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Commits on Nov 18, 2014

• 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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• to be moved to a separate project

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• map to individual HLA ALT for meaningful mapQ

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Commits on Nov 5, 2014

• optionally output debegging info

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Commits on Nov 4, 2014

• nothing, really

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• more command line help

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• change the default max_len

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• control min-match-length

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• type primary exons first and then the rest

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• a bit code cleanup

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• proper homozygous typing; fixed a low-level bug

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• backup

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Commits on Nov 3, 2014

• polished the run script

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• added the pipeline script

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• better CLI; more comments

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• not used any more

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• first HLA typing script

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