Additional General Alignment Options:

[-BW BandWidth (5)] [-G maxGap (50)] [-H maxHits (650)] [-M minMatch (25)] [-MD MaxDesert (50)] [-P minPercent-identity (0.9)] [-X Xdropoff (25)]

[-AGS (Y)|N] controls use of Affine Gap Scoring. If -AGS is off, a simple edit distance calculation is done. If on, the following are used:

[-GEC GapExtensionCost (2)] [-GOC GapOpenCost (5)] [-MS MatchScore (1)] [-RC ReplacementCost (3)]

[-OQC (Y)|N] controls use of the Optimal Query Coverage Algorithm. If -OQC if off, all alignments meeting above criteria are output. If on, a set of "primary" alignments are found that optimally cover the length of the query, using the following options:

[-BP BreakpointPenalty (5)] [-MGDP MaxGenomicDistancePenalty (5)] [-MNO MinNonOverlap (minMatch)]

The cost of inserting a breakpoint in the Optimal Coverage Set is BP*MIN(MGDP, Log10(genomic distance between reference loci)).

[-FBS Y|(N)] controls inclusion of "secondary" alignments similar to a primary alignment found using OQC. If -FBS is on, the following are used. A "secondary" alignemnt must satisfy BOTH criteria.

[-PRL PercentReciprocalLength (0.9)] [-PSS PercentSimilarScore (0.9)]

Additional experimental parameters: To compress a FASTA file to a nib2 file without creating an index: yaha -g fastaGenomeFile -c To uncompress a nib2 file back into a FASTA file: yaha -g nib2GenomeFile -u For finer control of alignments: [-I maxIntron (maxGap)] allows separate control of max deletion size vs. maxGap for insertion size. For a more detailed help message, type yaha -xh.

--version is not a valid option.

Usage (Default parameter values shown in parenthesis):

To create an index: yaha -g genomeFilename [-H maxHits (65525)] [-L wordLen (15)] [-S Skip-distance (1)] The genome file can be a FASTA file, or a nib2 file (created by a previous yaha index operation).

To align queries: yaha -x yahaIndexFile [-q queryFile|(stdin)] [-o8|(-osh)|-oss outputFile|(stdout)][AdditionalOptions] The query file can be either a FASTA file or a FASTQ file. -o8 produces alignment output in modified Blast8 format. -osh produces alignment output in SAM format with hard clipping. -oss produces alignment output in SAM format with soft clipping. [-t numThreads (1)]

Additional General Alignment Options:

[-BW BandWidth (5)] [-G maxGap (50)] [-H maxHits (650)] [-M minMatch (25)] [-MD MaxDesert (50)] [-P minPercent-identity (0.9)] [-X Xdropoff (25)]

[-AGS (Y)|N] controls use of Affine Gap Scoring. If -AGS is off, a simple edit distance calculation is done. If on, the following are used:

[-GEC GapExtensionCost (2)] [-GOC GapOpenCost (5)] [-MS MatchScore (1)] [-RC ReplacementCost (3)]

[-OQC (Y)|N] controls use of the Optimal Query Coverage Algorithm. If -OQC if off, all alignments meeting above criteria are output. If on, a set of "primary" alignments are found that optimally cover the length of the query, using the following options:

[-BP BreakpointPenalty (5)] [-MGDP MaxGenomicDistancePenalty (5)] [-MNO MinNonOverlap (minMatch)]

The cost of inserting a breakpoint in the Optimal Coverage Set is BP*MIN(MGDP, Log10(genomic distance between reference loci)).

[-FBS Y|(N)] controls inclusion of "secondary" alignments similar to a primary alignment found using OQC. If -FBS is on, the following are used. A "secondary" alignemnt must satisfy BOTH criteria.

[-PRL PercentReciprocalLength (0.9)] [-PSS PercentSimilarScore (0.9)]

Additional experimental parameters: To compress a FASTA file to a nib2 file without creating an index: yaha -g fastaGenomeFile -c To uncompress a nib2 file back into a FASTA file: yaha -g nib2GenomeFile -u For finer control of alignments: [-I maxIntron (maxGap)] allows separate control of max deletion size vs. maxGap for insertion size. For a more detailed help message, type yaha -xh.