.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.49.3.
.TH GMAP "1" "February 2024" "gmap 2024-02-22+ds-1" "User Commands"
.SH NAME
gmap \- Genomic Mapping and Alignment Program
.SH SYNOPSIS
.B gmap
[\fI\,OPTIONS\/\fR...] \fI\,<FASTA files\/\fR...\fI\,>, or\/\fR
cat <FASTA files...> | gmap [OPTIONS...]
.SH OPTIONS
.SS Input options (must include \fB\-d\fR or \fB\-g\fR)
.TP
\fB\-D\fR, \fB\-\-dir\fR=\fI\,directory\/\fR
Genome directory.  Default (as specified by \fB\-\-with\-gmapdb\fR to the configure program) is
\fI\,/var/cache/gmap\/\fP
.TP
\fB\-d\fR, \fB\-\-db\fR=\fI\,STRING\/\fR
Genome database.  If argument is '?' (with
the quotes), this command lists available databases.
.TP
\fB\-k\fR, \fB\-\-kmer\fR=\fI\,INT\/\fR
kmer size to use in genome database (allowed values: 16 or less).
If not specified, the program will find the highest available
kmer size in the genome database
.TP
\fB\-\-sampling\fR=\fI\,INT\/\fR
Sampling to use in genome database.  If not specified, the program
will find the smallest available sampling value in the genome database
within selected k\-mer size
.TP
\fB\-g\fR, \fB\-\-gseg\fR=\fI\,filename\/\fR
User\-supplied genomic segments.  If multiple segments are provided, then
every query sequence is aligned against every genomic segment
.TP
\fB\-1\fR, \fB\-\-selfalign\fR
Align one sequence against itself in FASTA format via stdin
(Useful for getting protein translation of a nucleotide sequence)
.TP
\fB\-2\fR, \fB\-\-pairalign\fR
Align two sequences in FASTA format via stdin, first one being
genomic and second one being cDNA
.TP
\fB\-\-cmdline\fR=\fI\,STRING\/\fR,STRING
Align these two sequences provided on the command line,
first one being genomic and second one being cDNA
.TP
\fB\-q\fR, \fB\-\-part\fR=\fI\,INT\/\fR/INT
Process only the i\-th out of every n sequences
e.g., 0/100 or 99/100 (useful for distributing jobs
to a computer farm).
.TP
\fB\-\-input\-buffer\-size\fR=\fI\,INT\/\fR
Size of input buffer (program reads this many sequences
at a time for efficiency) (default 1000)
.PP
Computation options
.TP
\fB\-B\fR, \fB\-\-batch\fR=\fI\,INT\/\fR
Batch mode (default = 2)

         Mode     Positions       Genome
           0      mmap            mmap
           1      mmap & preload  mmap
 (default) 2      mmap & preload  mmap & preload
           3      allocate        mmap & preload
           4      allocate        allocate
           5      allocate        allocate     (same as 4)
.TP
Note: For a single sequence, all data structures use mmap
If mmap not available and allocate not chosen, then will use fileio (very slow)
.TP
\fB\-\-use\-shared\-memory\fR=\fI\,INT\/\fR
If 1, then allocated memory is shared among all processes on this node
If 0 (default), then each process has private allocated memory
.TP
\fB\-\-nosplicing\fR
Turns off splicing (useful for aligning genomic sequences
onto a genome)
.TP
\fB\-\-max\-deletionlength\fR=\fI\,INT\/\fR
Max length for a deletion (default 30).  Above this size,
a genomic gap will be considered an intron rather than a deletion.
If the genomic gap is less than \fB\-\-max\-deletionlength\fR and greater
than \fB\-\-min\-intronlength\fR, a known splice site or splice site probabilities
of 0.80 on both sides will be reported as an intron.
.TP
\fB\-\-min\-intronlength\fR=\fI\,INT\/\fR
Min length for one internal intron (default 9).  Below this size,
a genomic gap will be considered a deletion rather than an intron.
If the genomic gap is less than \fB\-\-max\-deletionlength\fR and greater
than \fB\-\-min\-intronlength\fR, a known splice site or splice site probabilities
of 0.80 on both sides will be reported as an intron.
