[med-svn] [fastqtl] 04/04: Initial debian/*
Dylan Aïssi
bob.dybian-guest at moszumanska.debian.org
Mon May 2 21:52:57 UTC 2016
This is an automated email from the git hooks/post-receive script.
bob.dybian-guest pushed a commit to branch master
in repository fastqtl.
commit bf8a2e8eb13f316041018e3cdf1c1daf8179475c
Author: Dylan Aïssi <bob.dybian at gmail.com>
Date: Mon May 2 23:45:07 2016 +0200
Initial debian/*
---
debian/changelog | 5 +
debian/compat | 1 +
debian/control | 51 +++++
debian/copyright | 61 ++++++
debian/fastQTL.1 | 143 ++++++++++++++
debian/fastqtl-doc.doc-base | 9 +
debian/fastqtl-doc.install | 5 +
debian/fastqtl.install | 1 +
debian/fastqtl.lintian-overrides | 2 +
.../patches/01_Makefile_dynamic_hardenings.patch | 95 +++++++++
debian/patches/02_Replace_libtabix_by_libhts.patch | 216 +++++++++++++++++++++
debian/patches/series | 2 +
debian/rules | 21 ++
debian/source/format | 1 +
debian/tests/control | 2 +
debian/tests/output_tests/README | 17 ++
.../tests/output_tests/fastqtl_expected_output.log | 60 ++++++
.../tests/output_tests/fastqtl_expected_output.txt | 5 +
debian/tests/run-sample-analysis | 30 +++
debian/upstream/metadata | 10 +
debian/watch | 3 +
21 files changed, 740 insertions(+)
diff --git a/debian/changelog b/debian/changelog
new file mode 100644
index 0000000..36c70da
--- /dev/null
+++ b/debian/changelog
@@ -0,0 +1,5 @@
+fastqtl (2.184+dfsg-1) UNRELEASED; urgency=low
+
+ * Initial release. (Closes: #823115)
+
+ -- Dylan Aïssi <bob.dybian at gmail.com> Sat, 30 Apr 2016 23:21:54 +0200
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..39f6788
--- /dev/null
+++ b/debian/control
@@ -0,0 +1,51 @@
+Source: fastqtl
+Section: science
+Priority: optional
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Dylan Aïssi <bob.dybian at gmail.com>
+Build-Depends: debhelper (>= 9),
+ libboost-dev,
+ libboost-iostreams-dev,
+ libboost-program-options-dev,
+ libgsl0-dev,
+ r-mathlib,
+ zlib1g-dev,
+ libblas-dev,
+ libeigen3-dev,
+ libhts-dev
+Testsuite: autopkgtest
+Standards-Version: 3.9.8
+Vcs-Browser: https://anonscm.debian.org/git/debian-med/fastqtl.git
+Vcs-Git: https://anonscm.debian.org/git/debian-med/fastqtl.git
+Homepage: http://fastqtl.sourceforge.net/
+
+Package: fastqtl
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends}
+Suggests: fastqtl-doc
+Description: Quantitative Trait Loci (QTL) mapper in cis for molecular phenotypes
+ The goal of FastQTL is to identify single-nucleotide polymorphisms (SNPs)
+ which are significantly associated with various molecular phenotypes
+ (i.e. expression of known genes, cytosine methylation levels, etc).
+ It performs scans for all possible phenotype-variant pairs in cis
+ (i.e. variants located within a specific window around a phenotype).
+ FastQTL implements a new permutation scheme (Beta approximation) to accurately
+ and rapidly correct for multiple-testing at both the genotype and phenotype
+ levels.
+
+Package: fastqtl-doc
+Section: doc
+Architecture: all
+Depends: ${misc:Depends}
+Enhances: fastqtl
+Description: QTL mapper in cis for molecular phenotypes - documentation
+ The goal of FastQTL is to identify single-nucleotide polymorphisms (SNPs)
+ which are significantly associated with various molecular phenotypes
+ (i.e. expression of known genes, cytosine methylation levels, etc).
+ It performs scans for all possible phenotype-variant pairs in cis
+ (i.e. variants located within a specific window around a phenotype).
+ FastQTL implements a new permutation scheme (Beta approximation) to accurately
+ and rapidly correct for multiple-testing at both the genotype and phenotype
+ levels.
