Skip to content
Snippets Groups Projects
Select Git revision
  • brentp-fisher-include
  • jmarshall-warnings3
  • map-pfm
  • master default
  • merge-assume-stdin
  • nkindlon-master
  • nkindlon-master2
  • pfm_merge
  • v2.24.0
  • v2.23.0
  • v2.22.1
  • v2.22.0
  • v2.21.0
  • v2.20.1
  • v2.20.0
  • v2.19.1
  • v2.19.0
  • v2.18.2
  • v2.18.1
  • v2.18.0
20 results
You can move around the graph by using the arrow keys.
Created with Raphaël 2.2.011Dec96425Nov181413126229Oct2714119328Sep27262524231913111024Aug231615141328Jun271130May30Apr3226Mar21632112Feb3129Jan2827262524161514927Dec261918161312119825Nov14543231Oct302922111018Sep1731Aug30242214824Jul2321201817326Jun198623May20151426Apr230Mar2013119628Feb242321191817161513121187530Jan2928272624231816121085231Dec3029211713128729Nov282517161587432126Oct25242111730Sep2827232216151310865131Aug24Jul19131165130Jun29282423221716151414Apr83129Mar221817103124Feb23167231Jan272521191413765323Dec21Nov4Oct21Sep[DOC] update docs for new -g option in intersect for specifying custom sort order.[ENH] intergrate merge changes from @kcha.[BUG] case typo that OSX tolerated.[BUG] case typo that OSX tolerated.[TST] cleanup sample testsync docs[ENH] add -allowBeyondChromEnd feature to shuffle.Add sample to main menu[TST] tests for reldist[TST] resolve platform-specific issues with GNU cut.Actually needed j1.bed in test/intersect.Fixed sample and intersect unit tests; minor code changes; new repository.Added unit tests for sampleFile program.Added sample sub-program with needed changes to main, Makefiles, Context, FileRecordMgr, and RecordOutputMgr.Added unit test for unrecognized arguments.Added unit test and changed error message for empty files.New unit tests for sort order enforcement, non-existant file. Also added performance test for file input and compression types.Added 12 new tests to print header for files with large header from uncompressed files, gzip, and bgzip as file, redirect, pipe and fifo.Added more unit tests for bed, gzip, and bgzipped files with large headers from file, redirect, pipe and fifo.added unit tests and data file for sort order, genome file, and more Bam unmapped reads.Fixed a bug in BamRecord::printUnmapped, added a unit test with with data file for unmapped Bam reads.new unit tests for intersectFixed small memory leak in InputStreamMgr.Fixed test for Bam vs Bgzip to allow for empty references.Added support for Bgzip from files and stdin.added fifo handlingStopped BinTree from loading or getting hits for unmapped reads.Moved short circuit for BAM unmapped reads to Record::sameChromIntersect for when query record isn't BAM but DB record is.added BamRecord::printUnmapped method for noHit and count functionality.Fixed unmapped mate bugFixed chromId bug, removed debug metric from RecordOutputMgrAdded -g option and descriptor to intersect help message.Shortened output buffer, corrected Chromsweep errors with some print options due to early termination.handling for unmapped Bam recordsMerge pull request #1 from arq5x/masteradd missing include to prevent compilation errorImproved help and error msgs in Contextfixed negative coords, zero len intervals, Bed4 format errorresolved chromId problem when doing Chromsweep with BAM file sorted differently than genome file.-g (genomeFile) option now gives error if file is differently sorted than genome file.