GitHub - nishill/bam-entropy: Finds the entropy of data in a bam file based on the formula from information theory.

Branches Tags

Name		Name	Last commit message	Last commit date
Latest commit History 15 Commits
bamtools		bamtools
cramtools		cramtools
samtools		samtools
sdk		sdk
.vimrc		.vimrc
BamAlignmentIterator.cpp		BamAlignmentIterator.cpp
BamAlignmentIterator.h		BamAlignmentIterator.h
BamAlignmentIterator.o		BamAlignmentIterator.o
CompressionIterator.cpp		CompressionIterator.cpp
CompressionIterator.h		CompressionIterator.h
CompressionIterator.o		CompressionIterator.o
Makefile		Makefile
README		README
compress		compress
exampleBAM.bam		exampleBAM.bam
git-credential-osxkeychain		git-credential-osxkeychain
main.cpp		main.cpp
main.o		main.o
out1.txt		out1.txt
output.bam		output.bam
test.bam		test.bam

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# README
# $ID$

Files:

README
main.cpp
Makefile
BamAlignmentIterator.cpp
BamAlignmentIterator.h
CompressionIterator.cpp
CompressionIterator.h

Special Notes:

The bamtools c++ library is necessary to run and use code. 

The BamAlignmentIterator files were added to iterate through
the the alignments base by base. This program computes
the entropy of a given bam file based on information theory.

The CompressionIterator files are used as a new approach to 
analyze entropy. This time a tree structure is created as a 
list(genome position) of a map(base, QualInfo) of another
map ( QualScore, number of occureneces). This should allow for
the analysis of entropy on genetic variants.