+ .
+ This package provides documentation and example data to work with FastQTL.
diff --git a/debian/copyright b/debian/copyright
new file mode 100644
index 0000000..6630d43
--- /dev/null
+++ b/debian/copyright
@@ -0,0 +1,61 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: FastQTL
+Upstream-Contact: Olivier Delaneau <olivier.delaneau at gmail.com>
+Source: http://fastqtl.sourceforge.net/
+Comment: Exclude embedded Eigen and Tabix, and some other stuff.
+Files-Excluded: bin
+ lib
+ obj
+ Makefile.static
+ .dropbox
+ .project
+
+Files: *
+Copyright: 2014-2015 Olivier Delaneau, Alfonso Buil and Emmanouil T. Dermitzakis
+License: GPL-3+
+
+Files: src/utils/tabix.*pp
+Copyright: 2011-2016 Erik Garrison <erik.garrison at gmail.com> (tabixpp software)
+ 2014-2015 Olivier Delaneau, Alfonso Buil and Emmanouil T. Dermitzakis
+License: Expat
+
+Files: debian/*
+Copyright: 2016 Dylan Aïssi <bob.dybian at gmail.com>
+License: GPL-3+
+
+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 package; if not, write to the Free Software
+ Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
+ .
+ On Debian systems, the full text of the GNU General Public License
+ version 3 can be found in `/usr/share/common-licenses/GPL-3'.
+
+License: Expat
+ Permission is hereby granted, free of charge, to any person obtaining a copy
+ of this software and associated documentation files (the "Software"), to deal
+ in the Software without restriction, including without limitation the rights
+ to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+ copies of the Software, and to permit persons to whom the Software is
+ furnished to do so, subject to the following conditions:
+ .
+ The above copyright notice and this permission notice shall be included in
+ all copies or substantial portions of the Software.
+ .
+ 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 AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+ AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+ LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+ OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+ THE SOFTWARE.
diff --git a/debian/fastQTL.1 b/debian/fastQTL.1
new file mode 100644
index 0000000..02811e1
--- /dev/null
+++ b/debian/fastQTL.1
@@ -0,0 +1,143 @@
+.\"
+.TH FastQTL "1" "March 2016" "2.184"
+.SH NAME
+FastQTL \- Quantitative Trait Loci (QTL) mapper in cis for molecular phenotypes
+.SH SYNOPSIS
+.B fastQTL [\fIoptions\fR]
+.SH DESCRIPTION
+The goal of FastQTL is to identify single-nucleotide polymorphisms (SNPs)
+which are significantly associated with various molecular phenotypes
+(i.e. expression of known genes, cytosine methylation levels, etc).
+It performs scans for all possible phenotype-variant pairs in cis
+(i.e. variants located within a specific window around a phenotype).
+FastQTL implements a new permutation scheme (Beta approximation) to accurately
+and rapidly correct for multiple-testing at both the genotype and phenotype
+levels.
+.SH OPTIONS
+.SS Basic options
+.TP
+\fB\-\-help\fR
+.br
+Print help about options.
+.TP
+\fB\-\-silent\fR
+Silent mode on terminal.
+.TP
+\fB\-\-seed\fR arg (=1459232241)
+Random number generator seed.
+Useful to replicate runs of the software.
+
+.SS Input and Output files options
+.TP
+\fB\-L, \-\-log\fR
+Screen output is copied in this file.
+.TP
+\fB\-V, \-\-vcf\fR
+Genotypes in VCF format.
+.TP
+\fB\-B, \-\-bed\fR
+Phenotypes in BED format.
+.TP
+\fB\-C, \-\-cov\fR
+Covariates in TXT format.
+.TP
+\fB\-G, \-\-grp\fR
+Phenotype groups in TXT format.
+.TP
+\fB\-O, \-\-out\fR
+Output file.
+
+.SS Exclusion and Inclusion files options
+.TP
+\fB\-\-exclude\-samples\fR
+List of samples to exclude.
+.TP
+\fB\-\-include\-samples\fR
+List of samples to include.
+.TP
+\fB\-\-exclude\-sites\fR
+List of sites to exclude.
+.TP
+\fB\-\-include\-sites\fR
+List of sites to include.
