.gitignore

-Makefile.in
-aclocal.m4
-autom4te.cache
-config.h.in
-configure
-depcomp
-install-sh
-missing
-compile
-config.guess
-config.h.in~
-config.sub
-ltmain.sh
-*_cmdline.hpp
-test-driver

.gitmod

-develop

.travis.yml

-language: cpp
-before_install:
-  - mkdir -p ~/bin
-  - curl -L -o ~/bin/yaggo https://github.com/gmarcais/yaggo/releases/download/v1.5.9/yaggo
-  - chmod a+rx ~/bin/yaggo
-script: autoreconf -i && ./configure YAGGO=~/bin/yaggo && make && make check
-addons:
-  artifacts:
-    paths:
-      - $(git ls-files -o | grep '\.log$' | tr "\n" ":")
-  s3_region: "us-east-1"

CHANGES

-Version 1.1
-===========
-
-* Read input from pipes. For example, to count DNA from zipped files, run:
-
-% gunzip -c *.fa.gz | jellyfish [options] /dev/fd/0
-
-* Support fasta and fastq formats.
-
-* Support for counting 'q-mers', as defined by the Quake error
-  correcting software (http://www.cbcb.umd.edu/software/quake/).
-
-* New dump subcommands which replaces 'stats -f' and 'stats -c'.

HalfLICENSE

-Copyright (c) 2006, Industrial Light & Magic, a division of Lucasfilm
-Entertainment Company Ltd.  Portions contributed and copyright held by
-others as indicated.  All rights reserved.
-
-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.
-
-    * Neither the name of Industrial Light & Magic nor the names of
-      any other contributors to this software may be used to endorse or
-      promote products derived from this software without specific prior
-      written permission.
-
-THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "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 THE COPYRIGHT OWNER OR
-CONTRIBUTORS 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.
-

Makefile.simple

-# This Makefile is meant to be run in the traget directories. There
-# name start with a '_' by convention and contain a config.h.
-
-CC = g++
-CPPFLAGS = -Wall -Werror -g -O2 -D__STDC_CONSTANT_MACROS -D__STDC_FORMAT_MACROS -I.
-# Uncomment following to use SSE
-# CPPFLAGS += -msse -msse2 -DSSE
-LDFLAGS = -lpthread
-TARGETS = jellyfish 
-# old TARGETS = mer_counter dump_stats dump_stats_compacted hash_merge
-SOURCES = $(patsubst %,%.cc,$(TARGETS)) mer_count_thread.cc
-
-.SECONDARY:
-
-#VPATH=..:../lib
-
-%.d: %.cc
-	$(CC) -M -MM -MG -MP $(CPPFLAGS) $< > $@.tmp
-	sed -e 's/$*.o/& $@/g' $@.tmp > $@ && rm $@.tmp
-
-all: $(TARGETS)
-
-jellyfish: dump_stats_compacted.o square_binary_matrix.o hash_merge.o storage.o misc.o mer_count_thread.o mer_counter.o
-
-# compare_dump3: compare_dump3.o
-# dump_stats_compacted: dump_stats_compacted.o square_binary_matrix.o
-total_mers_single_fasta: total_mers_single_fasta.o
-mer_counter_C: mer_counter_C.o
-
-# hash_merge: hash_merge.o storage.o misc.o
-# mer_counter: mer_counter.o mer_count_thread.o storage.o misc.o
-# dump_mers: dump_mers.o storage.o misc.o
-dump_stats: dump_stats.o storage.o misc.o
-
-clean:
-	rm -f $(TARGETS) *.o *.d
-
-# Is the following OK? Shouldn't we include more than that?
-include $(SOURCES:.cc=.d)
--include local.mk

