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Explanation for binary files inside source package according to
http://lists.debian.org/debian-devel/2013/09/msg00332.html
Upstream has provided information about the binary files inside the
source package. The complete answer is recorded in the ITP bug log at
http://bugs.debian.org/728285
Files: inst/extdata/CaffeineTxdb.sqlite
Description: stale; removed in future versions.
sqlite tables derived from querying a public data base ('biomart.org').
Files: inst/extdata/ex1.bam
Description:
ex1.sam is the text representation of ex1.bam (using Rsamtools::asBam at the
time of file creation); ex1.bam.bai is an index created on ex1.bam (using
Rsamtools::indexBam at the time of file creation). ex1.sam is derived from files
originally distributed with 'samtools' software under an MIT license, see
Rsamtools/LICENSE
Files: inst/extdata/ex1.bcf
ex1.bcf is a file hand created in antiquity, and used in unit tests and man pages.
Files: inst/extdata/example.gtf.gz.*:
example.gtf.gz is gz-compressed text file used in unit tests and man pages, hand
curated from public data sources, the .tbi variant is an index
(Rsamtools::indexTabix)
Files: inst/extdata/example_from_SAM_Spec*:
This is a file useful to the developer, hand-curated from the SAM spec at
http://samtools.sourceforge.net/SAMv1.pdf
although SAM.pdf did not historically include version numbers so the precise
origin is unknown.
Files: inst/extdata/olaps.Rda
The script for creating this file is in the vignette Rsamtools-Overiew.Rnw
.
<<readGAlignmentsFromBam, eval=FALSE>>=
library(parallel)
options(srapply_fapply="parallel", mc.cores=detectCores())
olaps <- readGAlignmentsFromBam(bv)
@
Files: inst/unitTests/cases/ex1.sam.gz
Except of the first two lines this is a copy of file
inst/extdata/ex1.sam
Files: inst/unitTests/cases/ex1_*.bam*
Files are derived from file
inst/extdata/ex1.sam
and just used for verification of the correctness of
Rsamtools.
Files: inst/unitTests/cases/plp_refskip.bam*
This is a hand-crafted file used in a unit test
Source code duplication
=======================
The following files are copies of source code that is just contained in
other Debian packages. We are discussing this issue with upstream to
enable making use of dynamic linking for future versions of this package.
Files: src/samtools/*
Source is part of samtools (0.1.19-1)
For more details what was tried see
debian/patches/use-debian-packaged-libs.patch
Files: src/tabix/*
Source is part of tabix (0.2.6-1)
-- Andreas Tille <tille@debian.org> Fri, 25 Oct 2013 08:53:18 +0200
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