Import daligner_1.0+git20221215.bd26967-1.debian.tar.xz

[dgit import tarball daligner 1.0+git20221215.bd26967-1 daligner_1.0+git20221215.bd26967-1.debian.tar.xz]

22 files changed, 585 insertions, 0 deletions

diff --git a/README.source b/README.source
new file mode 100644
index 0000000..82fcd43
--- /dev/null
+++ b/README.source
@@ -0,0 +1,10 @@
+daligner for Debian
+===================
+
+Please note:
+
+  The files DB.[ch] and QV.[ch] are identical code copies from
+  dazzdb package.  It would make sense to create a real library
+  package from dazzdb and re-use the code here
+
+ -- Andreas Tille <tille@debian.org>  Tue, 28 Jan 2020 08:37:57 +0100
diff --git a/README.test b/README.test
new file mode 100644
index 0000000..b936868
--- /dev/null
+++ b/README.test
@@ -0,0 +1,9 @@
+Notes on how this package can be tested.
+────────────────────────────────────────
+
+This package can be tested by running the provided test:
+
+    sudo apt install dazzdb
+    sh run-unit-test
+
+in order to confirm its integrity.
diff --git a/changelog b/changelog
new file mode 100644
index 0000000..84a5049
--- /dev/null
+++ b/changelog
@@ -0,0 +1,146 @@
+daligner (1.0+git20221215.bd26967-1) unstable; urgency=medium
+
+  * New upstream version
+  * Standards-Version: 4.6.2 (routine-update)
+
+ -- Andreas Tille <tille@debian.org>  Mon, 06 Feb 2023 11:01:05 +0100
+
+daligner (1.0+git20210330.f61b8cf-1) unstable; urgency=medium
+
+  * New upstream version
+  * Standards-Version: 4.6.1 (routine-update)
+  * cppflags.patch: added to fortify hardened functions.
+  * typos.patch: added to fix typos caught by lintian.
+  * d/u/metadata: add repository information.
+  * d/control: add myself to uploaders.
+
+ -- Étienne Mollier <emollier@debian.org>  Wed, 03 Aug 2022 16:35:57 +0200
+
+daligner (1.0+git20200727.ed40ce5-3) unstable; urgency=medium
+
+  [ Helmut Grohne ]
+  * Do not hard code gcc
+    Closes: #968434
+
+ -- Andreas Tille <tille@debian.org>  Sat, 15 Aug 2020 21:39:59 +0200
+
+daligner (1.0+git20200727.ed40ce5-2) unstable; urgency=medium
+
+  * Team upload.
+  * added autopkgtests
+  * Install docs
+
+ -- Shruti Sridhar <shruti.sridhar99@gmail.com>  Wed, 12 Aug 2020 22:52:11 +0200
+
+daligner (1.0+git20200727.ed40ce5-1) unstable; urgency=medium
+
+  * Team upload.
+  * New upstream version
+
+ -- Steffen Moeller <moeller@debian.org>  Mon, 10 Aug 2020 16:01:48 +0200
+
+daligner (1.0+git20200608.c18a2fb-1) unstable; urgency=medium
+
+  * Team upload.
+  * New upstream version
+  * debhelper-compat 13 (routine-update)
+  * Add salsa-ci file (routine-update)
+  * Rules-Requires-Root: no (routine-update)
+  * Set upstream metadata fields: Bug-Database, Bug-Submit.
+
+ -- Steffen Moeller <moeller@debian.org>  Sat, 13 Jun 2020 15:37:29 +0200
+
+daligner (1.0+git20200115.c2b47da-1) unstable; urgency=medium
+
+  * New upstream version
+  * Afif removed himself from Uploaders
+  * Add myself to Uploaders
+  * New upstream version
+  * debhelper-compat 12
+  * Standards-Version: 4.5.0 (routine-update)
+  * debian/README.source: Document code copy from dazzdb
+
+ -- Andreas Tille <tille@debian.org>  Tue, 28 Jan 2020 09:32:56 +0100
+
+daligner (1.0+git20180524.fd21879-1) unstable; urgency=medium
+
+  * Team upload.
+
+  [ Jelmer Vernooij ]
+  * Use secure copyright file specification URI.