+.TP
+\fB\-\-exclude\-phenotypes\fR
+List of phenotypes to exclude.
+.TP
+\fB\-\-include\-phenotypes\fR
+List of phenotypes to include.
+.TP
+\fB\-\-exclude\-covariates\fR
+List of covariates to exclude.
+.TP
+\fB\-\-include\-covariates\fR
+List of covariates to include.
+
+.SS Parameters
+.TP
+\fB\-\-normal\fR
+To perform quantile normalization on the phenotype quantifications to make them normally distributed.
+Implemented as the rntransform function of the GenABEL package.
+
+.TP
+\fB\-W, \-\-window\fR
+Cis-window size.
+Default values is 1Mb (1e6).
+It means that all variants within 1e6 bp of the phenotype location (e.g. TSS) is analyzed.
+.TP
+\fB\-T, \-\-threshold\fR
+To filter out all phenotype-variant pairs with a p-value above the specified threshold in the output of a nominal pass.
+
+.SS Modes
+.TP
+\fB\-P, \-\-permute\fR
+Permutation pass to calculate corrected p-values for molecular phenotypes.
+.TP
+\fB\-\-psequence\fR
+Permutation sequence.
+.TP
+\fB\-\-map\fR
+Map best QTL candidates per molecular phenotype.
+.TP
+\fB\-\-map\-full\fR
+Scan full cis-window to discover independent signals.
+.TP
+\fB\-\-interaction\fR
+Test for interactions with variable specified in file.
+
+.SS Parallelization
+.TP
+\fB\-K, \-\-chunk\fR
+Specify which chunk needs to be processed.
+.TP
+\fB\-\-commands\fR
+Generates all commands.
+.TP
+\fB\-R, \-\-region\fR
+Region of interest.
+
+.SH EXAMPLE
+for c in $(seq 1 256); do
+.br
+ \fBfastQTL\fR \fB--vcf\fR genotypes.vcf.gz
+.br
+ \fB--bed\fR phenotypes.bed.gz
+.br
+ \fB--chunk\fR $c 256
+.br
+ \fB--permute\fR 1000
+.br
+ \fB--out\fR results.$c\.txt.gz
+.br
+done
+.br
+zcat results.*.txt.gz | gzip -c > fastqtl_expected_output.txt.gz
+.br
+
+.SH SEE ALSO
+.BR http://fastqtl.sourceforge.net/
+.SH AUTHOR
+FastQTL was written by Olivier Delaneau, Halit Ongen, Alfonso Buil and Manolis Dermitzakis.
+.PP
+This manual page was written by Dylan Aïssi <bob.dybian at gmail.com>,
+for the Debian project (but may be used by others).
diff --git a/debian/fastqtl-doc.doc-base b/debian/fastqtl-doc.doc-base
new file mode 100644
index 0000000..8442d9c
--- /dev/null
+++ b/debian/fastqtl-doc.doc-base
@@ -0,0 +1,9 @@
+Document: fastqtl
+Title: FastQTL
+Author: Olivier Delaneau <olivier.delaneau at gmail.com>
+Abstract: Description of FastQTL
+Section: Science/Biology
+
+Format: HTML
+Index: /usr/share/doc/fastqtl/doc/index.html
+Files: /usr/share/doc/fastqtl/doc/*
diff --git a/debian/fastqtl-doc.install b/debian/fastqtl-doc.install
new file mode 100644
index 0000000..e18b35c
--- /dev/null
+++ b/debian/fastqtl-doc.install
@@ -0,0 +1,5 @@
+README usr/share/doc/fastqtl/
+doc/* usr/share/doc/fastqtl/doc/
+example/examples.tar.xz usr/share/doc/fastqtl/examples/
+debian/tests/run-sample-analysis /usr/share/doc/fastqtl/examples/
+debian/tests/output_tests/* /usr/share/doc/fastqtl/examples/
diff --git a/debian/fastqtl.install b/debian/fastqtl.install
new file mode 100644
index 0000000..404a511
--- /dev/null
+++ b/debian/fastqtl.install
@@ -0,0 +1 @@
+bin/fastQTL usr/bin/
diff --git a/debian/fastqtl.lintian-overrides b/debian/fastqtl.lintian-overrides
new file mode 100644
index 0000000..e6e1027
--- /dev/null
+++ b/debian/fastqtl.lintian-overrides
@@ -0,0 +1,2 @@
+# This warning comes from libeigen3-dev (See https://bugs.debian.org/813233 )
+fastqtl: spelling-error-in-binary
\ No newline at end of file
diff --git a/debian/patches/01_Makefile_dynamic_hardenings.patch b/debian/patches/01_Makefile_dynamic_hardenings.patch
new file mode 100644
index 0000000..439697d
--- /dev/null
+++ b/debian/patches/01_Makefile_dynamic_hardenings.patch
@@ -0,0 +1,95 @@
+Author: Dylan Aïssi <bob.dybian at gmail.com>
+Description: Patch the makefile in order to use a full dynamic linking and to activate hardenings.
