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Created with Raphaël 2.2.016Sep151310865131Aug24Jul19131165130Jun29282423221716151414Apr83129Mar221817103124Feb23167231Jan272521191413765323Dec21Nov4Oct21Sep318Aug1665425Jul232221181715146543130Jun29876May543229Apr2826221514131229Mar2322181715141210319Feb126228Jan2723191110876543130Dec29201826Nov25191816141327Oct232120191521Sep17151428Aug22Jul25Jun1529May1912116528Apr272624232221159Moved nullBed reset to GetNextBedUpdated READMEUpdated READMEUpdated READMEUpdated READMEAdded newline before version.h EOFAdded new -sorted option to intersectBed. No memory and filthy fast.Gussy.chromsweep is a proper tool. Now to make it an iterable class.chromsweep 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 Vogel