+
+  [ Andreas Tille ]
+  * New upstream commit
+  * debhelper 11
+  * Point Vcs fields to salsa.debian.org
+  * Standards-Version: 4.2.1
+  * Remove trailing whitespace in debian/copyright
+  * hardening=+all
+
+ -- Andreas Tille <tille@debian.org>  Sun, 28 Oct 2018 08:34:03 +0100
+
+daligner (1.0+20180108-1) unstable; urgency=medium
+
+  * New upstream snapshot (git 233274a)
+  * Bump Standards-Version to 4.1.3
+  * Bump copyright years
+
+ -- Afif Elghraoui <afif@debian.org>  Sun, 04 Feb 2018 05:26:26 -0500
+
+daligner (1.0+20171010-2) unstable; urgency=low
+
+  [ Steffen Moeller ]
+  * [debian/upstream/metadata] Reference to OMICtools added.
+
+ -- Afif Elghraoui <afif@debian.org>  Thu, 19 Oct 2017 23:42:51 -0400
+
+daligner (1.0+20171010-1) unstable; urgency=medium
+
+  * New upstream snapshot (git b966696)
+  * Bump Standards Version to 4.1.1
+  * Bump copyright years
+
+ -- Afif Elghraoui <afif@debian.org>  Thu, 19 Oct 2017 23:18:52 -0400
+
+daligner (1.0+20161119-1) unstable; urgency=medium
+
+  * New upstream snapshot (git a9458dc)
+
+ -- Afif Elghraoui <afif@debian.org>  Wed, 18 Jan 2017 22:16:19 -0800
+
+daligner (1.0+20160927-2) unstable; urgency=low
+
+  * Use LDLIBS rather than LDFLAGS.
+    Thanks to Logan Rosen (Closes: #849431)
+  * Suggest dascrubber
+  * d/rules: Don't combine CPPFLAGS with CFLAGS
+  * Use debhelper compat 10
+
+ -- Afif Elghraoui <afif@debian.org>  Tue, 27 Dec 2016 13:03:16 -0800
+
+daligner (1.0+20160927-1) unstable; urgency=medium
+
+  * Imported Upstream version 1.0+20160927 (git ca167d3)
+  * Update patches
+  * Refer to upstream README for command reference
+  * Update Standards-Version
+  * Use encrypted protocols for VCS URLs
+  * Update email address and copyright years
+
+ -- Afif Elghraoui <afif@debian.org>  Tue, 11 Oct 2016 21:12:16 -0700
+
+daligner (1.0+20151214-1) unstable; urgency=medium
+
+  * New upstream revision (git2923450)
+  * Add manpages for new executables
+  * Stylistic consistency in packaging
+  * Refresh/adjust patches
+  * Suggest dazzdb
+
+ -- Afif Elghraoui <afif@ghraoui.name>  Fri, 08 Jan 2016 22:55:34 -0800
+
+daligner (1.0-1) unstable; urgency=low
+
+  * Initial release (Closes: #797352)
+
+ -- Afif Elghraoui <afif@ghraoui.name>  Sat, 29 Aug 2015 13:25:02 -0700
diff --git a/control b/control
new file mode 100644
index 0000000..b2867f7
--- /dev/null
+++ b/control
@@ -0,0 +1,24 @@
+Source: daligner
+Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+Uploaders: Andreas Tille <tille@debian.org>,
+           Étienne Mollier <emollier@debian.org>
+Section: science
+Priority: optional
+Build-Depends: debhelper-compat (= 13)
+Standards-Version: 4.6.2
+Vcs-Browser: https://salsa.debian.org/med-team/daligner
+Vcs-Git: https://salsa.debian.org/med-team/daligner.git
+Homepage: https://dazzlerblog.wordpress.com
+Rules-Requires-Root: no
+
+Package: daligner
+Architecture: any
+Depends: ${shlibs:Depends},
+         ${misc:Depends}
+Suggests: dazzdb,
+          dascrubber
+Description: local alignment discovery between long nucleotide sequencing reads
+ These tools permit one to find all significant local alignments between
+ reads encoded in a Dazzler database. The assumption is that the reads are
+ from a Pacific Biosciences RS II long read sequencer. That is, the reads
+ are long and noisy, up to 15% on average.
diff --git a/copyright b/copyright
new file mode 100644
index 0000000..f050988
--- /dev/null
+++ b/copyright
@@ -0,0 +1,36 @@
+Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: daligner
+Upstream-Contact: Eugene W. Myers, Jr. <gene.myers@gmail.com>
+Source: http://github.com/thegenemyers/DALIGNER
+
+Files: *
+Copyright: 2013-2018 Eugene W. Myers, Jr. <gene.myers@gmail.com>
+License: BSD-3-Clause~EWM
+
+Files: debian/*
+Copyright: 2015-2018 Afif Elghraoui <afif@debian.org>
+License: BSD-3-Clause~EWM
+
+License: BSD-3-Clause~EWM
+ Redistribution and use in source and binary forms, with or without modification,
+ are permitted provided that the following conditions are met:
+ .
