2.0.3

This release contains numerous bugfixes.

• Fix for issue #164, where SNAP was crashing with small headers and inputs, when all in memory.
• Fix for non-deterministic secondary alignments
• Fix that removes Hamming distance scoring when running the single end aligner standalone (snap-aligner single)

2.0.2

This release contains numerous bugfixes and several new features.

The features are adding a new -pfc option that will preserve comments in a FASTQ input into S/BAM tags; an option to attach the alignment time for each read as a BAM tag; cleaning up printf output formats by doing things like adding commas to large numbers so they're easier for humans to read; adding some options to reduce or eliminate status printing while aligning; updating to S/BAM format 1.6 and including the SO tag in the header when appropriate; increasing both the max read length and the maximum edit distance; various changes to the default parameters; and, fixes to the quick start guide and user manual.

The bugfixes include better handling of large indels enabled by the -i switch; supporting Windows-style (CRLF) FASTA files for index build; fixes in bam output; fixing some pathological cases that caused very slow read processing (during output, of all things); fix problems in non-affine gap single end alignments; fix an _int64 overflow in the Windows fine grained timer (which only affected performance measurements, but was still annoying); and, fix a bug for reads that aligned off the beginning of a contig.

2.0.1

This includes two new features and a number of bugfixes.

The features are support for reading compressed FASTA files during index build, and no longer requiring read names to have /1 and /2 for paired interleaved FASTQ inputs.

The bug fixes are:
A problem with sorting SAM format output files
A problem with CIGAR string generation in SAM format output files when using the -= option
Fixed some misleading error messages
Added description of previously undocumented command line switches in the manual

v2.0.0

This is the 2.0 release. It includes numerous features and bug fixes compared to 1.0, including:

• It supports soft clipping of reads based on both the alignment and base-call quality scores, using Hamming distance to determine when to do this.
• It supports liftover of alignments from ALT contigs to the corresponding regions of primary contigs
• It has the ability to quickly find large indels in the middle of reads by leveraging the pattern of index hits to detect where this might be happening and looking more carefully at those possible alignments
• It will by default report reads with two equally good possible alignments at MAPQ 0 rather than 3, because variant callers expect this regardless of the definition of MAPQ in the spec
• It has a mode that allows it to work well with the DRAGEN variant caller (this is just enabling a set of options that work well with DRAGEN but less well with Haplotype Caller)
• Some different default parameter settings
• 10% faster performance on some high-quality read sets that we measured.
• Many fixes for correctly calling short indels, sometimes by employing base call quality scores
• removing many memory leaks
• making the output BAM file have its contigs in the same order as those in the FASTA used to generate the index (though not required by the spec it is needed by the DRAGEN variant caller)
• fixing some problems in CIGAR string generation
• eliminating some problems writing very large BAM files on Linux
• not binding threads to processors when affinity is already set at process start time (Linux only)
• improvements to error messages

v1.0.0

This is the 1.0 release of SNAP. It includes support for affine gap indel scoring, ALT contig awareness and many bug fixes and performance improvements compared to the previous version.

1.0beta.18

Includes updates from the past several months of work in the dev branch, including lots of bug & perf fixes, better support for multiple alignment output (for example, limiting the number of mappings of a read per contig), an option to do index build with less memory, a daemon mode that allows SNAP to run and take commands from a pipe, and changes that make SNAP less likely to call indels when it can get the same edit distance with SNVs.