[med-svn] [dindel] 02/02: Added initial debian packaging.
Steffen Möller
moeller at moszumanska.debian.org
Fri Mar 18 15:37:00 UTC 2016
This is an automated email from the git hooks/post-receive script.
moeller pushed a commit to branch master
in repository dindel.
commit 68bc8f027e152241b48482039d8204f6eceba69a
Author: Steffen Moeller <moeller at debian.org>
Date: Fri Mar 18 16:34:54 2016 +0100
Added initial debian packaging.
---
debian/README.source | 15 ++
debian/changelog | 5 +
debian/compat | 1 +
debian/control | 39 ++++
debian/copyright | 58 +++++
debian/dindel.1 | 401 ++++++++++++++++++++++++++++++++
debian/docs | 1 +
debian/install | 1 +
debian/manpages | 1 +
debian/patches/compiler_errors.patch | 26 +++
debian/patches/modernize-Makefile.patch | 26 +++
debian/patches/series | 2 +
debian/rules | 5 +
debian/source/format | 1 +
debian/upstream/edam | 13 ++
debian/upstream/metadata | 17 ++
16 files changed, 612 insertions(+)
diff --git a/debian/README.source b/debian/README.source
new file mode 100644
index 0000000..08f8692
--- /dev/null
+++ b/debian/README.source
@@ -0,0 +1,15 @@
+dindel for Debian
+-----------------
+
+ * Substituted seqan source tree with ref to seqan-dev
+ * Current version of boost does not require the extension provided
+ * The description of the package is copied from the package's home page
+ * Created two patch files
+ - modernize-Makefile.patch
+ adjusting for the changed source tree
+ - compiler_errors.patch
+ resolved ambiguity (badly) for the hash function
+ * The man page was created with help2man and minimal manual editing
+
+ -- Steffen Moeller <moeller at debian.org> Fri, 18 Mar 2016 14:52:14 +0100
+
diff --git a/debian/changelog b/debian/changelog
new file mode 100644
index 0000000..f0bfc6c
--- /dev/null
+++ b/debian/changelog
@@ -0,0 +1,5 @@
+dindel (1.01+dfsg-1) unstable; urgency=low
+
+ * Initial release (Closes: #nnnn)
+
+ -- Animesh Sharma <sharma.animesh at gmail.com> Fri, 18 Mar 2016 10:51:19 +0100
diff --git a/debian/compat b/debian/compat
new file mode 100644
index 0000000..ec63514
--- /dev/null
+++ b/debian/compat
@@ -0,0 +1 @@
+9
diff --git a/debian/control b/debian/control
new file mode 100644
index 0000000..835f7d3
--- /dev/null
+++ b/debian/control
@@ -0,0 +1,39 @@
+Source: dindel
+Section: science
+Priority: optional
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders:
+ Animesh Sharma <sharma.animesh at gmail.com>,
+ Steffen Moeller <moeller at debian.org>
+Build-Depends: debhelper (>= 8.0.0), seqan-dev, libbam-dev,
+ libboost-program-options-dev, libboost-math-dev
+Standards-Version: 3.9.7
+Homepage: https://sites.google.com/site/keesalbers/soft/dindel
+#Vcs-Git: git://git.debian.org/collab-maint/dindel.git
+#Vcs-Browser: http://git.debian.org/?p=collab-maint/dindel.git;a=summary
+
+Package: dindel
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends}
+Description: determines indel calls from short-read data
+ Dindel is a program for calling small indels from short-read sequence
+ data ('next generation sequence data'). It currently is designed to
+ handle only Illumina data.
+ .
+ Dindel requires a BAM file containing the read-alignments as input. It
+ then extracts candidate indels from the BAM file, and realigns the reads
+ to candidate haplotypes consisting of these candidate indels. If there
+ is sufficient evidence for an alternative haplotype to the reference,
+ it will call an indel.
+ .
+ It is possible to test indels discovered with other methods using Dindel,
+ for instance longer indels obtained through assembly methods. Dindel
+ will then realign both mapped and unmapped reads to see if the candidate
+ indel is supported by the reads.
+ .
+ Dindel outputs both genotype likelihoods and includes a script to
+ convert these to a VCF file with indel and SNP calls.
+ .