+  · Redistributions of source code must retain the above copyright notice, this
+    list of conditions and the following disclaimer.
+ .
+  · Redistributions in binary form must reproduce the above copyright notice, this
+    list of conditions and the following disclaimer in the documentation and/or
+    other materials provided with the distribution.
+ .
+  · The name of EWM may not be used to endorse or promote products derived from
+    this software without specific prior written permission.
+ .
+ THIS SOFTWARE IS PROVIDED BY EWM ”AS IS” AND ANY EXPRESS OR IMPLIED WARRANTIES,
+ INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND
+ FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL EWM BE LIABLE
+ FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
+ (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS
+ OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
+ THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
+ NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN
+ IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
diff --git a/docs b/docs
new file mode 100644
index 0000000..06e0915
--- /dev/null
+++ b/docs
@@ -0,0 +1,3 @@
+README.md
+debian/README.*
+debian/tests/run-unit-test
diff --git a/man/daligner.1 b/man/daligner.1
new file mode 100644
index 0000000..2ab3eb8
--- /dev/null
+++ b/man/daligner.1
@@ -0,0 +1,12 @@
+.TH DALIGNER 1 "October 2016"
+.SH NAME
+daligner \- local alignment discovery between long nucleotide sequencing reads
+.SH SYNOPSIS
+.B daligner
+.RI [ options ] " files" ...
+.SH DESCRIPTION
+These tools permit one to find all significant local alignments between reads encoded in a Dazzler database.
+The assumption is that the reads are from a Pacific Biosciences RS II long read sequencer.
+That is, the reads are long and noisy, up to 15% on average.
+.SH OPTIONS
+For a complete description of available commands and their options, see /usr/share/doc/daligner/README.md
diff --git a/manpages b/manpages
new file mode 100644
index 0000000..13cdaf4
--- /dev/null
+++ b/manpages
@@ -0,0 +1 @@
+debian/man/*.1
diff --git a/patches/cflags.patch b/patches/cflags.patch
new file mode 100644
index 0000000..1d640ea
--- /dev/null
+++ b/patches/cflags.patch
@@ -0,0 +1,15 @@
+Description: Append to CFLAGS
+Author: Afif Elghraoui <afif@ghraoui.name>
+Forwarded: not-needed
+Last-Update: 2016-01-08
+--- a/Makefile
++++ b/Makefile
+@@ -3,7 +3,7 @@ DEST_DIR = ~/bin
+ # CFLAGS = -O0 -g -Wall -Wextra -Wno-unused-result -fno-strict-aliasing -fsanitize=address -fsanitize=undefined
+ # Above is for debug out of bound addresses, must compile with -lASAN -lUBSAN if gcc instead of clang
+ 
+-CFLAGS = -O3 -Wall -Wextra -Wno-unused-result -fno-strict-aliasing
++CFLAGS += -O3 -Wall -Wextra -Wno-unused-result -fno-strict-aliasing
+ 
+ ALL = daligner HPC.daligner LAsort LAmerge LAsplit LAcat LAshow LA2ONE LAcheck ONE2LA
+ 
diff --git a/patches/cppflags.patch b/patches/cppflags.patch
new file mode 100644
index 0000000..8a14c18
--- /dev/null
+++ b/patches/cppflags.patch
@@ -0,0 +1,54 @@
+Description: apply CPPFLAGS too.
+ Among other things, it enables fortifying sources.