.TP
\fB\-\-max\-intronlength\-middle\fR=\fI\,INT\/\fR
Max length for one internal intron (default 500000).  Note: for backward
compatibility, the \fB\-K\fR or \fB\-\-intronlength\fR flag will set both
\fB\-\-max\-intronlength\-middle\fR and \fB\-\-max\-intronlength\-ends\fR.
Also see \fB\-\-split\-large\-introns\fR below.
.TP
\fB\-\-max\-intronlength\-ends\fR=\fI\,INT\/\fR
Max length for first or last intron (default 10000).  Note: for backward
compatibility, the \fB\-K\fR or \fB\-\-intronlength\fR flag will set both
\fB\-\-max\-intronlength\-middle\fR and \fB\-\-max\-intronlength\-ends\fR.
.TP
\fB\-\-split\-large\-introns\fR
Sometimes GMAP will exceed the value for \fB\-\-max\-intronlength\-middle\fR,
if it finds a good single alignment.  However, you can force GMAP
to split such alignments by using this flag
.TP
\fB\-\-end\-trimming\-score\fR=\fI\,INT\/\fR
Trim ends if the alignment score is below this value
where a match scores +1 and a mismatch scores \fB\-3\fR
The value should be 0 (default) or negative.  A negative
allows some mismatches at the ends of the alignment
.TP
\fB\-\-trim\-end\-exons\fR=\fI\,INT\/\fR
Trim end exons with fewer than given number of matches
(in nt, default 12)
.TP
\fB\-w\fR, \fB\-\-localsplicedist\fR=\fI\,INT\/\fR
Max length for known splice sites at ends of sequence
(default 2000000)
.TP
\fB\-L\fR, \fB\-\-totallength\fR=\fI\,INT\/\fR
Max total intron length (default 2400000)
.TP
\fB\-x\fR, \fB\-\-chimera\-margin\fR=\fI\,INT\/\fR
Amount of unaligned sequence that triggers
search for the remaining sequence (default 30).
Enables alignment of chimeric reads, and may help
with some non\-chimeric reads.  To turn off, set to
zero.
.TP
\fB\-\-no\-chimeras\fR
Turns off finding of chimeras.  Same effect as \fB\-\-chimera\-margin\fR=\fI\,0\/\fR
.TP
\fB\-t\fR, \fB\-\-nthreads\fR=\fI\,INT\/\fR
Number of worker threads
.TP
\fB\-c\fR, \fB\-\-chrsubset\fR=\fI\,string\/\fR
Limit search to given chromosome
.TP
\fB\-\-strand\fR=\fI\,STRING\/\fR
Genome strand to try aligning to (plus, minus, or both default)
.TP
\fB\-z\fR, \fB\-\-direction\fR=\fI\,STRING\/\fR
cDNA direction (sense_force, antisense_force,
sense_filter, antisense_filter,or auto (default))
.TP
\fB\-\-canonical\-mode\fR=\fI\,INT\/\fR
Reward for canonical and semi\-canonical introns
0=low reward, 1=high reward (default), 2=low reward for
high\-identity sequences and high reward otherwise
.TP
\fB\-\-cross\-species\fR
Use a more sensitive search for canonical splicing, which helps especially
for cross\-species alignments and other difficult cases
.TP
\fB\-\-allow\-close\-indels\fR=\fI\,INT\/\fR
Allow an insertion and deletion close to each other
(0=no, 1=yes (default), 2=only for high\-quality alignments)
.TP
\fB\-\-microexon\-spliceprob\fR=\fI\,FLOAT\/\fR
Allow microexons only if one of the splice site probabilities is
greater than this value (default 0.95)
.TP
\fB\-\-indel\-open\fR
In dynamic programming, opening penalty for indel
.TP
\fB\-\-indel\-extend\fR
In dynamic programming, extension penalty for indel
Values for \fB\-\-indel\-open\fR and \fB\-\-indel\-extend\fR should be in [\-127,\-1].
If value is < \fB\-127\fR, then will use \fB\-127\fR instead.
