USeq_9.1.5

See commit logs.

USeq_9.1.3

See commit logs. Some bug fixes. New apps for annotating bed and vcf files.

USeq_9.1.2

Several new QC apps to finding concordance between related bam files. Some changes to the AggregatePlotter and Sam2USeq to facilitate scaling with spiked species. See the change logs!

USeq_9.1.1

Wanted to update the splice junction apps given the recent interest. No bug fixes, just more features. New app called KnownSpliceJunctionScanner for generating histograms, means, and stdevs for known 5' and 3' max ent scan scores when provided a ucsc refflat gene table.

USeq_9.1.0

See the commit logs!

USeq_9.0.9

See the commit logs!

USeq_9.0.8

See the commit logs! Threaded several apps, pipe input for the SamTranscriptomeParser, a variety of catches added for odd input data.

USeq_9.0.7

See the commit logs! Lots of modifications to the VCF parsers. New apps for estimating error rates in a normal bam files and comparing vcf records against background bams for variant artifacts.

USeq_9.0.6

Three new apps, a mpileup parser, an error rate estimator, and a tool for merging multiple vcf files enabling ensemble consensus calling.

USeq_9.0.5

First release of the QueryIndexer, an app for scanning an entire file system for tabix indexed genomic data files and building interval trees on them to enable rapid intersection. The output is used by the Query REST API tool, see https://github.com/HuntsmanCancerInstitute/Query . This first release version includes modifications supporting chr and no chr chrom names, is threaded for simultaneous file loading, and uses a better interval tree data structure implementation.