+Author: Étienne Mollier <emollier@debian.org>
+Forwarded: not-needed
+Last-Update: 2022-08-03
+---
+This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
+--- a/Makefile
++++ b/Makefile
+@@ -10,34 +10,34 @@ ALL = daligner HPC.daligner LAsort LAmer
+ all: $(ALL)
+ 
+ daligner: daligner.c filter.c filter.h lsd.sort.c lsd.sort.h align.c align.h DB.c DB.h QV.c QV.h
+-	$(CC) $(CFLAGS) -o daligner daligner.c filter.c lsd.sort.c align.c DB.c QV.c -lpthread -lm $(LDFLAGS)
++	$(CC) $(CPPFLAGS) $(CFLAGS) -o daligner daligner.c filter.c lsd.sort.c align.c DB.c QV.c -lpthread -lm $(LDFLAGS)
+ 
+ HPC.daligner: HPC.daligner.c DB.c DB.h QV.c QV.h
+-	$(CC) $(CFLAGS) -o HPC.daligner HPC.daligner.c DB.c QV.c -lm $(LDFLAGS)
++	$(CC) $(CPPFLAGS) $(CFLAGS) -o HPC.daligner HPC.daligner.c DB.c QV.c -lm $(LDFLAGS)
+ 
+ LAsort: LAsort.c align.h DB.c DB.h QV.c QV.h
+-	$(CC) $(CFLAGS) -o LAsort LAsort.c DB.c QV.c -lm $(LDFLAGS)
++	$(CC) $(CPPFLAGS) $(CFLAGS) -o LAsort LAsort.c DB.c QV.c -lm $(LDFLAGS)
+ 
+ LAmerge: LAmerge.c align.h DB.c DB.h QV.c QV.h
+-	$(CC) $(CFLAGS) -o LAmerge LAmerge.c DB.c QV.c -lm $(LDFLAGS)
++	$(CC) $(CPPFLAGS) $(CFLAGS) -o LAmerge LAmerge.c DB.c QV.c -lm $(LDFLAGS)
+ 
+ LAshow: LAshow.c align.c align.h DB.c DB.h QV.c QV.h
+-	$(CC) $(CFLAGS) -o LAshow LAshow.c align.c DB.c QV.c -lm $(LDFLAGS)
++	$(CC) $(CPPFLAGS) $(CFLAGS) -o LAshow LAshow.c align.c DB.c QV.c -lm $(LDFLAGS)
+ 
+ LA2ONE: LA2ONE.c align.c align.h DB.c DB.h QV.c QV.h ONElib.c ONElib.h
+-	$(CC) $(CFLAGS) -o LA2ONE LA2ONE.c align.c DB.c QV.c ONElib.c -lm $(LDFLAGS)
++	$(CC) $(CPPFLAGS) $(CFLAGS) -o LA2ONE LA2ONE.c align.c DB.c QV.c ONElib.c -lm $(LDFLAGS)
+ 
+ LAcat: LAcat.c align.h DB.c DB.h QV.c QV.h
+-	$(CC) $(CFLAGS) -o LAcat LAcat.c DB.c QV.c -lm $(LDFLAGS)
++	$(CC) $(CPPFLAGS) $(CFLAGS) -o LAcat LAcat.c DB.c QV.c -lm $(LDFLAGS)
+ 
+ LAsplit: LAsplit.c align.h DB.c DB.h QV.c QV.h
+-	$(CC) $(CFLAGS) -o LAsplit LAsplit.c DB.c QV.c -lm $(LDFLAGS)
++	$(CC) $(CPPFLAGS) $(CFLAGS) -o LAsplit LAsplit.c DB.c QV.c -lm $(LDFLAGS)
+ 
+ LAcheck: LAcheck.c align.c align.h DB.c DB.h QV.c QV.h
+-	$(CC) $(CFLAGS) -o LAcheck LAcheck.c align.c DB.c QV.c -lm $(LDFLAGS)
++	$(CC) $(CPPFLAGS) $(CFLAGS) -o LAcheck LAcheck.c align.c DB.c QV.c -lm $(LDFLAGS)
+ 
+ ONE2LA: ONE2LA.c align.c align.h DB.c DB.h QV.c QV.h ONElib.c ONElib.h
+-	$(CC) $(CFLAGS) -o ONE2LA ONE2LA.c align.c DB.c QV.c ONElib.c -lm $(LDFLAGS)
++	$(CC) $(CPPFLAGS) $(CFLAGS) -o ONE2LA ONE2LA.c align.c DB.c QV.c ONElib.c -lm $(LDFLAGS)
+ 
+ clean:
+ 	rm -f $(ALL)
diff --git a/patches/cross.patch b/patches/cross.patch
new file mode 100644
index 0000000..0b4babc
--- /dev/null
+++ b/patches/cross.patch
@@ -0,0 +1,52 @@
+Date: Sat, 15 Aug 2020 07:24:26 +0200
+From: Helmut Grohne <helmut@subdivi.de>
+Description: Do not hard code gcc
+Bug-Debian: https://bugs.debian.org/968434
+
+--- a/Makefile