+ There is basic support for outputting realigned BAM files for each
+ realignment-window. These realigned BAM files can be used to call SNPs
+ near (candidate) indels.
diff --git a/debian/copyright b/debian/copyright
new file mode 100644
index 0000000..0f87813
--- /dev/null
+++ b/debian/copyright
@@ -0,0 +1,58 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: dindel
+Source: https://sites.google.com/site/keesalbers/soft/dindel
+
+Files: *
+Copyright: 2010 Cornelis A. Albers
+ Sanger Center, Cambridge, UK
+License: GPL3
+
+Files: digamma.hpp
+Copyright: 2006 John Maddock
+License: Boost Software License, Version 1.0. (See accompanying file
+
+Files: foreach.hpp
+Copyright: 2004 Eric Niebler.
+License: Boost Software License, Version 1.0. (See accompanying file
+ Permission is hereby granted, free of charge, to any person or
+ organization obtaining a copy of the software and accompanying
+ documentation covered by this license (the "Software") to use, reproduce,
+ display, distribute, execute, and transmit the Software, and to prepare
+ derivative works of the Software, and to permit third-parties to whom
+ the Software is furnished to do so, all subject to the following:
+ .
+ The copyright notices in the Software and this entire statement,
+ including the above license grant, this restriction and the following
+ disclaimer, must be included in all copies of the Software, in whole or
+ in part, and all derivative works of the Software, unless such copies
+ or derivative works are solely in the form of machine-executable object
+ code generated by a source language processor.
+ .
+ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+ OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, TITLE AND
+ NON-INFRINGEMENT. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR ANYONE
+ DISTRIBUTING THE SOFTWARE BE LIABLE FOR ANY DAMAGES OR OTHER LIABILITY,
+ WHETHER IN CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
+ CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+ SOFTWARE.
+
+
+Files: debian/*
+Copyright: 2016 Animesh Sharma <sharma.animesh at gmail.com>
+License: GPL-3
+ This package is free software; you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation, either version 3 of the License, or
+ (at your option) any later version.
+ .
+ This package is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+ .
+ You should have received a copy of the GNU General Public License
+ along with this program. If not, see <http://www.gnu.org/licenses/>
+ .
+ On Debian systems, the complete text of the GNU General
+ Public License version 3 can be found in "/usr/share/common-licenses/GPL-3".
diff --git a/debian/dindel.1 b/debian/dindel.1
new file mode 100644
index 0000000..1cbbcdf
--- /dev/null
+++ b/debian/dindel.1
@@ -0,0 +1,401 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.40.10.
+.TH DINDEL "1" "March 2016" "" "User Commands"
+.SH NAME
+dindel \- finds of insertions and deletions from short nucleotide sequences
+.SH DESCRIPTION
+.SS "[Required] :"
+.TP
+\fB\-\-ref\fR arg
+fasta reference sequence (should be
+indexed with .fai file)
+.TP
+\fB\-\-outputFile\fR arg
+file\-prefix for output results
+.SS "[Required] Program option:"
+.TP
+\fB\-\-analysis\fR arg (=indels) Analysis type:
+getCIGARindels: Extract indels from CIGARs of
+mapped reads, and infer libary insert size
+distributions
+indels: infer indels
+realignCandidates: Realign/reposition candidates in
+candidate file
+.SS "[Required] BAM input. Choose one of the following:"
+.TP
+\fB\-\-bamFile\fR arg
+read alignment file (should be indexed)
+.TP
+\fB\-\-bamFiles\fR arg
+file containing filepaths for BAMs to be jointly
+analysed (not possible for \fB\-\-analysis\fR=\fI=indels\fR
+.PP
+[Required for analysis == getCIGARindels]:
+Region to be considered for extraction of candidate indels.:
+.TP
+\fB\-\-region\fR arg
+region to be analysed in format start\-end, eg.
+1000\-2000
+.TP
+\fB\-\-tid\fR arg
+target sequence (eg 'X')
+.SS "[Required for analysis == indels]:"
+.TP
+\fB\-\-varFile\fR arg
+file with candidate variants to be tested.
+.TP
+\fB\-\-varFileIsOneBased\fR
+coordinates in varFile are one\-based
+.SS "Output options:"
+.TP
+\fB\-\-outputRealignedBAM\fR
+output BAM file with realigned reads
+.TP
+\fB\-\-processRealignedBAM\fR arg ABSOLUTE path to script to process realigned BAM
+file
+.TP
+\fB\-\-quiet\fR
+quiet output
+.SS "parameters for analysis==indels option:"
+.TP
+\fB\-\-doDiploid\fR
+analyze data assuming a diploid sequence
+.TP
+\fB\-\-doPooled\fR
+estimate haplotype frequencies using Bayesian EM
+algorithm.