If \fB\-\-indel\-open\fR and \fB\-\-indel\-extend\fR are not specified, values are chosen
adaptively, based on the differences between the query and reference
.TP
\fB\-\-cmetdir\fR=\fI\,STRING\/\fR
Directory for methylcytosine index files (created using cmetindex)
(default is location of genome index files specified using \fB\-D\fR, \fB\-V\fR, and \fB\-d\fR)
.TP
\fB\-\-atoidir\fR=\fI\,STRING\/\fR
Directory for A\-to\-I RNA editing index files (created using atoiindex)
(default is location of genome index files specified using \fB\-D\fR, \fB\-V\fR, and \fB\-d\fR)
.TP
\fB\-\-mode\fR=\fI\,STRING\/\fR
Alignment mode: standard (default), cmet\-stranded, cmet\-nonstranded,
atoi\-stranded, atoi\-nonstranded, ttoc\-stranded, or ttoc\-nonstranded.
Non\-standard modes requires you to have previously run the cmetindex
or atoiindex programs (which also cover the ttoc modes) on the genome
.TP
\fB\-p\fR, \fB\-\-prunelevel\fR
Pruning level: 0=no pruning (default), 1=poor seqs,
2=repetitive seqs, 3=poor and repetitive
.PP
Output types
.TP
\fB\-S\fR, \fB\-\-summary\fR
Show summary of alignments only
.TP
\fB\-A\fR, \fB\-\-align\fR
Show alignments
.TP
\fB\-3\fR, \fB\-\-continuous\fR
Show alignment in three continuous lines
.TP
\fB\-4\fR, \fB\-\-continuous\-by\-exon\fR
Show alignment in three lines per exon
.TP
\fB\-E\fR, \fB\-\-exons\fR=\fI\,STRING\/\fR
Print exons ("cdna" or "genomic")
Will also print introns with "cdna+introns" or
"genomic+introns"
.TP
\fB\-P\fR, \fB\-\-protein_dna\fR
Print protein sequence (cDNA)
.TP
\fB\-Q\fR, \fB\-\-protein_gen\fR
Print protein sequence (genomic)
.TP
\fB\-f\fR, \fB\-\-format\fR=\fI\,INT\/\fR
Other format for output (also note the \fB\-A\fR and \fB\-S\fR options
and other options listed under Output types):
 mask_introns,
 mask_utr_introns,
 psl (or 1) = PSL (BLAT) format,
 gff3_gene (or 2) = GFF3 gene format,
 gff3_match_cdna (or 3) = GFF3 cDNA_match format,
 gff3_match_est (or 4) = GFF3 EST_match format,
 splicesites (or 6) = splicesites output (for GSNAP splicing file),
 introns = introns output (for GSNAP splicing file),
 map_exons (or 7) = IIT FASTA exon map format,
 map_ranges (or 8) = IIT FASTA range map format,
 coords (or 9) = coords in table format,
 sampe = SAM format (setting paired_read bit in flag),
 samse = SAM format (without setting paired_read bit),
 bedpe = indels and gaps in BEDPE format
.PP
Output options
.TP
\fB\-n\fR, \fB\-\-npaths\fR=\fI\,INT\/\fR
Maximum number of paths to show (default 5).  If set to 1, GMAP
will not report chimeric alignments, since those imply
two paths.  If you want a single alignment plus chimeric
alignments, then set this to be 0.
.TP
\fB\-\-suboptimal\-score\fR=\fI\,FLOAT\/\fR
Report only paths whose score is within this value of the
best path.
.TP
If specified between 0.0 and 1.0, then treated as a fraction
of the score of the best alignment (matches minus penalties for
mismatches and indels).  Otherwise, treated as an integer
number to be subtracted from the score of the best alignment.
Default value is 0.50.
