.TH YAHA "1" "July 2018" "YAHA version 0.1.83" "User Commands"
.SH NAME
YAHA \- find split-read mappings on single-end queries
.SH DESCRIPTION
.PP
Usage (Default parameter values shown in parenthesis):
.PP
To create an index:
yaha \fB\-g\fR 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).
.PP
To align queries:
yaha \fB\-x\fR yahaIndexFile [\-q queryFile|(stdin)] [\-o8|(\fB\-osh\fR)|\-oss outputFile|(stdout)][AdditionalOptions]
The query file can be either a FASTA file or a FASTQ file.
\fB\-o8\fR     produces alignment output in modified Blast8 format.
\fB\-osh\fR    produces alignment output in SAM format with hard clipping.
\fB\-oss\fR    produces alignment output in SAM format with soft clipping.
[\-t numThreads (1)]
.SS "Additional General Alignment Options:"
.IP
[\-BW BandWidth (5)] [\-G maxGap (50)] [\-H maxHits (650)] [\-M minMatch (25)]
[\-MD MaxDesert (50)] [\-P minPercent\-identity (0.9)] [\-X Xdropoff (25)]
.PP
[\-AGS (Y)|N] controls use of Affine Gap Scoring.
If \fB\-AGS\fR is off, a simple edit distance calculation is done.  If on, the following are used:
.IP
[\-GEC GapExtensionCost (2)] [\-GOC GapOpenCost (5)] [\-MS MatchScore (1)] [\-RC ReplacementCost (3)]
.PP
[\-OQC (Y)|N] controls use of the Optimal Query Coverage Algorithm.
If \fB\-OQC\fR 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:
.IP
[\-BP BreakpointPenalty (5)] [\-MGDP MaxGenomicDistancePenalty (5)] [\-MNO MinNonOverlap (minMatch)]
.PP
The cost of inserting a breakpoint in the Optimal Coverage Set is BP*MIN(MGDP, Log10(genomic distance between reference loci)).
.PP
[\-FBS Y|(N)] controls inclusion of "secondary" alignments similar to a primary alignment found using OQC.
If \fB\-FBS\fR is on, the following are used.  A "secondary" alignemnt must satisfy BOTH criteria.
.IP
[\-PRL PercentReciprocalLength (0.9)] [\-PSS PercentSimilarScore (0.9)]
.PP
Additional experimental parameters:
To compress a FASTA file to a nib2 file without creating an index:
yaha \fB\-g\fR fastaGenomeFile \fB\-c\fR
To uncompress a nib2 file back into a FASTA file:
yaha \fB\-g\fR nib2GenomeFile \fB\-u\fR
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 \fB\-xh\fR.
.PP
\fB\-\-version\fR is not a valid option.
.PP
Usage (Default parameter values shown in parenthesis):
.PP
To create an index:
yaha \fB\-g\fR 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).
.PP
To align queries:
yaha \fB\-x\fR yahaIndexFile [\-q queryFile|(stdin)] [\-o8|(\fB\-osh\fR)|\-oss outputFile|(stdout)][AdditionalOptions]
The query file can be either a FASTA file or a FASTQ file.
\fB\-o8\fR     produces alignment output in modified Blast8 format.
\fB\-osh\fR    produces alignment output in SAM format with hard clipping.
\fB\-oss\fR    produces alignment output in SAM format with soft clipping.
[\-t numThreads (1)]
.SS "Additional General Alignment Options:"
.IP
[\-BW BandWidth (5)] [\-G maxGap (50)] [\-H maxHits (650)] [\-M minMatch (25)]
[\-MD MaxDesert (50)] [\-P minPercent\-identity (0.9)] [\-X Xdropoff (25)]
.PP
[\-AGS (Y)|N] controls use of Affine Gap Scoring.
If \fB\-AGS\fR is off, a simple edit distance calculation is done.  If on, the following are used:
.IP
[\-GEC GapExtensionCost (2)] [\-GOC GapOpenCost (5)] [\-MS MatchScore (1)] [\-RC ReplacementCost (3)]
.PP
[\-OQC (Y)|N] controls use of the Optimal Query Coverage Algorithm.
If \fB\-OQC\fR 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:
.IP
[\-BP BreakpointPenalty (5)] [\-MGDP MaxGenomicDistancePenalty (5)] [\-MNO MinNonOverlap (minMatch)]
.PP
The cost of inserting a breakpoint in the Optimal Coverage Set is BP*MIN(MGDP, Log10(genomic distance between reference loci)).
.PP
[\-FBS Y|(N)] controls inclusion of "secondary" alignments similar to a primary alignment found using OQC.
If \fB\-FBS\fR is on, the following are used.  A "secondary" alignemnt must satisfy BOTH criteria.
.IP
[\-PRL PercentReciprocalLength (0.9)] [\-PSS PercentSimilarScore (0.9)]
.PP
Additional experimental parameters:
To compress a FASTA file to a nib2 file without creating an index:
yaha \fB\-g\fR fastaGenomeFile \fB\-c\fR
To uncompress a nib2 file back into a FASTA file:
yaha \fB\-g\fR nib2GenomeFile \fB\-u\fR
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 \fB\-xh\fR.
.SH "SEE ALSO"
https://github.com/GregoryFaust/yaha