Merge branch 'develop'

.gitignore

@@ -14,7 +14,8 @@ pprinseqc*.tar.gz
 src/*.fastq
 !src/test_F.fastq
 !src/test_R.fastq
-
+config.guess
+config.sub
 
 # Prerequisites
 *.d

Makefile.in

@@ -13,14 +13,15 @@ bindir = @bindir@
 srcdir = @srcdir@
 VPATH = @srcdir@
 
+ACLOCAL_AMFLAGS = -I m4 --install
 
 all test install uninstall pprinseqc:
 	cd src && $(MAKE) $@
 
 clean : FORCE
 	cd src && $(MAKE) $@
 	-rm -rf autom4te.cache 
-	-rm -f config.h config.log aclocal.m4 config.log config.status configure install-sh Makefile
+	-rm -f config.h config.log aclocal.m4 config.log config.status configure install-sh Makefile config.guess config.sub
 
 dist : $(distdir).tar.gz
 
@@ -35,12 +36,16 @@ $(distdir): FORCE
 	cp $(srcdir)/config.h.in $(distdir)
 	cp $(srcdir)/install-sh $(distdir)
 	cp $(srcdir)/Makefile.in $(distdir)
+	cp $(srcdir)/config.sub $(distdir)
+	cp $(srcdir)/config.guess $(distdir)
 	cp $(srcdir)/src/Makefile.in $(distdir)/src
 	cp $(srcdir)/src/main.cpp $(distdir)/src
 	cp $(srcdir)/src/reads.cpp $(distdir)/src
 	cp $(srcdir)/src/reads.h $(distdir)/src
 	cp $(srcdir)/src/test_F.fastq $(distdir)/src
 	cp $(srcdir)/src/test_R.fastq $(distdir)/src
+	cp $(srcdir)/src/test_F.fastq.gz $(distdir)/src
+	cp $(srcdir)/src/test_R.fastq.gz $(distdir)/src
 	cp $(srcdir)/src/bloom_filter.hpp $(distdir)/src
 	cp $(srcdir)/src/README $(distdir)/src
 

README.md

@@ -11,4 +11,5 @@ parallel c prinseq
 1. automake
 2. g++
 3. make
+4. boost-devel
 

configure.ac

@@ -2,7 +2,7 @@
 # Process this file with autoconf to produce a configure script.
 
 AC_PREREQ([2.69])
-AC_INIT([pprinseqc], [0.1], [garbanyo@gmail.com])
+AC_INIT([pprinseqc], [0.9], [garbanyo@gmail.com])
 ##AM_INIT_AUTOMAKE
 AC_CONFIG_SRCDIR([src/main.cpp])
 AC_LANG([C++])
@@ -15,6 +15,9 @@ AC_CONFIG_HEADERS([config.h])
 # Checks for programs.
 AC_PROG_CXX
 AC_PROG_INSTALL
+AX_BOOST_BASE([1.41], [], AC_MSG_ERROR([Could not find a useful version of boost]))
+AX_BOOST_FILESYSTEM
+AX_BOOST_IOSTREAMS
 