README.md

-Jellyfish
-=========
-
-Overview
---------
-
-Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA. A k-mer is a substring of length k, and counting the occurrences of all such substrings is a central step in many analyses of DNA sequence. Jellyfish can count k-mers using an order of magnitude less memory and an order of magnitude faster than other k-mer counting packages by using an efficient encoding of a hash table and by exploiting the "compare-and-swap" CPU instruction to increase parallelism.
-
-JELLYFISH is a command-line program that reads FASTA and multi-FASTA files containing DNA sequences. It outputs its k-mer counts in a binary format, which can be translated into a human-readable text format using the "jellyfish dump" command, or queried for specific k-mers with "jellyfish query". See the UserGuide provided on [Jellyfish's home page][1] for more details.
-
-If you use Jellyfish in your research, please cite:
-
-  Guillaume Marcais and Carl Kingsford, A fast, lock-free approach for efficient parallel counting of occurrences of k-mers. Bioinformatics (2011) 27(6): 764-770 ([first published online January 7, 2011](http://bioinformatics.oxfordjournals.org/cgi/content/abstract/27/6/764 "Paper on Oxford Bioinformatics website")) doi:10.1093/bioinformatics/btr011
-
-Installation
-------------
-
-To get an easier to compiled packaged tar ball of the source code, download a release from the [github release][3]. You need make and g++ version 4.4 or higher. To install in your home directory, do:
-
-```Shell
-./configure --prefix=$HOME
-make -j 4
-make install
-```
-
-To compile from the git tree, you will also need autoconf/automake, and [yaggo](https://github.com/gmarcais/yaggo/releases "Yaggo release on github"). Then to compile and install (in `/usr/local` in that example) with:
-
-```Shell
-autoreconf -i
-./configure
-make -j 4
-sudo make install
-```
-
-If the software is installed in system directories (hint: you needed to use `sudo` to install), like the example above, then the system library cache must be updated like such:
-
-```Shell
-sudo ldconfig
-```
-
-Extra / Examples
-----------------
-
-In the examples directory are potentially useful extra programs to query/manipulates output files of Jellyfish, using the shared library of Jellyfish in C++ or with scripting languages. The examples are not compiled by default. Each subdirectory of examples is independent and is compiled with a simple invocation of 'make'.
-
-
-Binding to script languages
----------------------------
-
-Bindings to Ruby, Python and Perl are provided. This binding allows to read the output file of Jellyfish directly in a scripting language. Compilation of the bindings is easier from the [release tarball][3]. The development files of the target scripting language are required.
-
-Compilation of the bindings from the git tree requires [SWIG][2] version 3 and adding the switch `--enable-swig` to the configure command lines show below.
-
-To compile all three bindings, configure and compile with:
-
-```Shell
-./configure --enable-ruby-binding --enable-python-binding --enable-perl-binding
-make -j 4
-sudo make install
-```
-
-By default, Jellyfish is installed in `/usr/local` and the bindings are installed in the proper system location. When the `--prefix` switch is passed, the bindings are installed in the given directory. For example:
-
-```Shell
-./configure --prefix=$HOME --enable-python-binding
-make -j 4
-make install
-```
-
-This will install the python binding in `$HOME/lib/python2.7/site-packages` (adjust based on your Python version).
-
-Then, for Python, Ruby or Perl to find the binding, an environment variable may need to be adjusted (`PYTHONPATH`, `RUBYLIB` and `PERL5LIB` respectively). For example:
-
-```Shell
-export PYTHONPATH=$HOME/lib/python2.7/site-packages
-```
-
-See the [swig directory](../../tree/master/swig) for examples on how to use the bindings.
-
-[1]: http://www.genome.umd.edu/jellyfish.html "Genome group at University of Maryland"
-[2]: http://www.swig.org/
-[3]: https://github.com/gmarcais/Jellyfish/releases "Jellyfish release"