+May be applied to single individual and pools.
+.SS "General algorithm parameters:"
+.TP
+\fB\-\-faster\fR
+use faster but less accurate ungapped
+read\-haplotype alignment model
+.TP
+\fB\-\-filterHaplotypes\fR
+prefilter haplotypes based on coverage
+.TP
+\fB\-\-flankRefSeq\fR arg (=2)
+#bases of reference sequence of indel
+region
+.TP
+\fB\-\-flankMaxMismatch\fR arg (=2)
+max number of mismatches in indel
+region
+.TP
+\fB\-\-priorSNP\fR arg (=0.001)
+prior probability of a SNP site
+.TP
+\fB\-\-priorIndel\fR arg (=0.0001)
+prior probability of a detected indel
+not being a sequencing error
+.TP
+\fB\-\-width\fR arg (=60)
+number of bases to left and right of
+indel
+.TP
+\fB\-\-maxHap\fR arg (=8)
+maximum number of haplotypes in
+likelihood computation
+.TP
+\fB\-\-maxRead\fR arg (=10000)
+maximum number of reads in likelihood
+computation
+.TP
+\fB\-\-mapQualThreshold\fR arg (=0.98999999999999999)
+lower limit for read mapping quality
+.TP
+\fB\-\-capMapQualThreshold\fR arg (=100)
+upper limit for read mapping quality in
+observationmodel_old (phred units)
+.TP
+\fB\-\-capMapQualFast\fR arg (=45)
+cap mapping quality in alignment using
+fast ungapped method
+.IP
+(WARNING: setting it too high (>50)
+.IP
+might result in significant
+overcalling!)
+.TP
+\fB\-\-skipMaxHap\fR arg (=200)
+skip computation if number of
+haplotypes exceeds this number
+.TP
+\fB\-\-minReadOverlap\fR arg (=20)
+minimum overlap between read and
+haplotype
+.TP
+\fB\-\-maxReadLength\fR arg (=500)
+maximum length of reads
+.TP
+\fB\-\-minCount\fR arg (=1)
+minimum number of WS observations of
+indel
+.TP
+\fB\-\-maxHapReadProd\fR arg (=10000000)
+skip if product of number of reads and
+haplotypes exceeds this value
+.TP
+\fB\-\-changeINStoN\fR
+change sequence of inserted sequence to
+\&'N', so that no penalty is incurred if
+a read mismatches the inserted sequence
+.SS "parameters for --pooled option:"
+.TP
+\fB\-\-bayesa0\fR arg (=0.001)
+Dirichlet a0 parameter haplotype frequency
+prior
+.TP
+\fB\-\-bayesType\fR arg (=singlevariant) Bayesian EM program type (all or
+singlevariant or priorpersite)
+.SS "General algorithm filtering options:"
+.HP
+\fB\-\-checkAllCIGARs\fR arg (=1) include all indels at the position of the call site
+.TP
+\fB\-\-filterReadAux\fR arg
+match string for exclusion of reads based on
+auxilary information
+.SS "Observation model parameters:"
+.TP
+\fB\-\-pError\fR arg (=0.00050000000000000001)
+probability of a read indel
+.TP
+\fB\-\-pMut\fR arg (=1.0000000000000001e\-05)
+probability of a mutation in the read
+.TP
+\fB\-\-maxLengthIndel\fR arg (=5)
+maximum length of a _sequencing error_
+indel in read [not for \fB\-\-faster\fR option]
+.SS "Library options:"
+.TP
+\fB\-\-libFile\fR arg
+file with library insert histograms (as generated by
+\fB\-\-analysis\fR getCIGARindels)
+.SS "Misc results analysis options:"
+.TP
+\fB\-\-compareReadHap\fR
+compare likelihood differences in reads
+against haplotypes
+.HP
+\fB\-\-compareReadHapThreshold\fR arg (=0.5) difference threshold for viewing
+.TP
+\fB\-\-showEmpirical\fR
+show empirical distribution over
+nucleotides
+.TP
+\fB\-\-showCandHap\fR
+show candidate haplotypes for fast
+method
+.TP
+\fB\-\-showHapAlignments\fR
+show for each haplotype which reads map
+to it
+.TP
+\fB\-\-showReads\fR
+show reads
+.TP
+\fB\-\-inferenceMethod\fR arg (=empirical)
+inference method
+.TP
+\fB\-\-opl\fR
+output likelihoods for every read and
+haplotype
+.SS "[Required] :"
+.TP
+\fB\-\-ref\fR arg
+fasta reference sequence (should be
+indexed with .fai file)
+.TP
+\fB\-\-outputFile\fR arg
+file\-prefix for output results
+.SS "[Required] Program option:"
+.TP
+\fB\-\-analysis\fR arg (=indels) Analysis type:
+getCIGARindels: Extract indels from CIGARs of
+mapped reads, and infer libary insert size
+distributions
+indels: infer indels
+realignCandidates: Realign/reposition candidates in
+candidate file
+.SS "[Required] BAM input. Choose one of the following:"
+.TP
+\fB\-\-bamFile\fR arg
+read alignment file (should be indexed)
+.TP
+\fB\-\-bamFiles\fR arg
+file containing filepaths for BAMs to be jointly
+analysed (not possible for \fB\-\-analysis\fR=\fI=indels\fR
+.PP
+[Required for analysis == getCIGARindels]:
+Region to be considered for extraction of candidate indels.:
+.TP
+\fB\-\-region\fR arg
+region to be analysed in format start\-end, eg.