 # Checks for libraries.
 

m4/ax_boost_base.m4

@@ -0,0 +1,301 @@
+# ===========================================================================
+#      https://www.gnu.org/software/autoconf-archive/ax_boost_base.html
+# ===========================================================================
+#
+# SYNOPSIS
+#
+#   AX_BOOST_BASE([MINIMUM-VERSION], [ACTION-IF-FOUND], [ACTION-IF-NOT-FOUND])
+#
+# DESCRIPTION
+#
+#   Test for the Boost C++ libraries of a particular version (or newer)
+#
+#   If no path to the installed boost library is given the macro searchs
+#   under /usr, /usr/local, /opt and /opt/local and evaluates the
+#   $BOOST_ROOT environment variable. Further documentation is available at
+#   <http://randspringer.de/boost/index.html>.
+#
+#   This macro calls:
+#
+#     AC_SUBST(BOOST_CPPFLAGS) / AC_SUBST(BOOST_LDFLAGS)
+#
+#   And sets:
+#
+#     HAVE_BOOST
+#
+# LICENSE
+#
+#   Copyright (c) 2008 Thomas Porschberg <thomas@randspringer.de>
+#   Copyright (c) 2009 Peter Adolphs
+#
+#   Copying and distribution of this file, with or without modification, are
+#   permitted in any medium without royalty provided the copyright notice
+#   and this notice are preserved. This file is offered as-is, without any
+#   warranty.
+
+#serial 43
+
+# example boost program (need to pass version)
+m4_define([_AX_BOOST_BASE_PROGRAM],
+          [AC_LANG_PROGRAM([[
+#include <boost/version.hpp>
+]],[[
+(void) ((void)sizeof(char[1 - 2*!!((BOOST_VERSION) < ($1))]));
+]])])
+
+AC_DEFUN([AX_BOOST_BASE],
+[
+AC_ARG_WITH([boost],
+  [AS_HELP_STRING([--with-boost@<:@=ARG@:>@],
+    [use Boost library from a standard location (ARG=yes),
+     from the specified location (ARG=<path>),
+     or disable it (ARG=no)
+     @<:@ARG=yes@:>@ ])],
+    [
+     AS_CASE([$withval],
+       [no],[want_boost="no";_AX_BOOST_BASE_boost_path=""],
+       [yes],[want_boost="yes";_AX_BOOST_BASE_boost_path=""],
+       [want_boost="yes";_AX_BOOST_BASE_boost_path="$withval"])
+    ],
+    [want_boost="yes"])
+
+
+AC_ARG_WITH([boost-libdir],
+  [AS_HELP_STRING([--with-boost-libdir=LIB_DIR],
+    [Force given directory for boost libraries.
+     Note that this will override library path detection,
+     so use this parameter only if default library detection fails
+     and you know exactly where your boost libraries are located.])],
+  [
+   AS_IF([test -d "$withval"],
+         [_AX_BOOST_BASE_boost_lib_path="$withval"],
+    [AC_MSG_ERROR([--with-boost-libdir expected directory name])])
+  ],
+  [_AX_BOOST_BASE_boost_lib_path=""])
+
+BOOST_LDFLAGS=""
+BOOST_CPPFLAGS=""
+AS_IF([test "x$want_boost" = "xyes"],
+      [_AX_BOOST_BASE_RUNDETECT([$1],[$2],[$3])])
+AC_SUBST(BOOST_CPPFLAGS)
+AC_SUBST(BOOST_LDFLAGS)
+])
+
+
+# convert a version string in $2 to numeric and affect to polymorphic var $1
+AC_DEFUN([_AX_BOOST_BASE_TONUMERICVERSION],[
+  AS_IF([test "x$2" = "x"],[_AX_BOOST_BASE_TONUMERICVERSION_req="1.20.0"],[_AX_BOOST_BASE_TONUMERICVERSION_req="$2"])
+  _AX_BOOST_BASE_TONUMERICVERSION_req_shorten=`expr $_AX_BOOST_BASE_TONUMERICVERSION_req : '\([[0-9]]*\.[[0-9]]*\)'`
+  _AX_BOOST_BASE_TONUMERICVERSION_req_major=`expr $_AX_BOOST_BASE_TONUMERICVERSION_req : '\([[0-9]]*\)'`
+  AS_IF([test "x$_AX_BOOST_BASE_TONUMERICVERSION_req_major" = "x"],
