Version 1.0.20

-Input reads can be in .bam or .sam format (no bam/sam output)
-Input reads file extension is now case insensitive
-More informative error message if input read file format cannot be parsed
-Bugfixes

GraphAligner.tar.gz

Version 1.0.19

• Tags in read name (eg methylation) are removed by default, can be kept with parameter --keep-sequence-name-tags
• Fixes to diploid heuristic

GraphAligner.tar.gz

Version 1.0.18

• bugfixes
• .gam output has mapping quality
• .gfa.gz input graph supported
• new hidden parameters "--diploid-heuristic" and "--diploid-heuristic-cache"

GraphAligner.tar.gz

v1.0.17b

-Bugfixes
-Compilation on osx works again

GraphAligner.tar.gz

Version 1.0.17

-Refactors for faster alignment and lower memory use
-New mxm seeding parameters "--low-memory-mem-index-construction" "--seeds-mxm-windowsize" "--mem-index-no-wavelet-tree"

GraphAligner.tar.gz

v1.0.16-osx

Compilation on osx is now supported
GraphAligner.tar.gz

Version 1.0.16

• MEM seeding is faster and uses less memory
• bugfix

GraphAligner.tar.gz

Updated tar from commit 3c33fec below to fix missing includes in bioconda compilation
GraphAligner.tar.gz

Version 1.0.15

• GraphAligner is now more strict about GFA correctness
• Minor bugfixes to --seeds-mem-count and --seeds-mum-count
• Minor bugfixes removing some sources of nondeterminism (but some remains)

GraphAligner.tar.gz

Version 1.0.14

• Alignment method overhauled: GraphAligner now clusters seeds and uses a sparse Smith-Waterman algorithm for extending each cluster
• Alignments now have mapping qualities
• Alignments are slightly more accurate
• Fixed a bug in alignment identity calculation
• New parameters --max-cluster-extend for the maximum number of seed clusters to extend, --max-trace-count for the maximum number of backtraces to compute per seed cluster
• Removed parameter --try-all-seeds

GraphAligner.tar.gz

v1.0.13

-Better alignment end clipping
-New parameter "--precise-clipping" to control the identity threshold used for clipping alignment ends
-New parameter "--X-drop" to control how far GraphAligner will try to align a read through low-identity parts
-New parameter "--min-alignment-score" to discard poor alignments
-Output log now reports how many base pairs in reads belong to an alignment
-Alignment cigar now uses =/X for matches/mismatches instead of M
-Allow graphs where edge overlaps are "*", assume that means zero overlap
-Bugfix for seed clustering in bubbles
-Bugfix for graphs whose node IDs are integers but larger than 32 bits
-Bugfix for empty output alignment gaf
-Removed lots of old parameters

GraphAligner.tar.gz