+Last-Update: 2016-04-30
+Forwarded: TODO
+
+--- a/Makefile
++++ b/Makefile
+@@ -1,13 +1,27 @@
+-#PLEASE SPECIFY THE R path here where you built the R math library standalone
+-RMATH=~/Software/R-3.1.3/src
++#!/usr/bin/make -f
++
++# Define DYNAMIC_LINK to compile using full dynamic linking
++DYNAMIC_LINK = 1
++
++ifndef DYNAMIC_LINK
++ #PLEASE SPECIFY THE R path here where you built the R math library standalone
++ RMATH=~/Software/R-3.1.3/src
++else
++ RMATH=
++endif
+
+ #compiler
+ CXX=g++
+
+ #internal paths
+ VPATH=$(shell for file in `find src -name *.cpp`; do echo $$(dirname $$file); done)
+-PATH_TABX=lib/Tabix
+-PATH_EIGN=lib/Eigen
++ifndef DYNAMIC_LINK
++ PATH_TABX=lib/Tabix
++ PATH_EIGN=lib/Eigen
++else
++ PATH_TABX=
++ PATH_EIGN=
++endif
+
+ #compiler flags
+ CXXFLAG_OPTI=-O3 -D_FAST_CORRELATION
+@@ -21,15 +35,25 @@
+ LDFLAG_MACX=-mmacosx-version-min=10.7 -stdlib=libc++
+
+ #includes
+-INC_BASE=-Isrc -I$(PATH_TABX) -I$(PATH_EIGN)
+-INC_MATH=-I$(RMATH)/include/
++ifndef DYNAMIC_LINK
++ INC_BASE=-Isrc -I$(PATH_TABX) -I$(PATH_EIGN)
++ INC_MATH=-I$(RMATH)/include/
++else
++ INC_BASE=-Isrc
++ INC_MATH=
++endif
+ INC_MACX=-I/usr/local/include/
+
+ #libraries
+ #LIB_BASE=-lm -lboost_iostreams -lboost_program_options -lz -lgsl -lblas
+ LIB_BASE=-lm -lz -lboost_iostreams -lboost_program_options -lgsl -lblas
+-LIB_MATH=$(RMATH)/nmath/standalone/libRmath.a
+-LIB_TABX=$(PATH_TABX)/libtabix.a
++ifndef DYNAMIC_LINK
++ LIB_MATH=$(RMATH)/nmath/standalone/libRmath.a
++ LIB_TABX=$(PATH_TABX)/libtabix.a
++else
++ LIB_MATH=-lRmath
++ LIB_TABX=-ltabix
++endif
+ LIB_MACX=-L/usr/local/lib/
+
+ #files (binary, objects, headers & sources)
+@@ -42,10 +66,10 @@
+ all: linux
+
+ #linux release
+-linux: CXXFLAG=$(CXXFLAG_OPTI) $(CXXFLAG_WARN)
++linux: CXXFLAG=$(CXXFLAG_OPTI) $(CXXFLAG_WARN) $(CXXFLAGS) $(CPPFLAGS)
+ linux: IFLAG=$(INC_BASE) $(INC_MATH)
+ linux: LIB=$(LIB_MATH) $(LIB_TABX) $(LIB_BASE)
+-linux: LDFLAG=$(LDFLAG_OPTI)
++linux: LDFLAG=$(LDFLAG_OPTI) $(LDFLAGS)
+ linux: $(FILE_BIN)
+
+ #macos release
+--- a/src/residualizer.h
++++ b/src/residualizer.h
+@@ -17,8 +17,8 @@
+ #ifndef _RESIDUALIZER_H
+ #define _RESIDUALIZER_H
+
+-#include <Dense>
+-#include <LU>
++#include <eigen3/Eigen/Dense>
++#include <eigen3/Eigen/LU>
+ #include "utils/utils.h"
+
+ using namespace Eigen;
diff --git a/debian/patches/02_Replace_libtabix_by_libhts.patch b/debian/patches/02_Replace_libtabix_by_libhts.patch
new file mode 100644
index 0000000..14c0bf2
--- /dev/null
+++ b/debian/patches/02_Replace_libtabix_by_libhts.patch
@@ -0,0 +1,216 @@
+Author: Dylan Aïssi <bob.dybian at gmail.com>
+Description: Merge src/utils/tabix.*pp with upstream (libtabixpp 1.0.0) in order to use libhts instead libtabix.
