Provided by: gmap_2021-12-17+ds-1_amd64 bug


       gmap - Genomic Mapping and Alignment Program


       gmap [OPTIONS...] <FASTA files...>, or cat <FASTA files...> | gmap [OPTIONS...]


   Input options (must include -d or -g)
       -D, --dir=directory
              Genome directory.  Default (as specified by --with-gmapdb to the configure program)
              is /var/cache/gmap

       -d, --db=STRING
              Genome database.  If  argument  is  '?'  (with  the  quotes),  this  command  lists
              available databases.

       -k, --kmer=INT
              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

              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

       -g, --gseg=filename
              User-supplied genomic segments.  If multiple  segments  are  provided,  then  every
              query sequence is aligned against every genomic segment

       -1, --selfalign
              Align  one  sequence  against  itself in FASTA format via stdin (Useful for getting
              protein translation of a nucleotide sequence)

       -2, --pairalign
              Align two sequences in FASTA format via stdin, first one being genomic  and  second
              one being cDNA

              Align these two sequences provided on the command line, first one being genomic and
              second one being cDNA

       -q, --part=INT/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).

              Size  of  input buffer (program reads this many sequences at a time for efficiency)
              (default 1000)

       Computation options

       -B, --batch=INT
              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)

       Note: For a single sequence, all data structures use mmap
              If mmap not available and allocate not chosen, then will use fileio (very slow)

              If 1, then allocated memory is shared  among  all  processes  on  this  node  If  0
              (default), then each process has private allocated memory

              Turns off splicing (useful for aligning genomic sequences onto a genome)

              Max  length  for  a deletion (default 100).  Above this size, a genomic gap will be
              considered an intron rather than a deletion.  If  the  genomic  gap  is  less  than
              --max-deletionlength  and  greater  than --min-intronlength, a known splice site or
              splice site probabilities of 0.80 on both sides will be reported as an intron.

              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 --max-deletionlength and greater than --min-intronlength, a known splice  site
              or splice site probabilities of 0.80 on both sides will be reported as an intron.

              Max   length  for  one  internal  intron  (default  500000).   Note:  for  backward
              compatibility,    the    -K    or    --intronlength    flag    will    set     both
              --max-intronlength-middle      and      --max-intronlength-ends.       Also     see
              --split-large-introns below.

              Max  length  for  first  or  last  intron  (default  10000).   Note:  for  backward
              compatibility,     the    -K    or    --intronlength    flag    will    set    both
              --max-intronlength-middle and --max-intronlength-ends.

              Sometimes GMAP will exceed the value for --max-intronlength-middle, if it  finds  a
              good  single  alignment.   However,  you can force GMAP to split such alignments by
              using this flag

              Trim ends if the alignment score is below this value where a match scores +1 and  a
              mismatch  scores -3 The value should be 0 (default) or negative.  A negative allows
              some mismatches at the ends of the alignment

              Trim end exons with fewer than given number of matches (in nt, default 12)

       -w, --localsplicedist=INT
              Max length for known splice sites at ends of sequence (default 2000000)

       -L, --totallength=INT
              Max total intron length (default 2400000)

       -x, --chimera-margin=INT
              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.

              Turns off finding of chimeras.  Same effect as --chimera-margin=0

       -t, --nthreads=INT
              Number of worker threads

       -c, --chrsubset=string
              Limit search to given chromosome

              Genome strand to try aligning to (plus, minus, or both default)

       -z, --direction=STRING
              cDNA direction  (sense_force,  antisense_force,  sense_filter,  antisense_filter,or
              auto (default))

              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

              Use a more sensitive search for canonical  splicing,  which  helps  especially  for
              cross-species alignments and other difficult cases

              Allow  an insertion and deletion close to each other (0=no, 1=yes (default), 2=only
              for high-quality alignments)

              Allow microexons only if one of the splice site probabilities is greater than  this
              value (default 0.95)

              In dynamic programming, opening penalty for indel

              In  dynamic  programming,  extension  penalty for indel Values for --indel-open and
              --indel-extend should be in [-127,-1].  If value is <  -127,  then  will  use  -127
              instead.   If  --indel-open and --indel-extend are not specified, values are chosen
              adaptively, based on the differences between the query and reference

              Directory for methylcytosine index files  (created  using  cmetindex)  (default  is
              location of genome index files specified using -D, -V, and -d)

              Directory  for A-to-I RNA editing index files (created using atoiindex) (default is
              location of genome index files specified using -D, -V, and -d)

              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

       -p, --prunelevel
              Pruning  level:  0=no pruning (default), 1=poor seqs, 2=repetitive seqs, 3=poor and

       Output types

       -S, --summary
              Show summary of alignments only

       -A, --align
              Show alignments

       -3, --continuous
              Show alignment in three continuous lines

       -4, --continuous-by-exon
              Show alignment in three lines per exon

       -E, --exons=STRING
              Print exons ("cdna" or "genomic") Will also print introns  with  "cdna+introns"  or

       -P, --protein_dna
              Print protein sequence (cDNA)

       -Q, --protein_gen
              Print protein sequence (genomic)

       -f, --format=INT
              Other  format  for output (also note the -A and -S options and other options listed
              under Output types):
               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

       Output options

       -n, --npaths=INT
              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.

