USeq Source Code

More static methods....

Fixed a warning message related to exon size, added methods related to strand.

Mods to support the Telescriptor....

New app and supporting classes for detailed Telescripting discovery.

Added more output options for showing sample names and their order.

Modified default bps to extract alignment counts from 250 to 150. This is a hidden option only used by telescriptors.

Added option to skip alt comparison when scoring matches. Corrected bug where SNP's with two SNP alternates were called nonSNP.

AlignmentEndTrimmer
Bug fix: mismatches are now counted properly on the reverse strand
VCFParser
Added support for awful varcsan VCF output.

AllelicExpressionDetector
* 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

AlignmentEndTrimmer: Option -s added to drop reads with -x number of mismatches. If option -e is specified, RNA editing changes are ignored.