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PROGRAM:

NAME


rabema_evaluate - RABEMA Evaluation

SYNOPSIS

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

-h, --help

Displays this help message.

--version

Display version information

-v, --verbose

Enable verbose output.

-vv, --very-verbose

Enable even more verbose output.

Input / Output:

-r, --reference FASTA

Path to load reference FASTA from. Valid filetypes are: fa and fasta.

-g, --in-gsi GSI

Path to load gold standard intervals from. If compressed using gzip, the file will
be decompressed on the fly. Valid filetypes are: gsi and gsi.gz.

-s, --in-sam SAM

Path to load the read mapper SAM output from. Valid filetype is: sam.

-b, --in-bam BAM

Path to load the read mapper BAM output from. Valid filetype is: bam.

--out-tsv TSV

Path to write the statistics to as TSV. Valid filetype is: tsv.

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. Usefull for
precision computation.

--match-N

When set, N matches all characters without penalty.

--distance-metric METRIC

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

-e, --max-error RATE

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 CAT

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.

--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

VERSION

rabema_evaluate version: 1.2.0 Last update March 14, 2013

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