++++ b/Makefile
+@@ -10,34 +10,34 @@ ALL = daligner HPC.daligner LAsort LAmer
+ all: $(ALL)
+ 
+ daligner: daligner.c filter.c filter.h lsd.sort.c lsd.sort.h align.c align.h DB.c DB.h QV.c QV.h
+-	gcc $(CFLAGS) -o daligner daligner.c filter.c lsd.sort.c align.c DB.c QV.c -lpthread -lm $(LDFLAGS)
++	$(CC) $(CFLAGS) -o daligner daligner.c filter.c lsd.sort.c align.c DB.c QV.c -lpthread -lm $(LDFLAGS)
+ 
+ HPC.daligner: HPC.daligner.c DB.c DB.h QV.c QV.h
+-	gcc $(CFLAGS) -o HPC.daligner HPC.daligner.c DB.c QV.c -lm $(LDFLAGS)
++	$(CC) $(CFLAGS) -o HPC.daligner HPC.daligner.c DB.c QV.c -lm $(LDFLAGS)
+ 
+ LAsort: LAsort.c align.h DB.c DB.h QV.c QV.h
+-	gcc $(CFLAGS) -o LAsort LAsort.c DB.c QV.c -lm $(LDFLAGS)
++	$(CC) $(CFLAGS) -o LAsort LAsort.c DB.c QV.c -lm $(LDFLAGS)
+ 
+ LAmerge: LAmerge.c align.h DB.c DB.h QV.c QV.h
+-	gcc $(CFLAGS) -o LAmerge LAmerge.c DB.c QV.c -lm $(LDFLAGS)
++	$(CC) $(CFLAGS) -o LAmerge LAmerge.c DB.c QV.c -lm $(LDFLAGS)
+ 
+ LAshow: LAshow.c align.c align.h DB.c DB.h QV.c QV.h
+-	gcc $(CFLAGS) -o LAshow LAshow.c align.c DB.c QV.c -lm $(LDFLAGS)
++	$(CC) $(CFLAGS) -o LAshow LAshow.c align.c DB.c QV.c -lm $(LDFLAGS)
+ 
+ LA2ONE: LA2ONE.c align.c align.h DB.c DB.h QV.c QV.h ONElib.c ONElib.h
+-	gcc $(CFLAGS) -o LA2ONE LA2ONE.c align.c DB.c QV.c ONElib.c -lm $(LDFLAGS)
++	$(CC) $(CFLAGS) -o LA2ONE LA2ONE.c align.c DB.c QV.c ONElib.c -lm $(LDFLAGS)
+ 
+ LAcat: LAcat.c align.h DB.c DB.h QV.c QV.h
+-	gcc $(CFLAGS) -o LAcat LAcat.c DB.c QV.c -lm $(LDFLAGS)
++	$(CC) $(CFLAGS) -o LAcat LAcat.c DB.c QV.c -lm $(LDFLAGS)
+ 
+ LAsplit: LAsplit.c align.h DB.c DB.h QV.c QV.h
+-	gcc $(CFLAGS) -o LAsplit LAsplit.c DB.c QV.c -lm $(LDFLAGS)
++	$(CC) $(CFLAGS) -o LAsplit LAsplit.c DB.c QV.c -lm $(LDFLAGS)
+ 
+ LAcheck: LAcheck.c align.c align.h DB.c DB.h QV.c QV.h
+-	gcc $(CFLAGS) -o LAcheck LAcheck.c align.c DB.c QV.c -lm $(LDFLAGS)
++	$(CC) $(CFLAGS) -o LAcheck LAcheck.c align.c DB.c QV.c -lm $(LDFLAGS)
+ 
+ ONE2LA: ONE2LA.c align.c align.h DB.c DB.h QV.c QV.h ONElib.c ONElib.h
+-	gcc $(CFLAGS) -o ONE2LA ONE2LA.c align.c DB.c QV.c ONElib.c -lm $(LDFLAGS)
++	$(CC) $(CFLAGS) -o ONE2LA ONE2LA.c align.c DB.c QV.c ONElib.c -lm $(LDFLAGS)
+ 
+ clean:
+ 	rm -f $(ALL)
diff --git a/patches/destdir-install.patch b/patches/destdir-install.patch
new file mode 100644
index 0000000..48e60f8
--- /dev/null
+++ b/patches/destdir-install.patch
@@ -0,0 +1,16 @@
+Description: Use DESTDIR during installation
+Author: Afif Elghraoui <afif@ghraoui.name>
+Forwarded: not-needed
+Last-Update: 2016-01-08
+--- a/Makefile
++++ b/Makefile
+@@ -45,7 +45,8 @@ clean:
+ 	rm -f daligner.tar.gz
+ 
+ install:
+-	cp $(ALL) $(DEST_DIR)
++	install -d $(DESTDIR)/usr/bin
++	install $(ALL) $(DESTDIR)/usr/bin
+ 
+ package:
+ 	make clean
diff --git a/patches/lddflags.patch b/patches/lddflags.patch
new file mode 100644
index 0000000..d4f5a52