+1000\-2000
+.TP
+\fB\-\-tid\fR arg
+target sequence (eg 'X')
+.SS "[Required for analysis == indels]:"
+.TP
+\fB\-\-varFile\fR arg
+file with candidate variants to be tested.
+.TP
+\fB\-\-varFileIsOneBased\fR
+coordinates in varFile are one\-based
+.SS "Output options:"
+.TP
+\fB\-\-outputRealignedBAM\fR
+output BAM file with realigned reads
+.TP
+\fB\-\-processRealignedBAM\fR arg ABSOLUTE path to script to process realigned BAM
+file
+.TP
+\fB\-\-quiet\fR
+quiet output
+.SS "parameters for analysis==indels option:"
+.TP
+\fB\-\-doDiploid\fR
+analyze data assuming a diploid sequence
+.TP
+\fB\-\-doPooled\fR
+estimate haplotype frequencies using Bayesian EM
+algorithm.
+May be applied to single individual and pools.
+.SS "General algorithm parameters:"
+.TP
+\fB\-\-faster\fR
+use faster but less accurate ungapped
+read\-haplotype alignment model
+.TP
+\fB\-\-filterHaplotypes\fR
+prefilter haplotypes based on coverage
+.TP
+\fB\-\-flankRefSeq\fR arg (=2)
+#bases of reference sequence of indel
+region
+.TP
+\fB\-\-flankMaxMismatch\fR arg (=2)
+max number of mismatches in indel
+region
+.TP
+\fB\-\-priorSNP\fR arg (=0.001)
+prior probability of a SNP site
+.TP
+\fB\-\-priorIndel\fR arg (=0.0001)
+prior probability of a detected indel
+not being a sequencing error
+.TP
+\fB\-\-width\fR arg (=60)
+number of bases to left and right of
+indel
+.TP
+\fB\-\-maxHap\fR arg (=8)
+maximum number of haplotypes in
+likelihood computation
+.TP
+\fB\-\-maxRead\fR arg (=10000)
+maximum number of reads in likelihood
+computation
+.TP
+\fB\-\-mapQualThreshold\fR arg (=0.98999999999999999)
+lower limit for read mapping quality
+.TP
+\fB\-\-capMapQualThreshold\fR arg (=100)
+upper limit for read mapping quality in
+observationmodel_old (phred units)
+.TP
+\fB\-\-capMapQualFast\fR arg (=45)
+cap mapping quality in alignment using
+fast ungapped method
+.IP
+(WARNING: setting it too high (>50)
+.IP
+might result in significant
+overcalling!)