+Last-Update: 2016-04-29
+Forwarded: No
+
+
+--- a/Makefile
++++ b/Makefile
+@@ -52,7 +52,7 @@
+ LIB_TABX=$(PATH_TABX)/libtabix.a
+ else
+ LIB_MATH=-lRmath
+- LIB_TABX=-ltabix
++ LIB_TABX=-lhts
+ endif
+ LIB_MACX=-L/usr/local/lib/
+
+--- a/src/utils/tabix.cpp
++++ b/src/utils/tabix.cpp
+@@ -8,6 +8,7 @@
+ Tabix::Tabix(void) { }
+
+ Tabix::Tabix(string& file) {
++ has_jumped = false;
+ filename = file;
+ const char* cfilename = file.c_str();
+ struct stat stat_tbi,stat_vcf;
+@@ -30,78 +31,99 @@
+ }
+ free(fnidx);
+
+- if ((t = ti_open(cfilename, 0)) == 0) {
++ if ((fn = hts_open(cfilename, "r")) == 0) {
+ cerr << "[tabix++] fail to open the data file." << endl;
+ exit(1);
+ }
+
+- if (ti_lazy_index_load(t) < 0) {
++ if ((tbx = tbx_index_load(cfilename)) == NULL) {
+ cerr << "[tabix++] failed to load the index file." << endl;
+ exit(1);
+ }
+
+- idxconf = ti_get_conf(t->idx);
++ int nseq;
++ const char** seq = tbx_seqnames(tbx, &nseq);
++ for (int i=0; i<nseq; i++) {
++ chroms.push_back(seq[i]);
++ }
++ free(seq);
++
++ idxconf = &tbx_conf_vcf;
+
+ // set up the iterator, defaults to the beginning
+- iter = ti_query(t, 0, 0, 0);
++ current_chrom = chroms.begin();
++ iter = tbx_itr_querys(tbx, current_chrom->c_str());
+
+ }
+
+ Tabix::~Tabix(void) {
+- ti_iter_destroy(iter);
+- ti_close(t);
++ tbx_itr_destroy(iter);
++ tbx_destroy(tbx);
+ }
+
+ void Tabix::getHeader(string& header) {
+ header.clear();
+- ti_iter_destroy(iter);
+- iter = ti_query(t, 0, 0, 0);
+- const char* s;
+- int len;
+- while ((s = ti_read(t, iter, &len)) != 0) {
+- if ((int)(*s) != idxconf->meta_char) {
+- firstline = string(s); // stash this line
++ kstring_t str = {0,0,0};
++ while ( hts_getline(fn, KS_SEP_LINE, &str) >= 0 ) {
++ if ( !str.l || str.s[0]!=tbx->conf.meta_char ) {
+ break;
+ } else {
+- header += string(s);
++ header += string(str.s);
+ header += "\n";
+ }
+ }
++ // set back to start
++ current_chrom = chroms.begin();
++ if (iter) tbx_itr_destroy(iter);
++ iter = tbx_itr_querys(tbx, current_chrom->c_str());
+ }
+
+ void Tabix::getLastHeader(string & header) {
+- header.clear();
+- ti_iter_destroy(iter);
+- iter = ti_query(t, 0, 0, 0);
+- const char* s;
+- int len;
+- while ((s = ti_read(t, iter, &len)) != 0) {
+- if ((int)(*s) != idxconf->meta_char) {
+- firstline = string(s); // stash this line
+- break;
+- } else header = string(s);
+- }
++ header.clear();
++ kstring_t str = {0,0,0};
++ while ( hts_getline(fn, KS_SEP_LINE, &str) >= 0 ) {
++ if ( !str.l || str.s[0]!=tbx->conf.meta_char ) {
++ break;
++ } else header = string(str.s);
++ }
++ // set back to start
++ current_chrom = chroms.begin();
++ if (iter) tbx_itr_destroy(iter);
++ iter = tbx_itr_querys(tbx, current_chrom->c_str());
+ }
+
+ bool Tabix::setRegion(string region) {
+- if (ti_parse_region(t->idx, region.c_str(), &tid, &beg, &end) == 0) {
+- firstline.clear();
+- ti_iter_destroy(iter);
+- iter = ti_queryi(t, tid, beg, end);
+- return true;