.TP
\fB\-O\fR, \fB\-\-ordered\fR
Print output in same order as input (relevant
only if there is more than one worker thread)
.TP
\fB\-5\fR, \fB\-\-md5\fR
Print MD5 checksum for each query sequence
.TP
\fB\-o\fR, \fB\-\-chimera\-overlap\fR
Overlap to show, if any, at chimera breakpoint
.TP
\fB\-\-failsonly\fR
Print only failed alignments, those with no results
.TP
\fB\-\-nofails\fR
Exclude printing of failed alignments
.TP
\fB\-V\fR, \fB\-\-snpsdir\fR=\fI\,STRING\/\fR
Directory for SNPs index files (created using snpindex) (default is
location of genome index files specified using \fB\-D\fR and \fB\-d\fR)
.TP
\fB\-v\fR, \fB\-\-use\-snps\fR=\fI\,STRING\/\fR
Use database containing known SNPs (in <STRING>.iit, built
previously using snpindex) for tolerance to SNPs
.TP
\fB\-\-split\-output\fR=\fI\,STRING\/\fR
Basename for multiple\-file output, separately for nomapping,
 uniq, mult, (and chimera, if \fB\-\-chimera\-margin\fR is selected)
.TP
\fB\-\-failed\-input\fR=\fI\,STRING\/\fR
Print completely failed alignments as input FASTA or FASTQ format
to the given file.  If the \fB\-\-split\-output\fR flag is also given, this file
is generated in addition to the output in the .nomapping file.
.TP
\fB\-\-append\-output\fR
When \fB\-\-split\-output\fR or \fB\-\-failedinput\fR is given, this flag will append output
to the existing files.  Otherwise, the default is to create new files.
.TP
\fB\-\-output\-buffer\-size\fR=\fI\,INT\/\fR
Buffer size, in queries, for output thread (default 1000).  When the number
of results to be printed exceeds this size, worker threads wait
until the backlog is cleared
.TP
\fB\-\-translation\-code\fR=\fI\,INT\/\fR
Genetic code used for translating codons to amino acids and computing CDS
Integer value (default=1) corresponds to an available code at
http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi
.TP
\fB\-\-alt\-start\-codons\fR
Also, use the alternate initiation codons shown in the above Web site
By default, without this option, only ATG is considered an initiation codon
.TP
\fB\-F\fR, \fB\-\-fulllength\fR
Assume full\-length protein, starting with Met
.TP
\fB\-a\fR, \fB\-\-cdsstart\fR=\fI\,INT\/\fR
Translate codons from given nucleotide (1\-based)
.TP
\fB\-T\fR, \fB\-\-truncate\fR
Truncate alignment around full\-length protein, Met to Stop
Implies \fB\-F\fR flag.
.TP
\fB\-Y\fR, \fB\-\-tolerant\fR
Translates cDNA with corrections for frameshifts
.PP
Options for GFF3 output
.TP
\fB\-\-gff3\-add\-separators\fR=\fI\,INT\/\fR
Whether to add a ### separator after each query sequence
Values: 0 (no), 1 (yes, default)
.TP
\fB\-\-gff3\-swap\-phase\fR=\fI\,INT\/\fR
Whether to swap phase (0 => 0, 1 => 2, 2 => 1) in gff3_gene format
Needed by some analysis programs, but deviates from GFF3 specification
Values: 0 (no, default), 1 (yes)
.TP
\fB\-\-gff3\-fasta\-annotation\fR=\fI\,INT\/\fR
Whether to include annotation from the FASTA header into the GFF3 output
Values: 0 (default): Do not include
.TP
1: Wrap all annotation as Annot="<header>"
2: Include key=value pairs, replacing brackets with quotation marks
.IP
and replacing spaces between key=value pairs with semicolons
.TP
\fB\-\-gff3\-cds\fR=\fI\,STRING\/\fR
Whether to use cDNA or genomic translation for the CDS coordinates
Values: cdna (default), genomic
.PP
Options for SAM output
.TP
\fB\-\-no\-sam\-headers\fR
Do not print headers beginning with '@'
.TP
\fB\-\-sam\-use\-0M\fR
Insert 0M in CIGAR between adjacent insertions and deletions
Required by Picard, but can cause errors in other tools
.TP
\fB\-\-sam\-extended\-cigar\fR
Use extended CIGAR format (using X and = symbols instead of M,
 to indicate matches and mismatches, respectively
.TP
\fB\-\-sam\-flipped\fR
Flip the query and genomic positions in the SAM output.
Potentially useful with the \fB\-g\fR flag when short reads are picked as query
sequences and longer reads as picked as genomic sequences
.TP
\fB\-\-force\-xs\-dir\fR
For RNA\-Seq alignments, disallows XS:A:? when the sense direction
is unclear, and replaces this value arbitrarily with XS:A:+.
May be useful for some programs, such as Cufflinks, that cannot
handle XS:A:?.  However, if you use this flag, the reported value
of XS:A:+ in these cases will not be meaningful.
