/p/picard/code/1937/Optimizing the subtractCount function by groupi...Nils HomerTue, 22 Apr 2014 20:18:50 -0000https://sourceforge.net/p/picard/code/1937/https://sourceforge.net/p/picard/code/1936/Unmapped reads could contribute to determing th...Nils HomerTue, 22 Apr 2014 19:46:44 -0000https://sourceforge.net/p/picard/code/1936/https://sourceforge.net/p/picard/code/1935/Require a reference dictionary for Tribble inde...Joel ThibaultTue, 22 Apr 2014 19:26:35 -0000https://sourceforge.net/p/picard/code/1935/https://sourceforge.net/p/picard/code/1934/do not check for OQ when we are not reverting OQsNils HomerTue, 22 Apr 2014 19:16:52 -0000https://sourceforge.net/p/picard/code/1934/https://sourceforge.net/p/picard/code/1933/First version of CollectWgsMetrics a program th...Tim FennellTue, 22 Apr 2014 16:37:23 -0000https://sourceforge.net/p/picard/code/1933/https://sourceforge.net/p/picard/code/1932/Changes to SamLocusIterator to a) check the map...Tim FennellTue, 22 Apr 2014 16:36:01 -0000https://sourceforge.net/p/picard/code/1932/https://sourceforge.net/p/picard/code/1931/Addition of a simple SamRecordFilter that filte...Tim FennellTue, 22 Apr 2014 16:35:08 -0000https://sourceforge.net/p/picard/code/1931/https://sourceforge.nethttp%3A//sourceforge.net/projects/picard/files/sam-jdk/1.112/sam-1.112.jar/downloadpicardMon, 21 Apr 2014 12:38:16 -0000http://sourceforge.net/projects/picard/files/sam-jdk/1.112/sam-1.112.jar/downloadhttps://sourceforge.nethttp%3A//sourceforge.net/projects/picard/files/picard-tools/1.112/README.txt/downloadpicardMon, 21 Apr 2014 12:38:16 -0000http://sourceforge.net/projects/picard/files/picard-tools/1.112/README.txt/downloadhttps://sourceforge.nethttp%3A//sourceforge.net/projects/picard/files/picard-tools/1.112/picard-tools-1.112.zip/downloadpicardMon, 21 Apr 2014 12:38:16 -0000http://sourceforge.net/projects/picard/files/picard-tools/1.112/picard-tools-1.112.zip/downloadhttps://sourceforge.net/p/picard/code/1930/Release 1.112Alec WysokerMon, 21 Apr 2014 12:18:25 -0000https://sourceforge.net/p/picard/code/1930/https://sourceforge.net/p/picard/code/1929/Release 1.112Alec WysokerMon, 21 Apr 2014 12:17:41 -0000https://sourceforge.net/p/picard/code/1929/https://sourceforge.net/p/picard/code/1928/Fixing unit tests for CheckIlluminaDirectoriesJoeFri, 18 Apr 2014 21:59:26 -0000https://sourceforge.net/p/picard/code/1928/https://sourceforge.net/p/picard/code/1927/Faker now produces the correct length faked fil...JoeFri, 18 Apr 2014 20:43:47 -0000https://sourceforge.net/p/picard/code/1927/https://sourceforge.net/p/picard/code/1926/Fixed multiple bugs in the MarkDuplicatesWithMa...Brad TaylorFri, 18 Apr 2014 19:55:54 -0000https://sourceforge.net/p/picard/code/1926/https://sourceforge.net/p/picard/code/1925/Deprecate VariantContextWriterFactoryJoel ThibaultFri, 18 Apr 2014 15:13:49 -0000https://sourceforge.net/p/picard/code/1925/https://sourceforge.net/p/picard/code/1924/Create Tabix indices for block-compressed VCFsJoel ThibaultFri, 18 Apr 2014 13:46:29 -0000https://sourceforge.net/p/picard/code/1924/https://sourceforge.net/p/picard/code/1923/PO-326 Removing checking PL valuesJoeThu, 17 Apr 2014 18:18:11 -0000https://sourceforge.net/p/picard/code/1923/https://sourceforge.net/p/picard/code/1922/Code clean up and optimization of SequenceUtil....jcareyThu, 17 Apr 2014 13:34:53 -0000https://sourceforge.net/p/picard/code/1922/https://sourceforge.net/p/picard/code/1921/Various