--- /dev/null
+++ b/patches/lddflags.patch
@@ -0,0 +1,54 @@
+Description: Support LDFLAGS in upstream build system
+ This patch was made using the following command:
+   sed -i 's/\(gcc.*\)/\1 \$(LDFLAGS)/' Makefile
+Author: Afif Elghraoui <afif@ghraoui.name>
+Forwarded: not-needed
+Last-Update: 2016-01-08
+
+--- a/Makefile
++++ b/Makefile
+@@ -10,34 +10,34 @@ ALL = daligner HPC.daligner LAsort LAmer
+ all: $(ALL)
+ 
+ daligner: daligner.c filter.c filter.h lsd.sort.c lsd.sort.h align.c align.h DB.c DB.h QV.c QV.h
+-	gcc $(CFLAGS) -o daligner daligner.c filter.c lsd.sort.c align.c DB.c QV.c -lpthread -lm
++	gcc $(CFLAGS) -o daligner daligner.c filter.c lsd.sort.c align.c DB.c QV.c -lpthread -lm $(LDFLAGS)
+ 
+ HPC.daligner: HPC.daligner.c DB.c DB.h QV.c QV.h
+-	gcc $(CFLAGS) -o HPC.daligner HPC.daligner.c DB.c QV.c -lm
++	gcc $(CFLAGS) -o HPC.daligner HPC.daligner.c DB.c QV.c -lm $(LDFLAGS)
+ 
+ LAsort: LAsort.c align.h DB.c DB.h QV.c QV.h
+-	gcc $(CFLAGS) -o LAsort LAsort.c DB.c QV.c -lm
++	gcc $(CFLAGS) -o LAsort LAsort.c DB.c QV.c -lm $(LDFLAGS)
+ 
+ LAmerge: LAmerge.c align.h DB.c DB.h QV.c QV.h
+-	gcc $(CFLAGS) -o LAmerge LAmerge.c DB.c QV.c -lm
++	gcc $(CFLAGS) -o LAmerge LAmerge.c DB.c QV.c -lm $(LDFLAGS)
+ 
+ LAshow: LAshow.c align.c align.h DB.c DB.h QV.c QV.h
+-	gcc $(CFLAGS) -o LAshow LAshow.c align.c DB.c QV.c -lm
++	gcc $(CFLAGS) -o LAshow LAshow.c align.c DB.c QV.c -lm $(LDFLAGS)
+ 
+ LA2ONE: LA2ONE.c align.c align.h DB.c DB.h QV.c QV.h ONElib.c ONElib.h
+-	gcc $(CFLAGS) -o LA2ONE LA2ONE.c align.c DB.c QV.c ONElib.c -lm
++	gcc $(CFLAGS) -o LA2ONE LA2ONE.c align.c DB.c QV.c ONElib.c -lm $(LDFLAGS)
+ 
+ LAcat: LAcat.c align.h DB.c DB.h QV.c QV.h
+-	gcc $(CFLAGS) -o LAcat LAcat.c DB.c QV.c -lm
++	gcc $(CFLAGS) -o LAcat LAcat.c DB.c QV.c -lm $(LDFLAGS)
+ 
+ LAsplit: LAsplit.c align.h DB.c DB.h QV.c QV.h
+-	gcc $(CFLAGS) -o LAsplit LAsplit.c DB.c QV.c -lm
++	gcc $(CFLAGS) -o LAsplit LAsplit.c DB.c QV.c -lm $(LDFLAGS)
+ 
+ LAcheck: LAcheck.c align.c align.h DB.c DB.h QV.c QV.h
+-	gcc $(CFLAGS) -o LAcheck LAcheck.c align.c DB.c QV.c -lm
++	gcc $(CFLAGS) -o LAcheck LAcheck.c align.c DB.c QV.c -lm $(LDFLAGS)
+ 
+ ONE2LA: ONE2LA.c align.c align.h DB.c DB.h QV.c QV.h ONElib.c ONElib.h
+-	gcc $(CFLAGS) -o ONE2LA ONE2LA.c align.c DB.c QV.c ONElib.c -lm
++	gcc $(CFLAGS) -o ONE2LA ONE2LA.c align.c DB.c QV.c ONElib.c -lm $(LDFLAGS)
+ 
+ clean:
+ 	rm -f $(ALL)
diff --git a/patches/series b/patches/series
new file mode 100644
index 0000000..cfd0cec
--- /dev/null
+++ b/patches/series
@@ -0,0 +1,6 @@
+cflags.patch
+lddflags.patch
+destdir-install.patch
+cross.patch
+cppflags.patch
+typos.patch
diff --git a/patches/typos.patch b/patches/typos.patch
new file mode 100644
index 0000000..93fc1b7
--- /dev/null
+++ b/patches/typos.patch
@@ -0,0 +1,59 @@
+Description: fix a couple of typos caught by lintian.
