NAME

       YAHA - find split-read mappings on single-end queries

DESCRIPTION

       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.

       --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.

SEE ALSO

       https://github.com/GregoryFaust/yaha

YAHA version 0.1.83                                 July 2018                                            YAHA(1)