Ngmlr Versions Save

• CMake fixes
• Dynamic linking is now default (use cmake -DSTATIC=ON for static linking)
• --bam-fix writes CS tag (Thanks Heng)
• Fix to handle missing write permission when writing index
• Improved handling of smaller duplications
• Typos corrected (Thanks wdecoster)
• Support for RG in output

• Fixed: reads wrongly sometimes wrongly spanned two chromosomes (issues #23)
• Match score reduced and low quality split + short inv detection enabeld for -x ont

• Fix for long MD strings (segfault)
• Fix for LMP extension at chromosome borders (segfault)
• Dynamic linking is now default

• 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 #13)
• Filtering changed to fix issue #12
• Primariy alignment flag fixed (issue #11)
• Set max length for read names to 500

• Compatibilty with (mini)conda
• SeqAn removed
• Switched from c++14 to c++11
• Option to switch off static build in CMake (-DSTATIC=OFF)

Mapping results should be the same as in v0.2.1

• 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)
• 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

• Docker image for building ngmlr added
• Gap decay parameter added
• Memory corruption fixed

• MD tag fixed