+- } else return false;
++ tbx_itr_destroy(iter);
++ iter = tbx_itr_querys(tbx, region.c_str());
++ has_jumped = true;
++ return true;
+ }
+
+ bool Tabix::getNextLine(string & line) {
+- const char* s;
+- int len;
+- if (!firstline.empty()) {
+- line = firstline; // recovers line read if header is parsed
+- firstline.clear();
+- return true;
+- }
+- if ((s = ti_read(t, iter, &len)) != 0) {
+- line = string(s);
+- return true;
+- } else return false;
++ kstring_t str = {0,0,0};
++ if (has_jumped) {
++ if (iter && tbx_itr_next(fn, tbx, iter, &str) >= 0) {
++ line = string(str.s);
++ return true;
++ } else return false;
++ } else { // step through all sequences in the file
++ // we've never jumped, so read everything
++ if (iter && tbx_itr_next(fn, tbx, iter, &str) >= 0) {
++ line = string(str.s);
++ return true;
++ } else {
++ ++current_chrom;
++ while (current_chrom != chroms.end()) {
++ tbx_itr_destroy(iter);
++ iter = tbx_itr_querys(tbx, current_chrom->c_str());
++ if (iter && tbx_itr_next(fn, tbx, iter, &str) >= 0) {
++ line = string(str.s);
++ return true;
++ } else {
++ ++current_chrom;
++ }
++ }
++ return false;
++ }
++ }
+ }
+--- a/src/utils/tabix.hpp
++++ b/src/utils/tabix.hpp
+@@ -9,24 +9,31 @@
+ #include <string>
+ #include <stdlib.h>
+ #include <sys/stat.h>
+-#include <bgzf.h>
+-#include <tabix.h>
++#include <htslib/bgzf.h>
++#include <htslib/tbx.h>
++#include <htslib/kseq.h>
+ #include <iostream>
++#include <cstring>
++#include <vector>
+
+
+ using namespace std;
+
+ class Tabix {
+
+- tabix_t *t;
+- ti_iter_t iter;
+- const ti_conf_t *idxconf;
++ htsFile* fn;
++ tbx_t* tbx;
++ hts_itr_t* iter;
++ const tbx_conf_t *idxconf;
+ int tid, beg, end;
+ string firstline;
++ bool has_jumped;
++ vector<string>::iterator current_chrom;
+
+ public:
+
+ string filename;
++ vector<string> chroms;
+
+ Tabix(void);
+ Tabix(string& file);
+@@ -36,6 +43,7 @@
+ void getLastHeader(string & header);
+ bool setRegion(string region);
+ bool getNextLine(string& line);
++
+ };
+
+ #endif
diff --git a/debian/patches/series b/debian/patches/series
new file mode 100644
index 0000000..cb0fd3c
--- /dev/null
+++ b/debian/patches/series
@@ -0,0 +1,2 @@
+01_Makefile_dynamic_hardenings.patch
+02_Replace_libtabix_by_libhts.patch
diff --git a/debian/rules b/debian/rules
new file mode 100755
index 0000000..b1b0686
--- /dev/null
+++ b/debian/rules
@@ -0,0 +1,21 @@
+#!/usr/bin/make -f
+
+# Don't override the upstream FLAG -O3
+CXXFLAGS:=$(shell dpkg-buildflags --get CXXFLAGS 2>/dev/null | sed -e 's/-O2//g')
+
+%:
+ dh $@
+
+override_dh_auto_build:
+ mkdir -p $(CURDIR)/obj/
+ mkdir -p $(CURDIR)/bin/
+ $(MAKE) CXXFLAGS='$(CXXFLAGS)'
+ cd $(CURDIR)/example/ && \
+ tar Jcvf examples.tar.xz *
+
+override_dh_installman:
+ dh_installman debian/fastQTL.1
+
+get-orig-source:
+ uscan --verbose --force-download --repack --compress xz
+
diff --git a/debian/source/format b/debian/source/format
new file mode 100644
index 0000000..46ebe02
