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