+.TP
+\fB\-\-skipMaxHap\fR arg (=200)
+skip computation if number of
+haplotypes exceeds this number
+.TP
+\fB\-\-minReadOverlap\fR arg (=20)
+minimum overlap between read and
+haplotype
+.TP
+\fB\-\-maxReadLength\fR arg (=500)
+maximum length of reads
+.TP
+\fB\-\-minCount\fR arg (=1)
+minimum number of WS observations of
+indel
+.TP
+\fB\-\-maxHapReadProd\fR arg (=10000000)
+skip if product of number of reads and
+haplotypes exceeds this value
+.TP
+\fB\-\-changeINStoN\fR
+change sequence of inserted sequence to
+\&'N', so that no penalty is incurred if
+a read mismatches the inserted sequence
+.SS "parameters for --pooled option:"
+.TP
+\fB\-\-bayesa0\fR arg (=0.001)
+Dirichlet a0 parameter haplotype frequency
+prior
+.TP
+\fB\-\-bayesType\fR arg (=singlevariant) Bayesian EM program type (all or
+singlevariant or priorpersite)
+.SS "General algorithm filtering options:"
+.HP
+\fB\-\-checkAllCIGARs\fR arg (=1) include all indels at the position of the call site
+.TP
+\fB\-\-filterReadAux\fR arg
+match string for exclusion of reads based on
+auxilary information
+.SS "Observation model parameters:"
+.TP
+\fB\-\-pError\fR arg (=0.00050000000000000001)
+probability of a read indel
+.TP
+\fB\-\-pMut\fR arg (=1.0000000000000001e\-05)
+probability of a mutation in the read
+.TP
+\fB\-\-maxLengthIndel\fR arg (=5)
+maximum length of a _sequencing error_
+indel in read [not for \fB\-\-faster\fR option]
+.SS "Library options:"
+.TP
+\fB\-\-libFile\fR arg
+file with library insert histograms (as generated by
+\fB\-\-analysis\fR getCIGARindels)
+.SS "Misc results analysis options:"
+.TP
+\fB\-\-compareReadHap\fR
+compare likelihood differences in reads
+against haplotypes
+.HP
+\fB\-\-compareReadHapThreshold\fR arg (=0.5) difference threshold for viewing
+.TP
+\fB\-\-showEmpirical\fR
+show empirical distribution over
+nucleotides
+.TP
+\fB\-\-showCandHap\fR
+show candidate haplotypes for fast
+method
+.TP
+\fB\-\-showHapAlignments\fR
+show for each haplotype which reads map
+to it
+.TP
+\fB\-\-showReads\fR
+show reads
+.TP
+\fB\-\-inferenceMethod\fR arg (=empirical)
+inference method
+.TP
+\fB\-\-opl\fR
+output likelihoods for every read and
+haplotype
+.SH "SEE ALSO"
+The full documentation for
+.B dindel
+you find referenced on https://sites.google.com/site/keesalbers/soft/dindel
diff --git a/debian/docs b/debian/docs
new file mode 100644
index 0000000..e845566
--- /dev/null
+++ b/debian/docs
@@ -0,0 +1 @@
+README
diff --git a/debian/install b/debian/install
new file mode 100644
index 0000000..4d26537
--- /dev/null
+++ b/debian/install
@@ -0,0 +1 @@
+dindel usr/bin
diff --git a/debian/manpages b/debian/manpages
new file mode 100644
index 0000000..0287bb2
--- /dev/null
+++ b/debian/manpages
@@ -0,0 +1 @@
+debian/dindel.1
diff --git a/debian/patches/compiler_errors.patch b/debian/patches/compiler_errors.patch
new file mode 100644
index 0000000..c680a62
--- /dev/null
+++ b/debian/patches/compiler_errors.patch
@@ -0,0 +1,26 @@
+Index: dindel-1.01+dfsg/StringHash.hpp
+===================================================================
+--- dindel-1.01+dfsg.orig/StringHash.hpp
++++ dindel-1.01+dfsg/StringHash.hpp
+@@ -32,7 +32,7 @@
+
+ struct my_hash_funct : public unary_function<string, size_t>
+ {
+- size_t operator()(const string & x) const { return hash<const char*>() (x.c_str()); }
++ size_t operator()(const string & x) const { return __gnu_cxx::hash<const char*>() (x.c_str()); }
+ };
+
+ template<class T> class string_hash : public hash_map<string, T, my_hash_funct> {};
+Index: dindel-1.01+dfsg/DInDel.cpp