--- /dev/null
+++ b/debian/source/format
@@ -0,0 +1 @@
+3.0 (quilt)
\ No newline at end of file
diff --git a/debian/tests/control b/debian/tests/control
new file mode 100644
index 0000000..3403f8a
--- /dev/null
+++ b/debian/tests/control
@@ -0,0 +1,2 @@
+Tests: run-sample-analysis
+Depends: @
diff --git a/debian/tests/output_tests/README b/debian/tests/output_tests/README
new file mode 100644
index 0000000..6ad7c39
--- /dev/null
+++ b/debian/tests/output_tests/README
@@ -0,0 +1,17 @@
+#!/bin/sh -e
+# Output files (i.e. fastqtl_expected_output.txt and fastqtl_expected_output.log) were generated following:
+
+wget http://fastqtl.sourceforge.net/files/FastQTL-2.184.linux.tgz
+tar -zxvf FastQTL-2.184.linux.tgz
+
+./FastQTL/bin/fastQTL.static \
+ --vcf ./FastQTL/example/genotypes.vcf.gz \
+ --bed ./FastQTL/example/phenotypes.bed.gz \
+ --cov ./FastQTL/example/covariates.txt.gz \
+ --interaction ./FastQTL/example/interaction.txt \
+ --chunk 1 100 \
+ --permute 100 \
+ --seed 1 \
+ --out fastqtl_expected_output.txt \
+ --log fastqtl_expected_output.log
+
diff --git a/debian/tests/output_tests/fastqtl_expected_output.log b/debian/tests/output_tests/fastqtl_expected_output.log
new file mode 100644
index 0000000..516aedb
--- /dev/null
+++ b/debian/tests/output_tests/fastqtl_expected_output.log
@@ -0,0 +1,60 @@
+
+Perform permutation based interaction analysis (used to calculate corrected p-values for MPs)
+ * Perform 100 permutations
+ * Test interaction with term from [./FastQTL/example/interaction.txt]
+ * Random number generator is seeded with 1
+ * Considering variants within 1e+06 bp of the MPs
+ * Chunk processed 1 / 100
+
+Scanning phenotype data in [./FastQTL/example/phenotypes.bed.gz]
+ * 364 phenotypes
+
+Reading phenotype data in [./FastQTL/example/phenotypes.bed.gz]
+ * region = 22:17517460-17739125
+ * 373 samples included
+ * 5 phenotypes included
+
+Reading genotype data in [./FastQTL/example/genotypes.vcf.gz] in VCF format
+ * region = 22:16517460-18739125
+ * 373 samples included
+ * 8684 sites included
+
+Reading covariates in [./FastQTL/example/covariates.txt.gz]
+ * 373 samples included
+ * 4 covariate(s) included
+
+Reading interaction term in [./FastQTL/example/interaction.txt]
+ * 373 samples included
+
+Imputing missing genotypes
+
+Imputing missing phenotypes
+
+Initialize covariate
+
+Processing gene [ENSG00000237438.1]
+ * Number of variants in cis = 7966
+ * Beta distribution parameters = 1.0382 2287.7101
+ * Progress = 20.0%
+
+Processing gene [ENSG00000177663.8]
+ * Number of variants in cis = 8165
+ * Beta distribution parameters = 0.7994 2826.0721
+ * Progress = 40.0%
+
+Processing gene [ENSG00000183307.3]
+ * Number of variants in cis = 8279
+ * Beta distribution parameters = 0.9595 9906.5566
+ * Progress = 60.0%
+
+Processing gene [ENSG00000069998.8]
+ * Number of variants in cis = 8466
+ * Beta distribution parameters = 0.9606 4564.2130
+ * Progress = 80.0%