+        [AC_MSG_ERROR([You should at least specify libboost major version])])
+  _AX_BOOST_BASE_TONUMERICVERSION_req_minor=`expr $_AX_BOOST_BASE_TONUMERICVERSION_req : '[[0-9]]*\.\([[0-9]]*\)'`
+  AS_IF([test "x$_AX_BOOST_BASE_TONUMERICVERSION_req_minor" = "x"],
+        [_AX_BOOST_BASE_TONUMERICVERSION_req_minor="0"])
+  _AX_BOOST_BASE_TONUMERICVERSION_req_sub_minor=`expr $_AX_BOOST_BASE_TONUMERICVERSION_req : '[[0-9]]*\.[[0-9]]*\.\([[0-9]]*\)'`
+  AS_IF([test "X$_AX_BOOST_BASE_TONUMERICVERSION_req_sub_minor" = "X"],
+        [_AX_BOOST_BASE_TONUMERICVERSION_req_sub_minor="0"])
+  _AX_BOOST_BASE_TONUMERICVERSION_RET=`expr $_AX_BOOST_BASE_TONUMERICVERSION_req_major \* 100000 \+  $_AX_BOOST_BASE_TONUMERICVERSION_req_minor \* 100 \+ $_AX_BOOST_BASE_TONUMERICVERSION_req_sub_minor`
+  AS_VAR_SET($1,$_AX_BOOST_BASE_TONUMERICVERSION_RET)
+])
+
+dnl Run the detection of boost should be run only if $want_boost
+AC_DEFUN([_AX_BOOST_BASE_RUNDETECT],[
+    _AX_BOOST_BASE_TONUMERICVERSION(WANT_BOOST_VERSION,[$1])
+    succeeded=no
+
+
+    AC_REQUIRE([AC_CANONICAL_HOST])
+    dnl On 64-bit systems check for system libraries in both lib64 and lib.
+    dnl The former is specified by FHS, but e.g. Debian does not adhere to
+    dnl this (as it rises problems for generic multi-arch support).
+    dnl The last entry in the list is chosen by default when no libraries
+    dnl are found, e.g. when only header-only libraries are installed!
+    AS_CASE([${host_cpu}],
+      [x86_64],[libsubdirs="lib64 libx32 lib lib64"],
+      [ppc64|s390x|sparc64|aarch64|ppc64le],[libsubdirs="lib64 lib lib64"],
+      [libsubdirs="lib"]
+    )
+
+    dnl allow for real multi-arch paths e.g. /usr/lib/x86_64-linux-gnu. Give
+    dnl them priority over the other paths since, if libs are found there, they
+    dnl are almost assuredly the ones desired.
+    AS_CASE([${host_cpu}],
+      [i?86],[multiarch_libsubdir="lib/i386-${host_os}"],
+      [multiarch_libsubdir="lib/${host_cpu}-${host_os}"]
+    )
+
+    dnl first we check the system location for boost libraries
+    dnl this location ist chosen if boost libraries are installed with the --layout=system option
+    dnl or if you install boost with RPM
+    AS_IF([test "x$_AX_BOOST_BASE_boost_path" != "x"],[
+        AC_MSG_CHECKING([for boostlib >= $1 ($WANT_BOOST_VERSION) includes in "$_AX_BOOST_BASE_boost_path/include"])
+         AS_IF([test -d "$_AX_BOOST_BASE_boost_path/include" && test -r "$_AX_BOOST_BASE_boost_path/include"],[
+           AC_MSG_RESULT([yes])
+           BOOST_CPPFLAGS="-I$_AX_BOOST_BASE_boost_path/include"
+           for _AX_BOOST_BASE_boost_path_tmp in $multiarch_libsubdir $libsubdirs; do
+                AC_MSG_CHECKING([for boostlib >= $1 ($WANT_BOOST_VERSION) lib path in "$_AX_BOOST_BASE_boost_path/$_AX_BOOST_BASE_boost_path_tmp"])
+                AS_IF([test -d "$_AX_BOOST_BASE_boost_path/$_AX_BOOST_BASE_boost_path_tmp" && test -r "$_AX_BOOST_BASE_boost_path/$_AX_BOOST_BASE_boost_path_tmp" ],[
+                        AC_MSG_RESULT([yes])
+                        BOOST_LDFLAGS="-L$_AX_BOOST_BASE_boost_path/$_AX_BOOST_BASE_boost_path_tmp";
+                        break;
+                ],
+      [AC_MSG_RESULT([no])])
+           done],[
+      AC_MSG_RESULT([no])])
+    ],[
+        if test X"$cross_compiling" = Xyes; then