+===================================================================
+--- dindel-1.01+dfsg.orig/DInDel.cpp
++++ dindel-1.01+dfsg/DInDel.cpp
+@@ -1566,7 +1566,7 @@
+ HDIterator2 hdi(hd, params.maxHap, pos, leftPos, rightPos, params.noIndelWindow);
+
+ double logNumHaps=hdi.getLogNumHaps();
+- if (logNumHaps>log(params.skipMaxHap)) {
++ if (logNumHaps>seqan::log(params.skipMaxHap)) {
+ cerr << "tid: " << params.tid << " pos: " << pos << " too many haplotypes [>exp(" << logNumHaps << ")]" << endl;
+ return true;
+ }
diff --git a/debian/patches/modernize-Makefile.patch b/debian/patches/modernize-Makefile.patch
new file mode 100644
index 0000000..be3c531
--- /dev/null
+++ b/debian/patches/modernize-Makefile.patch
@@ -0,0 +1,26 @@
+Index: dindel-1.01+dfsg/Makefile
+===================================================================
+--- dindel-1.01+dfsg.orig/Makefile
++++ dindel-1.01+dfsg/Makefile
+@@ -1,9 +1,9 @@
+-SAMTOOLDIR=/nfs/users/nfs_c/caa/source/samtools/
+-SEQANDIR=seqan_library/
++SAMTOOLDIR=/usr/include/samtools
++SEQANDIR=/usr/include/seqan
+
+ CPPFLAGS= -DNDEBUG -D_IOLIB=2 -DMINREADS=2 -DDINDEL
+ CXXFLAGS= -I$(SAMTOOLDIR) -I$(SEQANDIR) -I./ -Wno-deprecated -O3
+-LDFLAGS= -L$(SAMTOOLDIR) -lbam -lz -lboost_program_options -static
++LDFLAGS= -lbam -lz /usr/lib/x86_64-linux-gnu/libboost_program_options.so.1.55.0 -lpthread
+
+ SRCSDINDEL=DInDel.cpp HapBlock.cpp HaplotypeDistribution.cpp ObservationModelFB.cpp GetCandidates.cpp Faster.cpp
+ OBJSDINDEL=$(SRCSDINDEL:%.cpp=%.o)
+@@ -12,4 +12,7 @@
+ $(CXX) -o $@ $(CXXFLAGS) $(DINDELFLAGS) $(OBJSDINDEL) $(LDFLAGS)
+
+ clean:
+- rm -f $(OBJSDINDEL) $(OBJSCOMPAREVARIANTS) $(OBJSMAKEGLF)
++ rm -f $(OBJSDINDEL) $(OBJSCOMPAREVARIANTS) $(OBJSMAKEGLF) *.o
++
++distclean: clean
++ rm -f dindel
diff --git a/debian/patches/series b/debian/patches/series
new file mode 100644
index 0000000..a24c5c4
--- /dev/null
+++ b/debian/patches/series
@@ -0,0 +1,2 @@
+modernize-Makefile.patch
+compiler_errors.patch
diff --git a/debian/rules b/debian/rules
new file mode 100755
index 0000000..d003324
--- /dev/null
+++ b/debian/rules
@@ -0,0 +1,5 @@
+#!/usr/bin/make -f
+# -*- makefile -*-
+
+%:
+ dh $@
diff --git a/debian/source/format b/debian/source/format
new file mode 100644
index 0000000..163aaf8
--- /dev/null
+++ b/debian/source/format
@@ -0,0 +1 @@
+3.0 (quilt)
diff --git a/debian/upstream/edam b/debian/upstream/edam
new file mode 100644
index 0000000..ba2a509
--- /dev/null
+++ b/debian/upstream/edam
@@ -0,0 +1,13 @@
+ontology: EDAM (1.13)
+topic:
+ - DNA structural variation
+scopes:
+ - name: summary
+ function:
+ - Indel detection
+ inputs:
+ - data: Sequence alignment (nucleic acid)
+ formats: [BAM]
+ outputs:
+ - data: Sequence variations
+ formats: [VCF]
diff --git a/debian/upstream/metadata b/debian/upstream/metadata
new file mode 100644
index 0000000..15fd4d8
--- /dev/null
+++ b/debian/upstream/metadata
@@ -0,0 +1,17 @@
+Contact: Cornelis A. Albers
+Homepage: https://sites.google.com/site/keesalbers/soft/dindel
+Name: dindel
+Reference:
+ author: Cornelis A. Albers, Gerton Lunter, Daniel G. MacArthur, Gilean McVean, Willem H. Ouwehand, Richard Durbin
+ title:
+ Dindel: Accurate indel calls from short-read data
+ journal: Genome Research
+ volume: 21
+ number: 6
+ pages: 961-973
+ year: 2010
+ DOI: 10.1101/gr.112326.110
+ PMID: 20980555
+ URL: http://genome.cshlp.org/content/early/2010/10/25/gr.112326.110.abstract
+ eprint: http://genome.cshlp.org/content/early/2010/10/25/gr.112326.110.full.pdf+html
+ license: Open Access
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