Provided by: gmap_2015-12-31.v7-1_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, --genomefull
              Use full genome (all ASCII chars  allowed;  built  explicitly  during  setup),  not
              compressed version

       -g, --gseg=filename
              User-supplied 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     Offsets       Positions       Genome
                         0      see note      mmap            mmap
                         1      see note      mmap & preload  mmap
               (default) 2      see note      mmap & preload  mmap & preload
                         3      see note      allocate        mmap & preload
                         4      see note      allocate        allocate
                         5      expand        allocate        allocate

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

       Note about --batch and offsets: Expansion of offsets can be controlled
              independently by the --expand-offsets flag.  The --batch=5 option is equivalent  to
              --batch=4 plus --expand-offsets=1

              Whether  to  expand  the genomic offsets index Values: 0 (no, default), or 1 (yes).
              Expansion gives faster alignment, but requires more memory

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

              Min length for one internal intron (default 9).  Below this  size,  a  genomic  gap
              will be considered a deletion rather than an intron.

       -K, --intronlength=INT
              Max length for one internal intron (default 200000)

       -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

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

       -H, --trimendexons=INT
              Trim end exons with fewer than given number of matches (in nt, default 9)

              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)

              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

       -Z, --compress
              Print output in compressed format

       -E, --exons=STRING
              Print exons ("cdna" or "genomic")

       -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)

       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.  By default,
              if this option is not provided,
               the program prints all paths found.

       -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, the worker threads are halted until the
              backlog is cleared

       -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,

       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

              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), abort

              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

       -N, --nolengths
              No intron lengths in alignment

       -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

              Show version

       --help Show this help message

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