Provided by: gmap_2017-11-15-1_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 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.

              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 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

       -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)

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

              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  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

              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