---
name: "yaha"
section: "1"
platform: "linux"
package: "yaha"
version: "0.1.83-3"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/yaha"
---

# yaha(1)

find split-read mappings on single-end queries

## 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