Tags: t-nojiri/ngmlr
Tags
- Fixed: reads wrongly sometimes wrongly spanned two chromosomes (issues philres#23) - Match score reduced and low quality split + short inv detection enabeld for -x ont
- now reads from stdin if -q is skipped - fixes for increasing stability - updates and fixes for mapping ultra-long nanopore reads (https://github.com/nickloman/massive-nanopore-silliness) - Parameter --bam-fix added. Currently, BAM does not support reads with > 64k cigar elements. When --bam-fix is set all reads with >64k Cigar elements will be reported as unmapped to maintain compatibility with BAM
- Min residues check added to short read processing - Parameter "--skip-write" added: If specified, ngmlr won't write the reference index to disk - Fix for non-deterministic MAPQ (Issue philres#13) - Filtering changed to fix issue philres#12 - Primariy alignment flag fixed (issue philres#11) - Set max length for read names to 500
- Fixes for circular reference genomes - Memory corruption fixed - Filter for random short alignments added - Dynamic programming approach for choosing best combination of mapped segments (thanks to @bqminh) - Alignment computation speedup with SSE instructions (thanks to @smolkmo) - Mapping quality computation updates - Several memory leaks fixed - Small duplication detection improved - `--min-residues/-R` changed set to 25% (default). All reads that have less than 25% mapped are reported as unmapped per default - `--max-segments` added. Max number of segments reported for a single read
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