USeq Source Code

* Application for identifying allelic expression based on a table of snps and bam alignments filtered for alignment bias (see ReferenceMutator and SamComparator).
ReferenceMutator
* Given a table of snps and directory of reference fasta files. Introduces the non reference base into the fastas.
DefinedRegionDifferentialSeq
* Added option to collect counts from the 5' and 3' ends of genes
DifferentialReadCoverageComparator
* Takes the count table generated by DRDS with the -z option and looks for changes in 5'/3' read coverage between different conditions to identify short truncated transcripts
RandomMutationGenerator
* Creates snvs and indels for the BAMSurgeon application