1.1.0-beta12

Adding a very simple model for MAPQ: 255 for alignments having minimum penalty and 0 for others

1.1.0-beta11

Lower memory usage
Slightly higher accuracy

1.1.0-beta10

Usability/formatting adjustments, including:

Setting more paired-end flags in sam files
Adjusting sam header so samtools can read it
Sending status messages to stderr
Support for --out-sam - to send the sam file to stdout

1.1.0-beta09

Improvements to speed and accuracy

1.1.0-beta08

Support for --split-queries-past-size with very long input sequences

1.1.0-beta07

Some improvements to reliability, accuracy, and speed

1.1.0-beta06

release version 1.1.0-beta06

1.1.0-beta05

• Support to incorporate paired-endedness information from Illumina-style paired-end queries
• Automatically inferring ancestors of highly similar sequences, to compute more appropriate alignment penalties
• Assorted improvements to accuracy

1.1.0-beta04

Much faster performance via several optimizations including mostly parsing input files in parallel

Removed experimental --split-queries-past-size for now

1.1.0-beta03

Faster performance, particularly when many queries don't have a good alignment

Experimental option for rudimentary long-read support, which splits long queries into short queries before aligning: --split-queries-past-size