Bases can be shaded based on flow signal deviations from either the
the read base calls or the reference homopolymer length.
* preferences for shading bases was broken due to new Enum

Signed-off-by: Nils Homer <nilshomer@gmail.com>
Signed-off-by: Nils Homer <nils.homer@lifetech.com>
adding the ability to copy flow signal distribution to the clipboard.

Signed-off-by: Nils Homer <nilshomer@gmail.com>
Signed-off-by: Nils Homer <nils.homer@lifetech.com>
* re-implementing "shade base by" as a sub-menu and a checkbox item

Signed-off-by: Nils Homer <nils.homer@lifetech.com>
HiC updates -- fix O/E bug

git-svn-id: https://igv.googlecode.com/svn/trunk@2109 17392f64-ead8-4cea-ae29-09b3ab513800
Fix log4j properties error -- undefined appender "R"

git-svn-id: https://igv.googlecode.com/svn/trunk@2110 17392f64-ead8-4cea-ae29-09b3ab513800
Comment out insertion of IGV logo

git-svn-id: https://igv.googlecode.com/svn/trunk@2111 17392f64-ead8-4cea-ae29-09b3ab513800
Added commons-io jar

git-svn-id: https://igv.googlecode.com/svn/trunk@2112 17392f64-ead8-4cea-ae29-09b3ab513800
Fix potential NPE if frame is null (headless testing), remove some print statements

git-svn-id: https://igv.googlecode.com/svn/trunk@2113 17392f64-ead8-4cea-ae29-09b3ab513800
Changes to treatment of IGV directory management and startup sequence.

git-svn-id: https://igv.googlecode.com/svn/trunk@2114 17392f64-ead8-4cea-ae29-09b3ab513800
Modify CommandExecutor so viewAsPairs and setMaxDepth can both accept TrackNames as second argument.
Fix a few bugs regarding case sensitivity that was making some commands not work in CommandExecuter (batch scripts).

Create test for CommandExecutor, only put in skeleton for now.

git-svn-id: https://igv.googlecode.com/svn/trunk@2115 17392f64-ead8-4cea-ae29-09b3ab513800
JR: fixed bug in O/E calculation
NC: fixed bug in writing out of densities file

git-svn-id: https://igv.googlecode.com/svn/trunk@2116 17392f64-ead8-4cea-ae29-09b3ab513800
Add code to permit moving the "igv" folder

git-svn-id: https://igv.googlecode.com/svn/trunk@2117 17392f64-ead8-4cea-ae29-09b3ab513800
Tweak to preferences UI

git-svn-id: https://igv.googlecode.com/svn/trunk@2118 17392f64-ead8-4cea-ae29-09b3ab513800
Add backend code and tests for indexing a fasta file

git-svn-id: https://igv.googlecode.com/svn/trunk@2119 17392f64-ead8-4cea-ae29-09b3ab513800
Fix bug where size parameter of fasta index was being calculated incorrectly (was using bytes, not number of bases).
Clean up code a bit. Add more tests

git-svn-id: https://igv.googlecode.com/svn/trunk@2120 17392f64-ead8-4cea-ae29-09b3ab513800
Remove some window-specific hacks from DirectoryManager

git-svn-id: https://igv.googlecode.com/svn/trunk@2121 17392f64-ead8-4cea-ae29-09b3ab513800
HiC updates -- work on Pearsons correlation

git-svn-id: https://igv.googlecode.com/svn/trunk@2122 17392f64-ead8-4cea-ae29-09b3ab513800
Adjust AlignmentTrack so that getHeight returns minHeight whenever zoomed out (so track doesn't stay hugely large when zooming out)

git-svn-id: https://igv.googlecode.com/svn/trunk@2123 17392f64-ead8-4cea-ae29-09b3ab513800
Add a slight hack where USER_DIRECTORY falls back to USER_HOME if it's null.

git-svn-id: https://igv.googlecode.com/svn/trunk@2124 17392f64-ead8-4cea-ae29-09b3ab513800