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v2.05
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@mozack mozack released this 24 Apr 15:36
· 312 commits to master since this release
v2.05
6719f64

  • Enable usage of high quality soft clipping and observed indels to generate putative contigs by default
    ** Note: parameters around this behavior have changed

  • Remap reads equal to min mapq

  • Output unmapped read pairs in final BAM

  • Added deBruijn graph simplification

  • Cadabra - only use primary alignments for calling

  • Various speed optimizations
    ** More conservative assembly triggers
    ** Optimization of read to contig mapping
    ** sparse_hash --> dense_hash
    ** Introduce smaller chromosome "chunks" to improve parallelization
    ** Parallelize final BAM sorting/writing in multi-BAM cases
    ** More selective permuting of regional splice junctions combinations
    ** Discard low scoring contigs during assembly
    ** Cadabra - added multi-threading

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