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Created with Raphaël 2.2.01Sep31Aug24Jul19131165130Jun29282423221716151414Apr83129Mar221817103124Feb23167231Jan272521191413765323Dec21Nov4Oct21Sep318Aug1665425Jul232221181715146543130Jun29876May543229Apr2826221514131229Mar2322181715141210319Feb126228Jan2723191110876543130Dec29201826Nov25191816141327Oct232120191521Sep17151428Aug22Jul25Jun1529May1912116528Apr272624232221159Updated gzip detection. Weaker, but necessary for FIFO supportGzip detected by file extension. Weak, but only approach that works at this point.Need to rewind to start of file after Gzip check.Updated fastaFromBedfifo support add'lReverted the -full option in fastaFromBed. Use 06a7e24e294e06258c75 to retain it.BEDTools now supports FIFOs and named pipes. Many thanks Nate Weeks and Michael Hoffman for the suggestions.now allow "-" as well as "stdin".Added -Sm to windowBedAdded -S to subtractBedAdded -S to pairToBedAdded -S to closestBedAdded -S to annotateBedAdded -S to coverageBedAdded -S (opposite strand) logic to intersectBedAdded logic to keep dups and failed QC for multiBamCov. Thanks to Chip Stewart.GFF can't have 0-length features.Added -full to fastaFromBedCorrected start check in parseVcfLine. Thanks to Jan VogelMakefile tweakFirst cut at -scale for genomeCoverageBedcorrected a pull goofMerge branch 'master' of github.com:arq5x/bedtoolsincluded cstdlib in lineFileUtilities.h. Thanks to @dalerMerge pull request #7 from daler/masterinclude cstdlib for gcc 4.4.3Tweaks to Tokenize(), GetNextBed(), and detection of negative coordinates. Thanks to @agordon15% speedup for the tokenizer.tweak to Fasta.cppChanged version numberUpdated help messagesUpdated Makefile for 64bit BAM seeks.Latest BamTools. Commit 525fc971414d7f7b8b60Don't track BamTools/includeCleanup of bamtools directories and updated MakeNew region checks for multiBamCov. Thanks to Derek Barnett.Updated to 2.13.0.alphaUser can define their own tag type for tagBam.Moved FastaHack to the utils/ directoryCode gussying