USeq Source Code

Brought to you by: biotelerock, bmilash, elainegee, scourdy, tmosbruger

Commit [r95] Maximize Restore History

Added ParseExonMetrics, which takes the output from several sequencing diagnostic programs and creates PDF containing all of them. Several mods to existing Apps to support tomato v2. Added GenerateOverlapStats, which generates the same metrics as MergePairedSamAlignments, but does not require the time-intensive sort or sam manipulations.

Authored by: tmosbruger 2013-04-02

Browse code at this revision

Parent: [r94]

Child: [r96]

added	/trunk/Source/edu/utah/diagnostics
added	/trunk/Source/edu/utah/diagnostics/CountChromosomes.java
added	/trunk/Source/edu/utah/diagnostics/GenerateOverlapStats.java
added	/trunk/Source/edu/utah/diagnostics/NullOutputStream.java
added	/trunk/Source/edu/utah/diagnostics/ParseExonMetrics.java
changed	/trunk/Source/edu/utah/seq/data/CalculatePerCycleErrorRate.java
changed	/trunk/Source/edu/utah/seq/data/Sam2USeq.java
changed	/trunk/Source/util/gen/Gzipper.java
changed	/trunk/build.properties

/trunk/Source/edu/utah/diagnostics

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USeq Source Code

Commit [r95] Maximize Restore History

/trunk/Source/edu/utah/diagnostics

/trunk/Source/edu/utah/diagnostics/CountChromosomes.java Diff Switch to side-by-side view

/trunk/Source/edu/utah/diagnostics/GenerateOverlapStats.java Diff Switch to side-by-side view

/trunk/Source/edu/utah/diagnostics/NullOutputStream.java Diff Switch to side-by-side view

/trunk/Source/edu/utah/diagnostics/ParseExonMetrics.java Diff Switch to side-by-side view

/trunk/Source/edu/utah/seq/data/CalculatePerCycleErrorRate.java Diff Switch to side-by-side view

/trunk/Source/edu/utah/seq/data/Sam2USeq.java Diff Switch to side-by-side view

/trunk/Source/util/gen/Gzipper.java Diff Switch to side-by-side view

/trunk/build.properties Diff Switch to side-by-side view