Provided by: snap-aligner_1.0~beta.18+dfsg-3_amd64 bug


       snap-aligner_paired - scalable nucleotide alignment program


       Welcome to SNAP version 1.0beta.18.

       Too few parameters Usage: snap-aligner paired <index-dir> <inputFile(s)> [<options>] where
       <input file(s)> is a list of files to process.


       -o     filename  output alignments to filename in SAM or BAM format, depending on the file
              extension or explicit type specifier (see below).  Use a dash with an explicit type
              specifier to write to stdout, so for example -o -sam - would write  SAM  output  to

       -d     maximum edit distance allowed per read or pair (default: 15)

       -n     number of seeds to use per read

       -sc    Seed  coverage  (i.e.,  readSize/seedSize).   Floating  point.   Exclusive with -n.
              (default uses -n)

       -h     maximum hits to consider per seed (default: 300)

       -ms    minimum seed matches per location (default: 1)

       -t     number of threads (default is one per core)

       -b     bind each thread to its processor (this is the default)

       --b    Don't bind each thread to its processor (note the double dash)

       -P     disables cache prefetching in the genome; may be helpful for  machines  with  small
              caches or lots of cores/cache

       -so    sort output file by alignment location

       -sm    memory to use for sorting in Gb

       -x     explore some hits of overly popular seeds (useful for filtering)

       -f     stop on first match within edit distance limit (filtering mode)

       -F     filter  output  (a=aligned  only, s=single hit only (MAPQ >= 10), u=unaligned only,
              l=long enough to align (see -mrl))

       -S     suppress additional  processing  (sorted  BAM  output  only)  i=index,  d=duplicate

       -I     ignore IDs that don't match in the paired-end aligner

       -Cxx must be followed by two + or - symbols saying whether to clip low-quality

              bases from front and back of read respectively; default: back only (-C-+)

       -M     indicates  that  CIGAR  strings  in  the generated SAM file should use M (alignment
              match) rather than = and X (sequence (mis-)match).  This is the default

       -=     use the new style CIGAR strings with = and X rather than M.  The opposite of -M

       -G     specify a gap penalty to use when generating CIGAR strings

       -pf    specify the name of a file to contain the run speed

       --hp Indicates not to use huge  pages  (this  may  speed  up  index  load  and  slow  down
              This is the default

       -hp    Indicates to use huge pages (this may speed up alignment and slow down index load).

       -D     Specifies  the  extra search depth (the edit distance beyond the best hit that SNAP
              uses to compute MAPQ).  Default 2

       -rg    Specify the default read group if it is not specified in the input file

       -R     Specify the entire read group line for the SAM/BAM output.  This must include an ID
              tag.   If it doesn't start with '@RG' SNAP will add that.  Specify tabs by \t.  Two
              backslashes will generate a single backslash.  backslash followed by anything  else
              is illegal.  So, '-R @RG\tID:foo\tDS:my data' would generate reads with default tag
              foo, and an @RG line that also included the DS:my data field.

       -sa    Include reads from SAM or BAM files with the  secondary  (0x100)  or  supplementary
              (0x800) flag set; default is to drop them.

       -om    Output  multiple  alignments.  Takes as a parameter the maximum extra edit distance
              relative to the best alignment to allow for secondary alignments

       -omax Limit the number of alignments per read generated by -om.
              This means that if -om would generate more

              than -omax secondary alignments, SNAP will write out only the best -omax  of  them,
              where 'best' means 'with the lowest edit distance'.  Ties are broken arbitrarily.

       -mpc   Limit  the  number  of  alignments  generated  by  -om  to  this  many  per  contig
              (chromosome/FASTA entry);

       'mpc' means 'max per contig; default unlimited.
              This filter is applied prior to -omax.  The primary alignment

              is counted.

