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Commits on Dec 11, 2014

• wrong sentence in README-alt

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Commits on Dec 2, 2014

• more FAQs on ALT mapping

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Commits on Dec 1, 2014

• Updated READMEs a little

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Commits on Nov 26, 2014

• r1017: process I/O in a separate thread

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Commits on Nov 19, 2014

• added download link explicitly

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• moved directory structure to this README

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• smarter about path finding

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• minor changes

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• minor fix to a link

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• Split README-alt.md into two documentations

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• transfer read groups from the input BAM

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• r1005: insert arbitrary header lines

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• renamed extras to bwakit for clarity

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• update about bwa.kit

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• don't type empty files

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Commits on Nov 18, 2014

• fine tune the wrapper scripts

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• r998: smart pairing; allow mixture of SE/PE reads

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Commits on Nov 17, 2014

• minor change

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• added an evaluation section

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• Updated README for ALT mapping

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• Removed a comment on hs38 lacking EBV

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• polish

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• polish the run script

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Commits on Nov 16, 2014

• replace run-gen-hs38* with run-gen-ref

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Commits on Nov 14, 2014

• fine tune

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Commits on Nov 13, 2014

• smarter prefix finder

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• wrapper for bwa-mem

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• added scripts to generate hs38a.fa and hs38d6.fa

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• move bwa-typeHLA back to this repo

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• r985: fix bug due to the lack of _pri contigs d6

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• r984: updated to the latest kseq.h

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Commits on Nov 10, 2014

• r983: bugfix - wrong mate info

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• mate chr is sometimes wrong

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Commits on Nov 7, 2014

• removed contig weight & code cleanup

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Commits on Nov 6, 2014

• move to a new project bwa-typeHLA

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