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MethylationArrayDefinedRegionScanner

* Modified app so it works with non even numbers of t and c
SamParser
* Modified the way the mid point of an alignment is calculate. It is now the alignment start + 1/2 the read length. Did this to avoid problems with splice junction reads.
* Set the bam file reader stringency to silent.

biotelerock 2013-07-02

changed /trunk/Documentation/USeqDocumentation/releaseNotes.txt
changed /trunk/Source/edu/utah/seq/analysis/MethylationArrayDefinedRegionScanner.java
changed /trunk/Source/edu/utah/seq/base/BamIntensityJoiner.java
changed /trunk/Source/edu/utah/seq/data/MethylationArraySamplePair.java
changed /trunk/Source/edu/utah/seq/parsers/SamParser.java
changed /trunk/Source/util/gen/IO.java
/trunk/Documentation/USeqDocumentation/releaseNotes.txt Diff Switch to side-by-side view
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/trunk/Source/edu/utah/seq/analysis/MethylationArrayDefinedRegionScanner.java Diff Switch to side-by-side view
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/trunk/Source/edu/utah/seq/base/BamIntensityJoiner.java Diff Switch to side-by-side view
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/trunk/Source/edu/utah/seq/data/MethylationArraySamplePair.java Diff Switch to side-by-side view
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/trunk/Source/edu/utah/seq/parsers/SamParser.java Diff Switch to side-by-side view
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/trunk/Source/util/gen/IO.java Diff Switch to side-by-side view
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