Read and Write BAM (Binary Alignment) Files

Provides an interface to functions of the 'SAMtools' C-Library by Heng Li.


News

NEW FEATURES

o exonAlignDepth, exonLoessModel, geneAlignDepth classes added
o saveAldData, cutFlatAlignDepth, junctionSites, getNormFactor
    functions added

SIGNIFICANT USER-VISIBLE CHANGES

o (none)

BUG FIXES

o (none)

NEW FEATURES

o sampleBamFiles and samplesAlignDepth classes added

SIGNIFICANT USER-VISIBLE CHANGES

o (none)

BUG FIXES

o Corrected [extern "C" ] position in rbamtools.h

NEW FEATURES

o (none)

SIGNIFICANT USER-VISIBLE CHANGES

o (none)

BUG FIXES

o Corrected [extern "C" ] position in rbamtools.h

NEW FEATURES

o extractBamRegions

o rangeSegCount class

SIGNIFICANT USER-VISIBLE CHANGES

o The functions reader2fastq and range2fastq will be deprecated soon and
replaced by readerToFastq and rangeToFastq

BUG FIXES

o Corrected bug in gapSiteList.h which caused crashes in multiply repeated merges

o Changed Variable type from Integer to unsigned long long int in
C functions where alignment numbers are carried.

o Corrected a PROTECT / UNPROTECT imbalance which showed up incidentally.

NEW FEATURES

o Added support for Description (DS) segment in header program

o Added support for Supplementary Alignment (0x800) segment in alignment FLAG

SIGNIFICANT USER-VISIBLE CHANGES

o The functions create.index, load.index and create.idx.batch will
be deprecated soon and replaced by createIndex, loadIndex and
createIdxBatch.

BUG FIXES

o Fixed erroneous FLAG re-setting algorithm

o Enclosed range2fastq example in "\dontrun{}" in order to avoid
checking errors (File could not be opened) on OSX snowleopard

o Replaced rand() by runif() in (samtools) ksort.h
(due to NOTE in devel CRAN win-builder:
    "Compiled code should not call (...) the C RNG")

NEW FEATURES

o Included this NEWS file and a ChangeLog file

o Added test directory (tests are executed on R CMD check)

SIGNIFICANT USER-VISIBLE CHANGES

o Extended plotAlignDepth function: Option for plotting of exon positions added

BUG FIXES

o (none)

Reference manual

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install.packages("rbamtools")

2.16.6 by Wolfgang Kaisers, a month ago


Browse source code at https://github.com/cran/rbamtools


Authors: Wolfgang Kaisers


Documentation:   PDF Manual  


Artistic-2.0 license


Depends on methods, refGenome

Suggests xtable


See at CRAN