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Commits on Apr 4, 2016

• bump version #vc

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Commits on Feb 27, 2016

• Merge pull request #103 from pachterlab/MemoryFix

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Commits on Jan 22, 2016

• add a gulpfile #vc

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Commits on Oct 28, 2015

• Merge pull request #88 from pachterlab/devel

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• Merge pull request #87 from pachterlab/bias-to-hdf5

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Commits on Oct 24, 2015

• Merge pull request #85 from pachterlab/multicore

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Commits on Oct 4, 2015

• add snakemake and readme to test

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Commits on Aug 25, 2015

• Merge pull request #77 from pachterlab/devel

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• update to version 0.42.3

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• add option for standard deviation in fld. add some more msgs for fld

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• fix off-by-one error in trunc gaussian

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Commits on Aug 24, 2015

• Merge pull request #73 from pachterlab/unique-fasta-names

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Commits on Aug 22, 2015

• Merge pull request #69 from pachterlab/numprocessed

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• Merge pull request #62 from pachterlab/eff_len

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Commits on Jul 9, 2015

• general cleanup of comments and output

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• refactor mean_fl out of EM and Bootstrap

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• update_eff_lens has been refactored to remove const mean. remove some magic numbers

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• incorporate palls suggestions. technically works, but not benchmarked yet

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Commits on Jul 5, 2015

• updated bias to incorporate conditional mean

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Commits on Jul 3, 2015

• use truncated normal for single-end reads

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Commits on Jun 30, 2015

• stupid bugfix inserts frag len means into vector

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• lots of little refactoring to get eff len stuff to compile

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• calc eff lens based off of FL distribution instead of constant mean. still need SE logic

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• wip. helper function to give 'mean frag len' for each trans

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• compute the exact eff len based on the conditional distribution

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Commits on Jun 19, 2015

• Merge branch 'devel'

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• added note about devel and pull requests

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• Merge pull request #61 from pachterlab/devel

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Commits on Jun 17, 2015

• Minor release v0.42.2.1. Merge branch 'devel'

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• remove note about installing tests in INSTALL

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• Merge pull request #59 from pachterlab/devel

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Commits on Jun 13, 2015

• Merge pull request #55 from pachterlab/devel

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Commits on Jun 12, 2015

• Merge branch 'devel' -- fix single-end bug and pseudobam output

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• update pretty_num that got wiped out on merge

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• uncomment warning and uncomment threads. fixl inks in README

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