compile

+#! /bin/sh
+# Wrapper for compilers which do not understand '-c -o'.
+
+scriptversion=2016-01-11.22; # UTC
+
+# Copyright (C) 1999-2017 Free Software Foundation, Inc.
+# Written by Tom Tromey <tromey@cygnus.com>.
+#
+# This program 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 2, or (at your option)
+# any later version.
+#
+# This program 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/>.
+
+# As a special exception to the GNU General Public License, if you
+# distribute this file as part of a program that contains a
+# configuration script generated by Autoconf, you may include it under
+# the same distribution terms that you use for the rest of that program.
+
+# This file is maintained in Automake, please report
+# bugs to <bug-automake@gnu.org> or send patches to
+# <automake-patches@gnu.org>.
+
+nl='
+'
+
+# We need space, tab and new line, in precisely that order.  Quoting is
+# there to prevent tools from complaining about whitespace usage.
+IFS=" ""	$nl"
+
+file_conv=
+
+# func_file_conv build_file lazy
+# Convert a $build file to $host form and store it in $file
+# Currently only supports Windows hosts. If the determined conversion
+# type is listed in (the comma separated) LAZY, no conversion will
+# take place.
+func_file_conv ()
+{
+  file=$1
+  case $file in
+    / | /[!/]*) # absolute file, and not a UNC file
+      if test -z "$file_conv"; then
+	# lazily determine how to convert abs files
+	case `uname -s` in
+	  MINGW*)
+	    file_conv=mingw
+	    ;;
+	  CYGWIN*)
+	    file_conv=cygwin
+	    ;;
+	  *)
+	    file_conv=wine
+	    ;;
+	esac
+      fi
+      case $file_conv/,$2, in
+	*,$file_conv,*)
+	  ;;
+	mingw/*)
+	  file=`cmd //C echo "$file " | sed -e 's/"\(.*\) " *$/\1/'`
+	  ;;
+	cygwin/*)
+	  file=`cygpath -m "$file" || echo "$file"`
+	  ;;
+	wine/*)
+	  file=`winepath -w "$file" || echo "$file"`
+	  ;;
+      esac
+      ;;
+  esac
+}
+
+# func_cl_dashL linkdir
+# Make cl look for libraries in LINKDIR
+func_cl_dashL ()
+{
+  func_file_conv "$1"
+  if test -z "$lib_path"; then
+    lib_path=$file
+  else
+    lib_path="$lib_path;$file"
+  fi
+  linker_opts="$linker_opts -LIBPATH:$file"
+}
+
+# func_cl_dashl library
+# Do a library search-path lookup for cl
+func_cl_dashl ()
+{
+  lib=$1
+  found=no
+  save_IFS=$IFS
+  IFS=';'
+  for dir in $lib_path $LIB
+  do
+    IFS=$save_IFS
+    if $shared && test -f "$dir/$lib.dll.lib"; then
+      found=yes
+      lib=$dir/$lib.dll.lib
+      break
+    fi
+    if test -f "$dir/$lib.lib"; then
+      found=yes
+      lib=$dir/$lib.lib
+      break
+    fi
+    if test -f "$dir/lib$lib.a"; then
+      found=yes
+      lib=$dir/lib$lib.a
+      break
+    fi
+  done
+  IFS=$save_IFS
+
+  if test "$found" != yes; then
+    lib=$lib.lib
+  fi
+}
+
+# func_cl_wrapper cl arg...
+# Adjust compile command to suit cl
+func_cl_wrapper ()
+{
+  # Assume a capable shell
+  lib_path=
+  shared=:
+  linker_opts=
+  for arg
+  do
+    if test -n "$eat"; then
+      eat=
+    else
+      case $1 in
+	-o)
+	  # configure might choose to run compile as 'compile cc -o foo foo.c'.
+	  eat=1
+	  case $2 in
+	    *.o | *.[oO][bB][jJ])
+	      func_file_conv "$2"
+	      set x "$@" -Fo"$file"
+	      shift
+	      ;;
+	    *)
+	      func_file_conv "$2"
+	      set x "$@" -Fe"$file"
+	      shift
+	      ;;
+	  esac
+	  ;;
+	-I)
+	  eat=1
+	  func_file_conv "$2" mingw
+	  set x "$@" -I"$file"
+	  shift
+	  ;;
+	-I*)
+	  func_file_conv "${1#-I}" mingw
+	  set x "$@" -I"$file"
+	  shift
+	  ;;
+	-l)
+	  eat=1
+	  func_cl_dashl "$2"
+	  set x "$@" "$lib"
+	  shift
+	  ;;
+	-l*)
+	  func_cl_dashl "${1#-l}"
+	  set x "$@" "$lib"