+
+Processing gene [ENSG00000093072.10]
+ * Number of variants in cis = 8531
+ * Beta distribution parameters = 1.0645 1772.4331
+ * Progress = 100.0%
+
+Running time: 162 seconds
diff --git a/debian/tests/output_tests/fastqtl_expected_output.txt b/debian/tests/output_tests/fastqtl_expected_output.txt
new file mode 100644
index 0000000..1c6c843
--- /dev/null
+++ b/debian/tests/output_tests/fastqtl_expected_output.txt
@@ -0,0 +1,5 @@
+ENSG00000237438.1 7966 1.03823 2287.71 352.293 indel:1I_22_17834337 316877 1.89696e-05 0.0693069 0.0519815
+ENSG00000177663.8 8165 0.799377 2826.07 380.167 snp_22_17389156 -176688 6.27191e-05 0.178218 0.192496
+ENSG00000183307.3 8279 0.959492 9906.56 432.588 snp_22_17336410 -265847 0.000868799 0.940594 0.949806
+ENSG00000069998.8 8466 0.960617 4564.21 389.88 snp_22_18023838 377661 8.54998e-05 0.227723 0.216574
+ENSG00000093072.10 8531 1.06453 1772.43 334.203 snp_22_17738177 -948 0.000356058 0.683168 0.649116
diff --git a/debian/tests/run-sample-analysis b/debian/tests/run-sample-analysis
new file mode 100755
index 0000000..5403e7d
--- /dev/null
+++ b/debian/tests/run-sample-analysis
@@ -0,0 +1,30 @@
+#!/bin/sh -e
+# http://dep.debian.net/deps/dep8/
+# Autopkgtest: Test if fastqtl run analysis correctly
+# Author: Dylan Aïssi <bob.dybian at gmail.com>
+# Last-Update: 2016-04-02
+
+pkg=fastqtl
+if [ "$ADTTMP" = "" ] ; then
+ ADTTMP=`mktemp -d /tmp/${pkg}-test.XXXXXX`
+fi
+cd $ADTTMP
+cp -a /usr/share/doc/${pkg}/examples/* $ADTTMP
+
+tar Jxvf $ADTTMP/examples.tar.xz
+
+fastQTL \
+ --vcf genotypes.vcf.gz \
+ --bed phenotypes.bed.gz \
+ --cov covariates.txt.gz \
+ --interaction interaction.txt \
+ --chunk 1 100 \
+ --permute 100 \
+ --seed 1 \
+ --out fastqtl_output.txt \
+ --log fastqtl_output.log
+
+diff fastqtl_expected_output.txt fastqtl_output.txt
+
+rm -f $ADTTMP/*
+
diff --git a/debian/upstream/metadata b/debian/upstream/metadata
new file mode 100644
index 0000000..1c3d170
--- /dev/null
+++ b/debian/upstream/metadata
@@ -0,0 +1,10 @@
+Contact: Olivier Delaneau <olivier.delaneau at gmail.com>
+Name: FastQTL
+Reference:
+ - Author: Halit Ongen and Alfonso Buil and Andrew Anand Brown and Emmanouil T. Dermitzakis and and Olivier Delaneau
+ Title: "Fast and efficient QTL mapper for thousands of molecular phenotypes"
+ Journal: Bioinformatics
+ Year: 2015
+ DOI: 10.1093/bioinformatics/btv722
+ URL: https://bioinformatics.oxfordjournals.org/content/early/2016/02/19/bioinformatics.btv722
+ eprint: https://bioinformatics.oxfordjournals.org/content/early/2016/02/19/bioinformatics.btv722.full.pdf+html
diff --git a/debian/watch b/debian/watch
new file mode 100644
index 0000000..599d74a
--- /dev/null
+++ b/debian/watch
@@ -0,0 +1,3 @@
+version=3
+opts="repacksuffix=+dfsg,dversionmangle=s/\+dfsg//g" \
+ http://fastqtl.sourceforge.net/pages/install.html http://fastqtl.sourceforge.net/files/FastQTL-(\d\S*).linux\.tgz
--
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