NAME

       rabema_evaluate - RABEMA Evaluation

SYNOPSIS

       rabema_evaluate [OPTIONS] --reference REF.fa --in-gsi IN.gsi --in-bam MAPPING.{sam,bam}

DESCRIPTION

       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  sorted  by  queryname.   The  program will create a FASTA index file
       REF.fa.fai for fast random access to the reference.

OPTIONS

       -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, --reference INPUT_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-gsi INPUT_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-bam INPUT_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-tsv OUTPUT_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.

   Benchmark Parameters:
       --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-metric STRING
              Set distance metric.  Valid values: hamming, edit.   Default:  edit.  One  of  hamming  and  edit.
              Default: edit.

       -e, --max-error INTEGER
              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-category STRING
              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-tag STRING
              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.

RETURN VALUES

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

MEMORY REQUIREMENTS

       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.

REFERENCES

       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