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Commits on Apr 10, 2012

• change the --cssClass arg to flatfile-to-json.pl to be --className, to match what shows up eventually in the configuration. --cssClass still works though, for backcompat

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• add an example shell script that downloads and formats some fairly big tomato data

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• more additions to feature glyphs doc, just documenting things that were already there in the genome.css file

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• add more examples to the glyph docs, amazing what styles i'm finding by spelunking in the feature style CSS

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• split genome.css into main.css and feature_styles.css, so that all the styles for feature glyphs are not mixed in with the base styles for the app

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• little facelift to the feature glyph reference

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• make the transcript in the glyph reference be a better representation of how it actually looks

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• make a default classname for subfeatures that don't have an entry in subfeatureClasses

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• fix CDS example in featureglyphs docs

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Commits on Apr 9, 2012

• bugfix to lazy NClist building: correctly handle features that have so many subfeatures that they are bigger than the chunksize. fixes GMOD#90.

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• add a test for really-big-features nclist-builder bug

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• warning squash

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• make more tests use JBlibs earlier so they have a better chance of picking up Test::More

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• consistent spacing in setup.sh progress messages. no detail is too small to escape the gimlet (pedantic?) eye of rbuels.

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• be more explicit about what the BAM support is doing

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• add some more troubleshooting tips to setup.sh

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• add tips on development libraries to output of setup.sh

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• make JBlibs.pm use the copy of local::lib in extlibs/ if it's there

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• remove unnecessary use of List::MoreUtils

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• tweak dist.ini, try to make it easier to use dzil to build

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• update Makefile.PL, made by a newer dzil

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• make setup.sh check for missing perl core modules. EC2 instances in particular don't always have these. >:-{

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• make command-line scripts correctly update the style and other config opts of existing tracks. fixes GMOD#91

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• add a test for flatfile-to-json.pl correctly updating style information. references GMOD#91

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• correct ucsc-to-json feature modification callback to use the most recent feature getters

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• make FeatureTrack cope with string start/end coords. defensive programming, and turns out to not to have much of a speed penalty. references GMOD#96.

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Commits on Apr 8, 2012

• JBlibs: don't die if the extlib/ isn't found. people might want to run with their own libs

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• numify end coordinates of features for correct JSON encoding. fixes GMOD#96

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• fix wig-to-json.pl test

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• add autotools cache dir to gitignore

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• add Makefile.deploy rules for managing the makefile and configure scripts in wig2png/

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Commits on Apr 7, 2012

• back off a bit on the track-label margins now that the y-scales are centered

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• change the wiggle "metadata" data item to "stats", which is more descriptive of what it actually does

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• draw Y-axis labels in the center instead of on the left. rename updateStaticElements() methods to the more accurate updateViewDimensions()

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Commits on Apr 6, 2012

• better document --type option to flatfile-to-json.pl

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