Began abstracting to variable number of callesr
Untested query construction scheme for consensus variant detection. Now must abstract the genotype consensus selection to variable number of callers
Added Average depth and GATK PL fields. The output is still funky funky.
The mean depth and GATKs PL fields are now appropriately handled. Need a better abstraction for adding branches to the consensus, as well as preserving specific metrics from the branches, or extending the output.
updating genotypers
Merge branch 'master' into haplotypecaller
Init. Sucessfully opens up VCF readers for an arbitrary number of vcf files. Now we have to figure out how to walk these along variation lock step.
update to the vcf iterator
Merge branch 'master' of https://github.com/vtrubets/galaxy.consensus into stream_refactor
Merge branch 'master' of https://github.com/vtrubets/galaxy.consensus into stream_refactor
moved tourette specific scripts out of the repository
Merge branch 'master' of https://github.com/vtrubets/galaxy.consensus into stream_refactor
Removed problematic reference encodings in the contig ID section.
Can now walk concordant sites.
Changed the name of the file containing the class for the new concordant site wlker
Switched to reporting _Record objects during iteration rather than just physical position. This allows us to operate on sets of records when calculating consensus.
Genotyper for the stream-based code refactor.
Init for a new VCF writer class
We now have a barebones consensus caller! As of now, it can only do a strict consensus, and no information beyond genotypes are passed along from the original VCF files.
init for the main loop of the consensus refactor