de-wildcarding of imports."mmcowan"Wed, 16 Apr 2014 20:53:49 -0000https://sourceforge.net/p/picard/code/1921/https://sourceforge.net/p/picard/code/1920/Move BLOCK_COMPRESSED_EXTENSIONS to Tribble so ...Joel ThibaultWed, 16 Apr 2014 18:29:41 -0000https://sourceforge.net/p/picard/code/1920/https://sourceforge.net/p/picard/code/1919/Adding support for gzipped and block gzipped fi...JoeWed, 16 Apr 2014 16:02:14 -0000https://sourceforge.net/p/picard/code/1919/https://sourceforge.net/p/picard/code/1918/Moved output directory creation to constructor....Brad TaylorTue, 15 Apr 2014 15:19:28 -0000https://sourceforge.net/p/picard/code/1918/https://sourceforge.net/p/picard/code/1917/assert file structure for bcl only on uncompres...jcareyTue, 15 Apr 2014 13:56:20 -0000https://sourceforge.net/p/picard/code/1917/https://sourceforge.net/p/picard/code/1916/Fix tile filtering for multi tile bcl files.jcareyTue, 15 Apr 2014 13:05:37 -0000https://sourceforge.net/p/picard/code/1916/https://sourceforge.net/p/picard/code/1915/Initial pass on making sure we are cleaning up/...jcareyMon, 14 Apr 2014 19:19:53 -0000https://sourceforge.net/p/picard/code/1915/https://sourceforge.net/p/picard/code/1914/PO-326 Updating test data to include the platfo...JoeMon, 14 Apr 2014 18:13:41 -0000https://sourceforge.net/p/picard/code/1914/https://sourceforge.net/p/picard/code/1913/Make public.Alec WysokerMon, 14 Apr 2014 16:10:35 -0000https://sourceforge.net/p/picard/code/1913/https://sourceforge.net/p/picard/code/1912/Fixed BCLReader tests and added back support fo...jcareyMon, 14 Apr 2014 16:05:10 -0000https://sourceforge.net/p/picard/code/1912/https://sourceforge.net/p/picard/code/1911/PO-326 Validating the PL attribute in SAMFileVa...JoeMon, 14 Apr 2014 15:15:19 -0000https://sourceforge.net/p/picard/code/1911/https://sourceforge.net/p/picard/code/1910/PO-326 Validating the PL attribute in SAMFileVa...JoeMon, 14 Apr 2014 14:57:40 -0000https://sourceforge.net/p/picard/code/1910/https://sourceforge.net/p/picard/code/1909/Adding the name of the file to the error string...JoeMon, 14 Apr 2014 14:19:33 -0000https://sourceforge.net/p/picard/code/1909/https://sourceforge.net/p/picard/code/1908/Added better Bcl parsing. Reader test is still ...jcareyThu, 10 Apr 2014 20:27:19 -0000https://sourceforge.net/p/picard/code/1908/https://sourceforge.net/p/picard/code/1907/Writing the proper size to faked-out BCL filesJoeThu, 10 Apr 2014 18:06:51 -0000https://sourceforge.net/p/picard/code/1907/https://sourceforge.net/p/picard/code/1906/fixed imports the point to the correct SamPairU...YossiThu, 10 Apr 2014 15:53:00 -0000https://sourceforge.net/p/picard/code/1906/https://sourceforge.net/p/picard/code/1905/Basic refactor of per tile and per cycle per ti...jcareyWed, 09 Apr 2014 21:36:57 -0000https://sourceforge.net/p/picard/code/1905/https://sourceforge.net/p/picard/code/1904/Pulled subclasses out of IlluminaFileUtil.jcareyTue, 08 Apr 2014 20:45:41 -0000https://sourceforge.net/p/picard/code/1904/https://sourceforge.net/p/picard/code/1903/Remove extraneous test data files.jcareyTue, 08 Apr 2014 14:53:00 -0000https://sourceforge.net/p/picard/code/1903/https://sourceforge.net/p/picard/code/1902/Add ability to remap sample names for single-sa...droazenMon, 07 Apr 2014 19:46:00 -0000https://sourceforge.net/p/picard/code/1902/https://sourceforge.nethttp%3A//sourceforge.net/projects/picard/files/sam-jdk/1.111/sam-1.111.jar/downloadpicardMon, 07 Apr 2014 15:11:36 -0000http://sourceforge.net/projects/picard/files/sam-jdk/1.111/sam-1.111.jar/downloadhttps://sourceforge.nethttp%3A//sourceforge.net/projects/picard/files/picard-tools/1.111/picard-tools-1.111.zip/downloadpicardMon, 07 Apr 2014 15:11:36 -0000http://sourceforge.net/projects/picard/files/picard-tools/1.111/picard-tools-1.111.zip/downloadhttps://sourceforge.nethttp%3A//sourceforge.net/projects/picard/files/picard-tools/1.111/README.txt/downloadpicardMon, 07 Apr 2014 15:11:36 -0000http://sourceforge.net/projects/picard/files/picard-tools/1.111/README.txt/downloadhttps://sourceforge.net/p/picard/code/1901/Release 1.111Alec WysokerMon, 07 Apr 2014 14:49:53 -0000https://sourceforge.net/p/picard/code/1901/https://sourceforge.net/p/picard/code/1900/Release 1.111Alec WysokerMon, 07 Apr 2014 13:43:54 -0000https://sourceforge.net/p/picard/code/1900/https://sourceforge.net/p/picard/code/1899/setting ADD_MATE_CIGAR to default to true in Fi...Nils HomerFri, 04 Apr 2014 21:20:27 -0000https://sourceforge.net/p/picard/code/1899/https://sourceforge.net/p/picard/code/1898/Fixed two bugs related to subtracting alignment...Brad TaylorFri, 04 Apr 2014 21:16:30 -0000https://sourceforge.net/p/picard/code/1898/https://sourceforge.net/p/picard/code/1897/Fixed two bugs related to subtracting alignment...Brad TaylorFri, 04 Apr 2014 21:14:10 -0000https://sourceforge.net/p/picard/code/1897/https://sourceforge.net/p/picard/code/1896/New VariantContextWriterBuilder class and testsJoel ThibaultFri, 04 Apr 2014 17:59:13 -0000https://sourceforge.net/p/picard/code/1896/https://sourceforge.net/p/picard/code/1895/Sync the nh_mark_duplicates branch with /trunk ...Nils HomerThu, 03 Apr 2014 15:56:46 -0000https://sourceforge.net/p/picard/code/1895/https://sourceforge.net/p/picard/code/1894/Added support for VCFv4.2 Version tags in heade...Eric BanksThu, 03 Apr 2014 02:55:51 -0000https://sourceforge.net/p/picard/code/1894/https://sourceforge.net/p/picard/code/1893/Removed support for Qseq, Cif and Cnf file form...jcareyWed, 02 Apr 2014 19:31:14 -0000https://sourceforge.net/p/picard/code/1893/https://sourceforge.net/p/picard/code/1892/Adding a new branch for the Illumina file util ...jcareyWed, 02 Apr 2014 19:18:18 -0000https://sourceforge.net/p/picard/code/1892/https://sourceforge.net/p/picard/code/1891/Merged nh_mate_cigar_refactoring r1775:r1889 in...jcareyTue, 01 Apr 2014 20:17:17 -0000https://sourceforge.net/p/picard/code/1891/https://sourceforge.net/p/picard/code/1890/Revert modified function arguments.jcareyTue, 01 Apr 2014 20:12:33 -0000https://sourceforge.net/p/picard/code/1890/https://sourceforge.net/p/picard/code/1889/Reassign the file util when checking symlinks s...jcareyTue, 01 Apr 2014 19:51:17 -0000https://sourceforge.net/p/picard/code/1889/https://sourceforge.net/p/picard/code/1888/Set ADD_MATE_CIGAR to false by default.jcareyTue, 01 Apr 2014 19:29:23 -0000https://sourceforge.net/p/picard/code/1888/https://sourceforge.net/p/picard/code/1887/Moved DuplicationMetrics back out of markduplic...Brad TaylorTue, 01 Apr 2014 18:56:51 -0000https://sourceforge.net/p/picard/code/1887/https://sourceforge.net/p/picard/code/1886/Adding a utility RemoveSamAttributes that will ...Nils HomerTue, 01 Apr 2014 17:58:40 -0000https://sourceforge.net/p/picard/code/1886/