+Author: Étienne Mollier <emollier@debian.org>
+Forwarded: no
+Last-Update: 2022-08-03
+---
+This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
+--- daligner.orig/DB.c
++++ daligner/DB.c
+@@ -2208,7 +2208,7 @@
+     }
+   if (accum != extra->accum)
+     { EPRINTF(EPLACE,
+-           "%s: Reduction indicator of extra %s does not agree with previos .anno block files\n",
++           "%s: Reduction indicator of extra %s does not agree with previous .anno block files\n",
+            Prog_Name,name);
+       goto error;
+     }
+@@ -2829,7 +2829,7 @@
+     first = last = -1;
+   else
+     { if (index(ppnt+1,BLOCK_SYMBOL) != NULL)
+-        { EPRINTF(EPLACE,"%s: Two or more occurences of %c-sign in source name '%s'\n",
++        { EPRINTF(EPLACE,"%s: Two or more occurrences of %c-sign in source name '%s'\n",
+                          Prog_Name,BLOCK_SYMBOL,root);
+           goto error;
+         }
+--- daligner.orig/LAsplit.c
++++ daligner/LAsplit.c
+@@ -105,7 +105,7 @@
+       exit (1);
+     }
+   if (index(root2+1,BLOCK_SYMBOL) != NULL)
+-    { fprintf(stderr,"%s: Two or more occurences of %c-sign in source name '%s'\n",
++    { fprintf(stderr,"%s: Two or more occurrences of %c-sign in source name '%s'\n",
+                      Prog_Name,BLOCK_SYMBOL,root);
+       exit (1);
+     }
+--- daligner.orig/lsd.sort.c
++++ daligner/lsd.sort.c
+@@ -55,7 +55,7 @@
+     int64  thresh[256];   //  If check then multiple of LEX_zdiv to check for thread assignment
+     int64  tptr[256];     //  Finger for each 8-bit value
+     int64 *sptr;          //  Conceptually [256][NTHREADS].  At end of sorting pass
+-  } Lex_Arg;              //    sprtr[b][n] = # of occurences of value b in rangd of
++  } Lex_Arg;              //    sprtr[b][n] = # of occurrences of value b in rangd of
+                           //    thread n for the *next* pass
+ 
+ //  Threaded sorting pass
+--- daligner.orig/daligner.c
++++ daligner/daligner.c
+@@ -531,7 +531,7 @@
+             ARG_POSITIVE(HIT_MIN,"Hit threshold (in bp.s)")
+             break;
+           case 't':
+-            ARG_POSITIVE(MAX_REPS,"Tuple supression frequency")
++            ARG_POSITIVE(MAX_REPS,"Tuple suppression frequency")
+             break;
+           case 'H':
+             ARG_POSITIVE(HGAP_MIN,"HGAP threshold (in bp.s)")
diff --git a/rules b/rules
new file mode 100755
index 0000000..080b3d0
--- /dev/null
+++ b/rules
@@ -0,0 +1,21 @@
+#!/usr/bin/make -f
+
+#DH_VERBOSE = 1
+include /usr/share/dpkg/default.mk
+
+export DEB_BUILD_MAINT_OPTIONS=hardening=+all
+
+%:
+	dh $@
+
+override_dh_auto_install:
+	dh_auto_install
+	mkdir -p $(CURDIR)/debian/$(DEB_SOURCE)/usr/share/man/man1
+	for command in $(CURDIR)/debian/$(DEB_SOURCE)/usr/bin/*; \
+	do \
+		if [ $$(basename $$command) != daligner ] ; \
+		then \
+			ln -s daligner.1 \
