rabema_evaluate - RABEMA Evaluation

       Compare  the  SAM/bam  output MAPPING.sam/MAPPING.bam of any read mapper against the RABEMA gold standard
       previously built with rabema_build_gold_standard.  The input is a reference FASTA file, a  gold  standard
       interval (GSI) file and the SAM/BAM input to evaluate.

       The  input  SAM/BAM  file  must  be  sortedbyqueryname.   The  program will create a FASTA index file
       REF.fa.fai for fast random access to the reference.

       From version 1.1, great care has been taken to keep the memory requirements as low as possible.

       The evaluation step needs to store the whole reference sequence in memory but little  more  memory.   So,
       for  the  human  genome,  the  memory  requirements  are below 4 GB, regardless of the size of the GSI or
       SAM/BAM file.

       rabema_evaluate - RABEMA Evaluation

-h, --help
              Display the help message.

       --version
              Display version information.

       -v, --verbose
              Enable verbose output.

       -vv, --very-verbose
              Enable even more verbose output.

   Input/Output:-r, --referenceINPUT_FILE
              Path to load reference FASTA from. Valid filetypes are: .sam[.*],  .raw[.*],  .gbk[.*],  .frn[.*],
              .fq[.*], .fna[.*], .ffn[.*], .fastq[.*], .fasta[.*], .faa[.*], .fa[.*], .embl[.*], and .bam, where
              * is any of the following extensions: gz, bz2, and bgzf for transparent (de)compression.

       -g, --in-gsiINPUT_FILE
              Path to load gold standard intervals from. If compressed using gzip, the file will be decompressed
              on  the  fly.  Valid  filetype  is:  .gsi[.*],  where * is any of the following extensions: gz for
              transparent (de)compression.

       -b, --in-bamINPUT_FILE
              Path to load the read mapper SAM or BAM output from. Valid filetypes are: .sam[.*] and .bam, where
              * is any of the following extensions: gz, bz2, and bgzf for transparent (de)compression.

       --out-tsvOUTPUT_FILE
              Path to write the statistics to as TSV. Valid filetype is: .rabema_report_tsv.

       --dont-check-sorting
              Do not check sortedness (by name) of input SAM/BAM files.  This is required if the reads  are  not
              sorted by name in the original FASTQ files.  Files from the SRA and ENA generally are sorted.

   BenchmarkParameters:--oracle-mode
              Enable  oracle  mode.   This  is used for simulated data when the input GSI file gives exactly one
              position that is considered as the true sample position.  For simulated data.

       --only-unique-reads
              Consider only reads that a single alignment in the  mapping  result  file.  Useful  for  precision
              computation.

       --match-N
              When set, N matches all characters without penalty.

       --distance-metricSTRING
              Set  distance  metric.   Valid  values:  hamming,  edit.   Default: edit. One of hamming and edit.
              Default: edit.

       -e, --max-errorINTEGER
              Maximal error rate to build gold standard for in  percent.   This  parameter  is  an  integer  and
              relative  to  the read length.  The error rate is ignored in oracle mode, here the distance of the
              read at the sample position is taken, individually for each read.  Default: 0 Default: 0.

       -c, --benchmark-categorySTRING
              Set benchmark category.  One of {all, all-best, any-best.  Default: all One of all, all-best,  and
              any-best. Default: all.

       --trust-NM
              When  set,  we trust the alignment and distance from SAM/BAM file and no realignment is performed.
              Off by default.

       --extra-pos-tagSTRING
              If the CIGAR string is absent, the missing alignment end position can be provided by this BAM tag.

       --ignore-paired-flags
              When set, we ignore all SAM/BAM flags related to pairing.  This is necessary  when  analyzing  SAM
              from SOAP's soap2sam.pl script.

       --DONT-PANIC
              Do not stop program execution if an additional hit was found that indicates that the gold standard
              is incorrect.

   Logging:--show-missed-intervals
              Show details for each missed interval from the GSI.

       --show-invalid-hits
              Show details for invalid hits (with too high error rate).

       --show-additional-hits
              Show details for additional hits (low enough error rate but not in gold standard.

       --show-hits
              Show details for hit intervals.

       --show-try-hit
              Show details for each alignment in SAM/BAM input.

              The  occurrence  of  "invalid"  hits  in  the  read mapper's output is not an error.  If there are
              additional hits, however, this shows an error in the gold standard.

       M. Holtgrewe, A.-K. Emde, D. Weese and K. Reinert.  A Novel  And  Well-Defined  Benchmarking  Method  For
       Second Generation Read Mapping, BMC Bioinformatics 2011, 12:210.

       http://www.seqan.de/rabema
              RABEMA Homepage

       http://www.seqan.de/mason
              Mason Homepage

rabema_evaluate 1.2.10 [tarball]                                                              RABEMA_EVALUATE(1)

       A return value of 0 indicates success, any other value indicates an error.

rabema_evaluate [OPTIONS] --referenceREF.fa--in-gsiIN.gsi--in-bamMAPPING.{sam,bam}