.TP
\fB\-\-md\-lowercase\-snp\fR
In MD string, when known SNPs are given by the \fB\-v\fR flag,
 prints difference nucleotides as lower\-case when they,
 differ from reference but match a known alternate allele
.TP
\fB\-\-action\-if\-cigar\-error\fR
Action to take if there is a disagreement between CIGAR length and sequence length
Allowed values: ignore, warning (default), noprint, abort
Note that the noprint option does not print the CIGAR string at all if there
is an error, so it may break a SAM parser
.TP
\fB\-\-read\-group\-id\fR=\fI\,STRING\/\fR
Value to put into read\-group id (RG\-ID) field
.TP
\fB\-\-read\-group\-name\fR=\fI\,STRING\/\fR
Value to put into read\-group name (RG\-SM) field
.TP
\fB\-\-read\-group\-library\fR=\fI\,STRING\/\fR
Value to put into read\-group library (RG\-LB) field
.TP
\fB\-\-read\-group\-platform\fR=\fI\,STRING\/\fR
Value to put into read\-group library (RG\-PL) field
.PP
Options for quality scores
.TP
\fB\-\-quality\-protocol\fR=\fI\,STRING\/\fR
Protocol for input quality scores.  Allowed values:
illumina (ASCII 64\-126) (equivalent to \fB\-J\fR 64 \fB\-j\fR \fB\-31\fR)
sanger   (ASCII 33\-126) (equivalent to \fB\-J\fR 33 \fB\-j\fR 0)
.TP
Default is sanger (no quality print shift)
SAM output files should have quality scores in sanger protocol
.IP
Or you can specify the print shift with this flag:
.TP
\fB\-j\fR, \fB\-\-quality\-print\-shift\fR=\fI\,INT\/\fR
Shift FASTQ quality scores by this amount in output
(default is 0 for sanger protocol; to change Illumina input
to Sanger output, select \fB\-31\fR)
.PP
External map file options
.TP
\fB\-M\fR, \fB\-\-mapdir\fR=\fI\,directory\/\fR
Map directory
.TP
\fB\-m\fR, \fB\-\-map\fR=\fI\,iitfile\/\fR
Map file.  If argument is '?' (with the quotes),
 this lists available map files.
.TP
\fB\-e\fR, \fB\-\-mapexons\fR
Map each exon separately
.TP
\fB\-b\fR, \fB\-\-mapboth\fR
Report hits from both strands of genome
.TP
\fB\-u\fR, \fB\-\-flanking\fR=\fI\,INT\/\fR
Show flanking hits (default 0)
.TP
\fB\-\-print\-comment\fR
Show comment line for each hit
.PP
Alignment output options
.TP
\fB\-\-nolengths\fR
No intron lengths in alignment
.TP
\fB\-\-nomargin\fR
No left margin in GMAP standard output (with the \fB\-A\fR flag)
.TP
\fB\-I\fR, \fB\-\-invertmode\fR=\fI\,INT\/\fR
Mode for alignments to genomic (\-) strand:
0=Don't invert the cDNA (default)
1=Invert cDNA and print genomic (\-) strand
2=Invert cDNA and print genomic (+) strand
.TP
\fB\-i\fR, \fB\-\-introngap\fR=\fI\,INT\/\fR
Nucleotides to show on each end of intron (default 3)
.TP
\fB\-l\fR, \fB\-\-wraplength\fR=\fI\,INT\/\fR
Wrap length for alignment (default 50)
.PP
Filtering output options
.TP
\fB\-\-min\-trimmed\-coverage\fR=\fI\,FLOAT\/\fR
Do not print alignments with trimmed coverage less
this value (default=0.0, which means no filtering)
Note that chimeric alignments will be output regardless
of this filter
.TP
\fB\-\-min\-identity\fR=\fI\,FLOAT\/\fR
Do not print alignments with identity less
this value (default=0.0, which means no filtering)
Note that chimeric alignments will be output regardless
of this filter
Help options
.TP
\fB\-\-check\fR
Check compiler assumptions
.TP
\fB\-\-version\fR
Show version
.TP
\fB\-\-help\fR
Show this help message

.TP
Other tools of GMAP suite are located in /usr/lib/gmap