       -pc    Preserve the soft clipping for reads coming from SAM or BAM files

       -xf    Increase expansion factor for BAM and GZ files (default 1.0)

       -hdp  Use  Hadoop-style  prefixes  (reporter:status:...)  on  error  messages,  and   emit
              hadoop-style progress messages

       -mrl  Specify  the  minimum read length to align, reads shorter than this (after clipping)
       stay unaligned.
              This should be

       a good bit bigger than the seed length or you might get some questionable alignments.
              Default 50

       -map Use file mapping to load the index rather than reading it.
              This might speed up index loading in cases

              where SNAP is run repatedly on the same index, and the index is larger than half of
              the  memory  size of the machine.  On some operating systems, loading an index with
              -map is much slower than without if the index is not in memory.  You might consider
              adding -pre to prefetch the index into system cache when loading with -map when you
              don't expect the index to be in cache.

       -pre Prefetch the index into system cache.
              This is only meaningful with -map, and only helps if the index is not

              already in memory and your operating system is slow at reading mapped files  (i.e.,
              some versions of Linux, but not Windows).

       -lp    Run SNAP at low scheduling priority (Only implemented on Windows)

       -nu    No  Ukkonen:  don't  reduce  edit  distance  search based on prior candidates. This
              option is purely for evaluating the performance effect of using Ukkonen's algorithm
              rather  than  Smith-Waterman,  and  specifying  it will slow down execution without
              improving the alignments.

       -no    No Ordering: don't order the evalutation of reads  so  as  to  select  more  likely
              candidates  first.   This option is purely for evaluating the performance effect of
              the read evaluation order, and specifying  it  will  slow  down  execution  without
              improving alignments.

       -nt    Don't  truncate  searches  based  on  missed  seed hits.  This option is purely for
              evaluating the performance effect of candidate truncation, and specifying  it  will
              slow down execution without improving alignments.

       -wbs   Write  buffer  size in megabytes.  Don't specify this unless you've gotten an error
              message saying to make it bigger.  Default 16.

       You may process more than one alignment without restarting SNAP, and if  possible  without
       reloading  the index.  In order to do this, list on the command line all of the parameters
       for the first alignment, followed by  a  comma  (separated  by  a  space  from  the  other
       parameters)  followed  by  the  parameters  for  the  next  alignment (including single or
       paired).  You may have as many of these as you please.  If two consecutive alignments  use
       the  same  index,  it  will  not be reloaded.  So, for example, you could do 'snap-aligner
       single hg19-20 foo.fq -o foo.sam , paired hg19-20 end1.fq end2.fq -o  paired.sam'  and  it
       would  not  reload the index between the single and paired alignments.  When specifying an
       input or output file, you can simply list the filename, in which case SNAP will infer  the
       type of the file from the file extension (.sam or .bam for example), or you can explicitly
       specify the file type by preceding the filename with one of the

              following type specifiers (which are case sensitive):








       So, for example, you could specify -bam input.file to make SNAP treat input.file as a  BAM
       file,  even  though  it  would  ordinarily assume a FASTQ file for input or a SAM file for
       output when it doesn't recoginize the file extension.  In order to use a  file  name  that
       begins  with a '-' and not have SNAP treat it as a switch, you must explicitly specify the
       type.  But really, that's just confusing and you shouldn't do it.  Input  and  output  may
       also  be  from/to  stdin/stdout. To do that, use a - for the input or output file name and
       give an explicit type specifier.  So, for example,  snap-aligner  aligner  single  myIndex
       -fastq - -o -sam - would read FASTQ from stdin and write SAM to stdout.

       -s     min and max spacing to allow between paired ends (default: 50 1000).

       -fs    force spacing to lie between min and max.

       -H     max hits for intersecting aligner (default: 2000).

       -mcp specifies the maximum candidate pool size (An internal data structure.

              Only  increase  this if you get an error message saying to do so. If you're running
              out of memory, you may want to reduce it.  Default: 1000000)

       -F b additional option to -F to require both mates to satisfy filter (default is just one)

              If you specify -F b together with one of the other -F options, -F b MUST be second

       -ku    Keep unpaired-looking reads in  SAM/BAM  input.   Ordinarily,  if  a  read  doesn't
              specify  mate  information  (RNEXT field is * and/or PNEXT is 0) then the code that
              matches reads will immdeiately discard it.  Specifying this flag  may  cause  large
              memory  usage  for  some  input  files,  but  may  be  necessary for some strangely
              formatted input files.  You'll also need to specify this  flag  for  SAM/BAM  files
              that were aligned by a single-end aligner.