M ReleaseNote.txt
M scripts/blast2psl.pl
M README.txt
M README.txt
M README
A scripts
AM README
M src/misc/filter/PairInDistance.java
M scripts/sMonitor.pl
AM scripts/rearrangeDetector.pl
M scripts/blast2psl.pl
AM scripts/consistentIndel.pl
M scripts/MappingMinimap2.pl
M README.txt
M galaxy/OneStopWrapper.pl
M galaxy/OneStopWrapper.pl
D build.in.xml.EXAMPLE
M scripts/RPKMcorrelation.pl
A src/misc/SAM2PSL.java
AM scripts/sMonitor.pl
M scripts/cgff2PSL.pl
AM scripts/FastqReverse.pl
AM scripts/MastPairCompareWrapper.pl
M build.xml
M src/special/PromoterCGFF.java
M scripts/MutationAnnotation.pl
M src/graph/Graph.java
AM scripts/mergeExonCount.pl
M scripts/MappingBlat.pl
A src/misc/filter/MonoSeq.java
M scripts/consistentBlocks.pl
M scripts/consistentBlocks.pl
M scripts/consistentBlocks.pl
M scripts/consistentIterator.pl
M scripts/consistentBlocks.pl
M scripts/consistentBlocks.pl
D scripts/consistent.pl
M src/misc/GffTree.java
M src/graph/Graph.java
M build.in.xml.EXAMPLE
M scripts/MergeSam2.pl
M scripts/MergeSam2.pl
M scripts/MutationAnnotation.pl
M scripts/MutationAnnotation.pl
M scripts/MutationAnnotation.pl
M scripts/MutationAnnotation.pl
A src/bio301
M ReleaseNote.txt
AM scripts/MergeSam.pl
M scripts/pipeline/MergeSam2.pl
M scripts/pipeline/MappingMinimap2.pl
M scripts/special/MutationAnnotation.pl
M scripts/special/MutationAnnotation.pl
M scripts/special/MutationAnnotation.pl
M src/reseq/NtFreqCounter.java
M scripts/psl2sam.pl
M scripts/galaxy/VariantAnnotateFilter.pl
M scripts/galaxy/VariantAnnotateFilter.pl
M scripts/galaxy/VariantAnnotateFilter.pl
M scripts/pipeline/MergeSam2.pl
M scripts/pipeline/MergeSam2.pl