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Commits on Jun 3, 2015

• Merge pull request cole-trapnell-lab#27 from wookietreiber/detect-eigen-via-pkg-config

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Commits on May 27, 2015

• detects eigen3 via pkg-config

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  wookietreiber

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Commits on Jan 10, 2015

• Merge pull request cole-trapnell-lab#7 from gaborcsardi/README-link

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Commits on Jan 9, 2015

• Fix CuffCompare link in README

  gaborcsardi

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Commits on Nov 25, 2014

• Merge pull request cole-trapnell-lab#1 from smowton/master

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• Don't try to look up reference scaffolds in a depth-of-coverage map; this leads to undefined behaviour.

  

  Chris Smowton

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• Don't blank the skipped.gtf file when running in reference guided mode.

  

  Chris Smowton

  committed
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• Replace the map-of-lists mate-finding data structure with a much more efficient hashmap. This prevents long stalls when a large number of as-yet-unpaired mates are looking for the same genome offset.

  

  Chris Smowton

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Commits on Jul 26, 2014

• Convert svn:ignore properties to .gitignore.

  ctrapnell

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Commits on Jun 9, 2014

• don't include low abundance transcripts in coverage normalization calculation, use all isoforms

  ctrapnell

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Commits on May 15, 2014

• simpler, more robust method for finding the coverage scaling constant

  ctrapnell

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• some tweaks to mode calculation

  ctrapnell

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Commits on May 14, 2014

• use mode instead of median

  ctrapnell

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• try the mean coverage instead of the median for estimated absolute norm

  ctrapnell

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Commits on May 12, 2014

• use a single table to hold all the id to locus mapping data

  ctrapnell

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Commits on May 8, 2014

• more fixes for duplicate entries in cuffnorm tables

  ctrapnell

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• fixed the build errors associated with last checkin

  ctrapnell

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Commits on May 7, 2014

• DOES NOT COMPILE. Deal with genes that span multiple disjoint loci

  ctrapnell

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• adjust locks on TestLauncher

  ctrapnell

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• needed to lock _launcher_lock in the output writer

  ctrapnell

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Commits on May 6, 2014

• more memory reductions - don't load all of the metadata associated with LocusCount objects during deserialization

  ctrapnell

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• disabled deep copying for cuffnorm

  ctrapnell

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• clear the read group count tables after cuffnorm normalization

  ctrapnell

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• use ints instead of strings to index read group count tables

  ctrapnell

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• boost/version.hpp errors

  ctrapnell

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• boost/version.hpp at the top

  ctrapnell

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Commits on May 5, 2014

• removed tracked objects after they are written out

  ctrapnell

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• fixed a #define issue

  ctrapnell

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• first steps toward immediate write-out of tracking data

  ctrapnell

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• only use the most abundant transcript for median coverage calculation

  ctrapnell

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• a little cleanup

  ctrapnell

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• print median transcript coverage in sample attribute table

  ctrapnell

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• only use transcripts hit by at least one whole fragment for estimated absolute normalization

  ctrapnell

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• apply estimated absolute scaling via the internal_scale_factor

  ctrapnell

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Commits on May 1, 2014

• disabled bundle caching during inspect_map to reduce memory footprint of cuffnorm

  ctrapnell

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