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Created with Raphaël 2.2.016Sep151310865131Aug24Jul19131165130Jun29282423221716151414Apr83129Mar221817103124Feb23167231Jan272521191413765323Dec21Nov4Oct21Sep318Aug1665425Jul232221181715146543130Jun29876May543229Apr2826221514131229Mar2322181715141210319Feb126228Jan2723191110876543130Dec29201826Nov25191816141327Oct232120191521Sep17151428Aug22Jul25Jun1529May1912116528Apr272624232221159chromsweep is now a python-style generator. Big smile\!chromsweep demogcB no longer requires a genome file for BAM. New chromsweep tool.Changed error message when BAM is not qeury sorted in pairToBedAdded Seek and Rewind (destroy?) to BedFile.Added -scores option to tagBamFixed pairToPair's -type notBoth modeVersion 2.13.1: Added -s, -S, and -names to tagBam.Added -s, -S, and -names to tagBam.Avoid deleting bedStream iff stdinReasoning for GZIP detection change.Proper Gzip checkUpdated 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.