+			$(CURDIR)/debian/$(DEB_SOURCE)/usr/share/man/man1/$$(basename $$command).1 ; \
+		fi; \
+	done
diff --git a/salsa-ci.yml b/salsa-ci.yml
new file mode 100644
index 0000000..33c3a64
--- /dev/null
+++ b/salsa-ci.yml
@@ -0,0 +1,4 @@
+---
+include:
+  - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/salsa-ci.yml
+  - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/pipeline-jobs.yml
diff --git a/source/format b/source/format
new file mode 100644
index 0000000..163aaf8
--- /dev/null
+++ b/source/format
@@ -0,0 +1 @@
+3.0 (quilt)
diff --git a/tests/control b/tests/control
new file mode 100644
index 0000000..bedafb6
--- /dev/null
+++ b/tests/control
@@ -0,0 +1,3 @@
+Tests: run-unit-test
+Depends: @, dazzdb
+Restrictions: allow-stderr
diff --git a/tests/run-unit-test b/tests/run-unit-test
new file mode 100644
index 0000000..463e336
--- /dev/null
+++ b/tests/run-unit-test
@@ -0,0 +1,29 @@
+#!/bin/bash
+set -e
+
+pkg=daligner
+
+export LC_ALL=C.UTF-8
+if [ "${AUTOPKGTEST_TMP}" = "" ] ; then
+  AUTOPKGTEST_TMP=$(mktemp -d /tmp/${pkg}-test.XXXXXX)
+  trap "rm -rf ${AUTOPKGTEST_TMP}" 0 INT QUIT ABRT PIPE TERM
+fi
+
+cd "${AUTOPKGTEST_TMP}"
+
+rangen 1.0 -r2020 >R.fasta           
+fasta2DAM R R.fasta           
+dsimulator R -c20. -r2020 >G.fasta   
+fasta2DB G G.fasta            
+rm G.fasta                    
+DBsplit -s11 G                
+DBdust G.1                    
+DBdust G.2                
+DBstats -mdust G              
+cat G.db
+
+HPC.daligner -mdust -t5 G | sh -v
+LAshow -c G -w50 G.1 | head
+
+# Since the output is not consistent.
+#It cannot be compared with the reference. 
diff --git a/upstream/metadata b/upstream/metadata
new file mode 100644
index 0000000..4d55e0e
--- /dev/null
+++ b/upstream/metadata
@@ -0,0 +1,23 @@
+Bug-Database: https://github.com/thegenemyers/DALIGNER/issues
+Bug-Submit: https://github.com/thegenemyers/DALIGNER/issues/new
+Reference:
+  Author: Gene Myers
+  Title: Efficient Local Alignment Discovery amongst Noisy Long Reads
+  Booktitle: Algorithms in Bioinformatics
+  ISSN: 0302-9743
+  Year: 2014
+  Volume: 8701
+  Pages: 52-67
+  DOI: 10.1007/978-3-662-44753-6_5
+  URL: http://link.springer.com/chapter/10.1007%2F978-3-662-44753-6_5
+Registry:
+  - Name: OMICtools
+    Entry: OMICS_08897
+  - Name: bio.tools
+    Entry: NA
+  - Name: SciCrunch
+    Entry: SCR_016066
+  - Name: conda:bioconda
+    Entry: daligner
+Repository: https://github.com/thegenemyers/DALIGNER.git
+Repository-Browse: https://github.com/thegenemyers/DALIGNER
diff --git a/watch b/watch
new file mode 100644
index 0000000..3698f95
--- /dev/null
+++ b/watch
@@ -0,0 +1,7 @@
+version=4
+
+opts="mode=git,pretty=1.0+git%cd.%h" \
+    https://github.com/thegenemyers/DALIGNER.git HEAD
+
+#opts="filenamemangle=s/(?:.*)?v?(\d[\d\.]*)\.tar\.gz/daligner-$1.tar.gz/" \
+#    https://github.com/thegenemyers/DALIGNER/tags (?:.*/)?[vV]?(\d[\d\.]*)\.tar\.gz