+	  shift
+	  ;;
+	-L)
+	  eat=1
+	  func_cl_dashL "$2"
+	  ;;
+	-L*)
+	  func_cl_dashL "${1#-L}"
+	  ;;
+	-static)
+	  shared=false
+	  ;;
+	-Wl,*)
+	  arg=${1#-Wl,}
+	  save_ifs="$IFS"; IFS=','
+	  for flag in $arg; do
+	    IFS="$save_ifs"
+	    linker_opts="$linker_opts $flag"
+	  done
+	  IFS="$save_ifs"
+	  ;;
+	-Xlinker)
+	  eat=1
+	  linker_opts="$linker_opts $2"
+	  ;;
+	-*)
+	  set x "$@" "$1"
+	  shift
+	  ;;
+	*.cc | *.CC | *.cxx | *.CXX | *.[cC]++)
+	  func_file_conv "$1"
+	  set x "$@" -Tp"$file"
+	  shift
+	  ;;
+	*.c | *.cpp | *.CPP | *.lib | *.LIB | *.Lib | *.OBJ | *.obj | *.[oO])
+	  func_file_conv "$1" mingw
+	  set x "$@" "$file"
+	  shift
+	  ;;
+	*)
+	  set x "$@" "$1"
+	  shift
+	  ;;
+      esac
+    fi
+    shift
+  done
+  if test -n "$linker_opts"; then
+    linker_opts="-link$linker_opts"
+  fi
+  exec "$@" $linker_opts
+  exit 1
+}
+
+eat=
+
+case $1 in
+  '')
+     echo "$0: No command.  Try '$0 --help' for more information." 1>&2
+     exit 1;
+     ;;
+  -h | --h*)
+    cat <<\EOF
+Usage: compile [--help] [--version] PROGRAM [ARGS]
+
+Wrapper for compilers which do not understand '-c -o'.
+Remove '-o dest.o' from ARGS, run PROGRAM with the remaining
+arguments, and rename the output as expected.
+
+If you are trying to build a whole package this is not the
+right script to run: please start by reading the file 'INSTALL'.
+
+Report bugs to <bug-automake@gnu.org>.
+EOF
+    exit $?
+    ;;
+  -v | --v*)
+    echo "compile $scriptversion"
+    exit $?
+    ;;
+  cl | *[/\\]cl | cl.exe | *[/\\]cl.exe | \
+  icl | *[/\\]icl | icl.exe | *[/\\]icl.exe )
+    func_cl_wrapper "$@"      # Doesn't return...
+    ;;
+esac
+
+ofile=
+cfile=
+
+for arg
+do
+  if test -n "$eat"; then
+    eat=
+  else
+    case $1 in
+      -o)
+	# configure might choose to run compile as 'compile cc -o foo foo.c'.
+	# So we strip '-o arg' only if arg is an object.
+	eat=1
+	case $2 in
+	  *.o | *.obj)
+	    ofile=$2
+	    ;;
+	  *)
+	    set x "$@" -o "$2"
+	    shift
+	    ;;
+	esac
+	;;
+      *.c)
+	cfile=$1
+	set x "$@" "$1"
+	shift
+	;;
+      *)
+	set x "$@" "$1"
+	shift
+	;;
+    esac
+  fi
+  shift
+done
+
+if test -z "$ofile" || test -z "$cfile"; then
+  # If no '-o' option was seen then we might have been invoked from a
+  # pattern rule where we don't need one.  That is ok -- this is a
+  # normal compilation that the losing compiler can handle.  If no
+  # '.c' file was seen then we are probably linking.  That is also
+  # ok.
+  exec "$@"
+fi
+
+# Name of file we expect compiler to create.
+cofile=`echo "$cfile" | sed 's|^.*[\\/]||; s|^[a-zA-Z]:||; s/\.c$/.o/'`
+
+# Create the lock directory.
+# Note: use '[/\\:.-]' here to ensure that we don't use the same name
+# that we are using for the .o file.  Also, base the name on the expected
+# object file name, since that is what matters with a parallel build.
+lockdir=`echo "$cofile" | sed -e 's|[/\\:.-]|_|g'`.d
+while true; do
+  if mkdir "$lockdir" >/dev/null 2>&1; then
+    break
+  fi
+  sleep 1
+done
+# FIXME: race condition here if user kills between mkdir and trap.
+trap "rmdir '$lockdir'; exit 1" 1 2 15
+
+# Run the compile.
+"$@"
+ret=$?
+
+if test -f "$cofile"; then
+  test "$cofile" = "$ofile" || mv "$cofile" "$ofile"
+elif test -f "${cofile}bj"; then
+  test "${cofile}bj" = "$ofile" || mv "${cofile}bj" "$ofile"
+fi
+
+rmdir "$lockdir"
+exit $ret
+
+# Local Variables:
+# mode: shell-script
+# sh-indentation: 2
+# eval: (add-hook 'write-file-hooks 'time-stamp)
+# time-stamp-start: "scriptversion="
+# time-stamp-format: "%:y-%02m-%02d.%02H"
+# time-stamp-time-zone: "UTC0"
+# time-stamp-end: "; # UTC"
+# End:

configure.ac

-AC_INIT([jellyfish], [2.2.8], [gmarcais@umd.edu])
+AC_INIT([jellyfish], [2.2.9], [gmarcais@umd.edu])
 AC_CANONICAL_HOST
 AC_CONFIG_MACRO_DIR([m4])
 AM_INIT_AUTOMAKE([subdir-objects foreign parallel-tests color-tests])

debian/changelog

+jellyfish (2.2.9-1) UNRELEASED; urgency=medium
+
+  * New upstream version
+  * Point Vcs fields to salsa.debian.org
+  * Standards-Version: 4.1.4
+
+ -- Andreas Tille <tille@debian.org>  Thu, 26 Apr 2018 15:51:15 +0200
+
 jellyfish (2.2.8-3) unstable; urgency=medium
 
   * Build and install fastq2sam, which fixes Debci tests

debian/control

@@ -18,9 +18,9 @@ Build-Depends: debhelper (>= 11~),
                dh-python,
                perl,
                chrpath
-Standards-Version: 4.1.3
-Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/jellyfish.git
-Vcs-Git: https://anonscm.debian.org/git/debian-med/jellyfish.git
+Standards-Version: 4.1.4
+Vcs-Browser: https://salsa.debian.org/med-team/jellyfish
+Vcs-Git: https://salsa.debian.org/med-team/jellyfish.git
 Homepage: http://www.cbcb.umd.edu/software/jellyfish/
 
 Package: jellyfish

debian/patches/series

 manpage_whatis_entry.patch
-pkg-config-with-name
-drop-rpath
-modern-g++
-spelling
-gcc-7.patch
+# pkg-config-with-name
+# drop-rpath
+# modern-g++
+# spelling
+# gcc-7.patch
 reproducible.patch
 portability.patch
-add_small_mers.sh.patch
-6dfc57b516249454dc0a708ceb4833623cbf0ffd.patch
+# add_small_mers.sh.patch
+# 6dfc57b516249454dc0a708ceb4833623cbf0ffd.patch

debian/rules

@@ -43,14 +43,6 @@ override_dh_install:
 override_dh_auto_configure:
 	dh_auto_configure -- --enable-swig --enable-perl-binding
 
-override_dh_auto_clean:
-	set -e && for i in $(build3vers); do \
-	  cd swig/python ; \
-          python$$i ./setup.py clean --all 2> /dev/null; \
-	  cd ../.. ; \
-	done
-	dh_auto_clean
-
 override_dh_clean:
 	dh_clean
 	if [ -d debian/tmp_save_tests ] ; then \