              Report only paths whose score is within this value of the best path.

       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.

       -O, --ordered
              Print output in same order as input (relevant only if there is more than one worker

       -5, --md5
              Print MD5 checksum for each query sequence

       -o, --chimera-overlap
              Overlap to show, if any, at chimera breakpoint

              Print only failed alignments, those with no results

              Exclude printing of failed alignments

       -V, --snpsdir=STRING
              Directory  for  SNPs  index  files (created using snpindex) (default is location of
              genome index files specified using -D and -d)

       -v, --use-snps=STRING
              Use database  containing  known  SNPs  (in  <STRING>.iit,  built  previously  using
              snpindex) for tolerance to SNPs

              Basename for multiple-file output, separately for nomapping,
               uniq, mult, (and chimera, if --chimera-margin is selected)

              Print  completely  failed  alignments  as  input FASTA or FASTQ format to the given
              file.  If the --split-output flag is also given, this file is generated in addition
              to the output in the .nomapping file.

              When  --split-output or --failedinput is given, this flag will append output to the
              existing files.  Otherwise, the default is to create new files.

              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

              Genetic code used for translating codons to amino acids and computing  CDS  Integer
              value      (default=1)      corresponds     to     an     available     code     at

              Also, use the alternate initiation codons shown in the above Web site  By  default,
              without this option, only ATG is considered an initiation codon

       -F, --fulllength
              Assume full-length protein, starting with Met

       -a, --cdsstart=INT
              Translate codons from given nucleotide (1-based)

       -T, --truncate
              Truncate alignment around full-length protein, Met to Stop Implies -F flag.

       -Y, --tolerant
              Translates cDNA with corrections for frameshifts

       Options for GFF3 output

              Whether  to  add  a ### separator after each query sequence Values: 0 (no), 1 (yes,

              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

              Whether to include annotation from the FASTA header into the GFF3 output Values:  0
              (default): Do not include

       1: Wrap all annotation as Annot="<header>"
              2: Include key=value pairs, replacing brackets with quotation marks

              and replacing spaces between key=value pairs with semicolons

              Whether  to  use  cDNA  or genomic translation for the CDS coordinates Values: cdna
              (default), genomic

       Options for SAM output

              Do not print headers beginning with '@'

              Insert 0M in CIGAR between adjacent insertions and deletions  Required  by  Picard,
              but can cause errors in other tools

              Use extended CIGAR format (using X and = symbols instead of M,
               to indicate matches and mismatches, respectively

              Flip  the  query  and genomic positions in the SAM output.  Potentially useful with
              the -g flag when short reads are picked as query  sequences  and  longer  reads  as
              picked as genomic sequences

              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.

              In MD string, when known SNPs are given by the -v flag,
               prints difference nucleotides as lower-case when they,
               differ from reference but match a known alternate allele

              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

              Value to put into read-group id (RG-ID) field

              Value to put into read-group name (RG-SM) field

              Value to put into read-group library (RG-LB) field

              Value to put into read-group library (RG-PL) field

       Options for quality scores

              Protocol  for  input  quality  scores.   Allowed  values:  illumina  (ASCII 64-126)
              (equivalent to -J 64 -j -31) sanger   (ASCII 33-126) (equivalent to -J 33 -j 0)

       Default is sanger (no quality print shift)
              SAM output files should have quality scores in sanger protocol

              Or you can specify the print shift with this flag:

       -j, --quality-print-shift=INT
              Shift FASTQ quality scores by this amount  in  output  (default  is  0  for  sanger
              protocol; to change Illumina input to Sanger output, select -31)

       External map file options

       -M, --mapdir=directory
              Map directory

       -m, --map=iitfile
              Map file.  If argument is '?' (with the quotes),
               this lists available map files.

       -e, --mapexons
              Map each exon separately

       -b, --mapboth
              Report hits from both strands of genome

       -u, --flanking=INT
              Show flanking hits (default 0)

              Show comment line for each hit

       Alignment output options

              No intron lengths in alignment

              No left margin in GMAP standard output (with the -A flag)

       -I, --invertmode=INT
              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  (+)

       -i, --introngap=INT
              Nucleotides to show on each end of intron (default 3)

       -l, --wraplength=INT
              Wrap length for alignment (default 50)

       Filtering output options

              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

              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

              Check compiler assumptions

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       --help Show this help message

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