1.2.0-beta05

• Enabling the cache more often when using the Api
• SequenceAlignment.formatVerbose now outputting query length rather than alignment length

1.2.0-beta04

Fixes:

• Larger maximum reference contig length
• Fixing a small nondeterminism in hashing the reference genome
• Fix for the case of low indel extension penalty

Performance:

• Better parallelization of hashing of the reference when there is a long contig or a single query
• Flushing worker messages more often

Additions/adjustments to the output:

• Small text-based graphs of alignment penalty and indel lengths
• More accurate timing when running a single query
• Replacing empty vcf fields with '.'

Augmenting the library API:

• QueryAlignment.formatVerbose() function now available to users of the API
• Api.newDatabase support for custom sequence names

1.2.0-beta03

Adding an ambiguity penalty for ambiguous basepairs in queries too

Some diagnostics: disallowing sequences of length 0 and disallowing duplicate contig names by default

1.2.0-beta02

--vcf-omit-support-reads flag to control support read display in VCF

Some more API methods to make it easier to use Mapper as a library

1.2.0-beta01

Added a --cache-dir argument to allow caching analyses of the reference genome ( see #2 )

Added a simple Api class to make it easier to interact with Mapper as a library

No longer skipping some hashblocks having the longest analyzed length in their batch

1.1.0

Rereleasing 1.1.0-beta13 without a qualifier, to indicate stability

1.1.0-beta13

Renaming Mapper to X-Mapper to be more unique

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