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lomereiterlomereiter
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fixed a bug in markdup; updated docs
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‎Makefile‎

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D_COMPILER=dmd
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D_FLAGS=-IBioD -O -release -inline -g -version=serial
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D_FLAGS=-IBioD #-O -release -inline -g# -version=serial
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RDMD_FLAGS=--compiler=$(D_COMPILER) --build-only $(D_FLAGS)
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‎man/sambamba-flagstat.1‎

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.\" generated with Ronn/v0.7.3
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.\" http://github.com/rtomayko/ronn/tree/0.7.3
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.
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.TH "SAMBAMBA\-FLAGSTAT" "1" "April 2013" "" ""
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.TH "SAMBAMBA\-FLAGSTAT" "1" "July 2013" "" ""
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.
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.SH "NAME"
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\fBsambamba\-flagstat\fR \- getting flag statistics from BAM file

‎man/sambamba-flagstat.1.ronn‎

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## SYNOPSIS
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`sambamba-flagstat` [OPTIONS] <input.bam>
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`sambamba flagstat` [OPTIONS] <input.bam>
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## DESCRIPTION
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## OPTIONS
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* `-t`, `--nthreads`=<NTHREADS>:
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Specify number of threads to use for BAM decompression
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Specify number of threads to use for BAM decompression
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* `-p`, `--show-progress`:
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Show progressbar in STDERR
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Show progressbar in STDERR

‎man/sambamba-index.1‎

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.\" generated with Ronn/v0.7.3
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.\" http://github.com/rtomayko/ronn/tree/0.7.3
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.
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.TH "SAMBAMBA\-INDEX" "1" "April 2013" "" ""
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.TH "SAMBAMBA\-INDEX" "1" "July 2013" "" ""
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.
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.SH "NAME"
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\fBsambamba\-index\fR \- tool for building standard index files for BAM data

‎man/sambamba-index.1.ronn‎

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## SYNOPSIS
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`sambamba-index` [`-p`|`--show-progress`] [`-n`|`--threads`=NTHREADS] <input.bam> [<output.bai>]
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`sambamba index` [`-p`|`--show-progress`] [`-n`|`--threads`=NTHREADS] <input.bam> [<output.bai>]
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## DESCRIPTION
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`sambamba-index` builds an index for a sorted by coordinate BAM file.
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`sambamba index` builds an index for a sorted by coordinate BAM file.
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This step is required for effective region querying in most tools for working
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with BAM data.
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Build index file example.bam.bai given a sorted BAM file example.bam:
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$ sambamba-index example.bam
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$ sambamba index example.bam
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Build index file at custom location showing progress:
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$ sambamba-index --show-progress example.bam /tmp/example.bam.bai
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$ sambamba index --show-progress example.bam /tmp/example.bam.bai

‎man/sambamba-markdup.1.ronn‎

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sambamba-markdup(1) -- finding duplicate reads in BAM file
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=============================================================
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## SYNOPSIS
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`sambamba markdup` [OPTIONS] <input.bam> <output.bam>
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## DESCRIPTION
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Marks (by default) or removes duplicate reads. For determining
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whether a read is a duplicate or not, the same criteria as in Picard
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are used.
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## OPTIONS
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* `-r`, `--remove-duplicates`:
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remove duplicates instead of just marking them
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* `-t`, `--nthreads`=<NTHREADS>:
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number of threads to use
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* `-l`, `--compression-level`=<N>:
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specify compression level of the resulting file (from 0 to 9)");
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* `-p`, `--show-progress`:
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show progressbar in STDERR
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* `--tmpdir`=<TMPDIR>:
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specify directory for temporary files; default is `/tmp`
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* `--hash-table-size`=<HASHTABLESIZE>:
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size of hash table for finding read pairs (default is 262144 reads);
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will be rounded down to the nearest power of two;
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should be `> (average coverage) * (insert size)` for good performance
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* `--overflow-list-size`=<OVERFLOWLISTSIZE>:
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size of the overflow list where reads, thrown away from the hash table,
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get a second chance to meet their pairs (default is 200000 reads);
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increasing the size reduces the number of temporary files created
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* `--io-buffer-size`=<BUFFERSIZE>:
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controls sizes of two buffers of BUFFERSIZE *megabytes* each, used
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for reading and writing BAM during the second pass (default is 128)
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## BUGS
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External sort is not implemented.
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Thus, memory consumption grows by 2Gb per each 100M reads.
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Check that you have enough RAM before running the tool.

‎man/sambamba-merge.1‎

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.\" generated with Ronn/v0.7.3
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.\" http://github.com/rtomayko/ronn/tree/0.7.3
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.
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.TH "SAMBAMBA\-MERGE" "1" "April 2013" "" ""
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.TH "SAMBAMBA\-MERGE" "1" "July 2013" "" ""
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.
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.SH "NAME"
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\fBsambamba\-merge\fR \- tool for merging several BAM files into one

‎man/sambamba-merge.1.ronn‎

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## SYNOPSIS
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`sambamba-merge` [OPTIONS] <output.bam> <input1.bam> <input2.bam> [...]
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`sambamba merge` [OPTIONS] <output.bam> <input1.bam> <input2.bam> [...]
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## DESCRIPTION
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`sambamba-merge` is used for merging several sorted BAM files into one.
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`sambamba merge` is used for merging several sorted BAM files into one.
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The sorting order of all the files must be the same, and it is maintained in the output file.
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SAM headers are merged automatically like in Picard merging tool.
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## OPTIONS
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* `-t`, `--nthreads`=<NTHREADS>:
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Specify number of threads to use for compression/decompression tasks.
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Specify number of threads to use for compression/decompression tasks.
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* `-l`, `--compression-level`=<COMPRESSION_LEVEL>:
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Specify compression level of output file as a number from 0 to 9
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Specify compression level of output file as a number from 0 to 9
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* `-H`, `--header`:
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Output only merged header to stdout in SAM format (e.g. for debugging purposes).
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Other options are ignored.
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Output only merged header to stdout in SAM format (e.g. for debugging purposes).
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Other options are ignored.
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* `-p`, `--show-progress`:
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Show progressbar in STDERR.
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Show progressbar in STDERR.

‎man/sambamba-slice.1‎

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.\" generated with Ronn/v0.7.3
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.\" http://github.com/rtomayko/ronn/tree/0.7.3
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.
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.TH "SAMBAMBA\-SLICE" "1" "December 2012" "" ""
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.TH "SAMBAMBA\-SLICE" "1" "July 2013" "" ""
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.
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.SH "NAME"
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\fBsambamba\-slice\fR \- copying a slice of BAM file
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.
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.SH "OPTIONS"
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.
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.nf
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.TP
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\fB\-o\fR, \fB\-\-output\-filename\fR=\fIOUTPUTFILE\fR
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* `\-o`, `\-\-output\-filename`=<OUTPUTFILE>:
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Name of output file
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.
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.fi
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‎man/sambamba-slice.1.ronn‎

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## SYNOPSIS
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`sambamba-slice` [OPTIONS] <input.bam> <region>
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`sambamba slice` [OPTIONS] <input.bam> <region>
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## DESCRIPTION
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## OPTIONS
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* `-o`, `--output-filename`=<OUTPUTFILE>:
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Name of output file
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Name of output file

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