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Commits on Apr 17, 2017

• Merge branch 'master' into 0.2.13_cram_support

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Commits on Mar 28, 2017

• allow argument for reference fasta

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• Merge branch 'ernfrid-0.2.13_cram_support' into 0.2.13_cram_support

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• resolve conflicts

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Commits on May 30, 2016

• ignored paired-end libraries that comprise <0.1% of the BAM file. I think this is the cause of arq5x#104

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Commits on Sep 23, 2015

• removed deprecated lsort and lmerge

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Commits on Sep 3, 2015

• use gawk instead of awk, since some versions of awk do not support i=1;i<=k;++i style for loops

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Commits on Jun 2, 2015

• fix shifting of intervals with slop

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• not sure what i did here

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• repair algorithm reporting

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• actually fixed probability slop of 1e-100

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• don't alter the peak value when adding slop to intervals

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Commits on May 16, 2015

• Merge branch 'master' of github.com:cc2qe/lumpy-sv

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Commits on May 14, 2015

• add dependency version issue per arq5x#80

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Commits on May 1, 2015

• add missing FORMAT item to VCF header

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• bump bamkit

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Commits on Apr 28, 2015

• put SNAME info tag at bottom of header

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• removed lumpyexpress without -S and -D from README until we fix this functionality

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• removed lumpyexpress without -S and -D from README until we fix this functionality

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Commits on Apr 27, 2015

• fix SVLEN for DUP and INV

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• marker for BND dev. too difficult to solve right now.

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• don't print columns 9-end after merging

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• preserve header order. also fix SVNAME --> SNAME typo

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• fix breakend variant reporting

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Commits on Apr 3, 2015

• remove old README

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• sync

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• update

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• update

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• update

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• update

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• update

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• update

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• update

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• update

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• update

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