+            search_libsubdirs=$multiarch_libsubdir
+        else
+            search_libsubdirs="$multiarch_libsubdir $libsubdirs"
+        fi
+        for _AX_BOOST_BASE_boost_path_tmp in /usr /usr/local /opt /opt/local ; do
+            if test -d "$_AX_BOOST_BASE_boost_path_tmp/include/boost" && test -r "$_AX_BOOST_BASE_boost_path_tmp/include/boost" ; then
+                for libsubdir in $search_libsubdirs ; do
+                    if ls "$_AX_BOOST_BASE_boost_path_tmp/$libsubdir/libboost_"* >/dev/null 2>&1 ; then break; fi
+                done
+                BOOST_LDFLAGS="-L$_AX_BOOST_BASE_boost_path_tmp/$libsubdir"
+                BOOST_CPPFLAGS="-I$_AX_BOOST_BASE_boost_path_tmp/include"
+                break;
+            fi
+        done
+    ])
+
+    dnl overwrite ld flags if we have required special directory with
+    dnl --with-boost-libdir parameter
+    AS_IF([test "x$_AX_BOOST_BASE_boost_lib_path" != "x"],
+          [BOOST_LDFLAGS="-L$_AX_BOOST_BASE_boost_lib_path"])
+
+    AC_MSG_CHECKING([for boostlib >= $1 ($WANT_BOOST_VERSION)])
+    CPPFLAGS_SAVED="$CPPFLAGS"
+    CPPFLAGS="$CPPFLAGS $BOOST_CPPFLAGS"
+    export CPPFLAGS
+
+    LDFLAGS_SAVED="$LDFLAGS"
+    LDFLAGS="$LDFLAGS $BOOST_LDFLAGS"
+    export LDFLAGS
+
+    AC_REQUIRE([AC_PROG_CXX])
+    AC_LANG_PUSH(C++)
+        AC_COMPILE_IFELSE([_AX_BOOST_BASE_PROGRAM($WANT_BOOST_VERSION)],[
+        AC_MSG_RESULT(yes)
+    succeeded=yes
+    found_system=yes
+        ],[
+        ])
+    AC_LANG_POP([C++])
+
+
+
+    dnl if we found no boost with system layout we search for boost libraries
+    dnl built and installed without the --layout=system option or for a staged(not installed) version
+    if test "x$succeeded" != "xyes" ; then
+        CPPFLAGS="$CPPFLAGS_SAVED"
+        LDFLAGS="$LDFLAGS_SAVED"
+        BOOST_CPPFLAGS=
+        if test -z "$_AX_BOOST_BASE_boost_lib_path" ; then
+            BOOST_LDFLAGS=
+        fi
+        _version=0
+        if test -n "$_AX_BOOST_BASE_boost_path" ; then
+            if test -d "$_AX_BOOST_BASE_boost_path" && test -r "$_AX_BOOST_BASE_boost_path"; then
+                for i in `ls -d $_AX_BOOST_BASE_boost_path/include/boost-* 2>/dev/null`; do
+                    _version_tmp=`echo $i | sed "s#$_AX_BOOST_BASE_boost_path##" | sed 's/\/include\/boost-//' | sed 's/_/./'`
+                    V_CHECK=`expr $_version_tmp \> $_version`
+                    if test "x$V_CHECK" = "x1" ; then
+                        _version=$_version_tmp
+                    fi
+                    VERSION_UNDERSCORE=`echo $_version | sed 's/\./_/'`
+                    BOOST_CPPFLAGS="-I$_AX_BOOST_BASE_boost_path/include/boost-$VERSION_UNDERSCORE"
+                done
+                dnl if nothing found search for layout used in Windows distributions
+                if test -z "$BOOST_CPPFLAGS"; then
+                    if test -d "$_AX_BOOST_BASE_boost_path/boost" && test -r "$_AX_BOOST_BASE_boost_path/boost"; then
+                        BOOST_CPPFLAGS="-I$_AX_BOOST_BASE_boost_path"
+                    fi
+                fi
+                dnl if we found something and BOOST_LDFLAGS was unset before
+                dnl (because "$_AX_BOOST_BASE_boost_lib_path" = ""), set it here.
+                if test -n "$BOOST_CPPFLAGS" && test -z "$BOOST_LDFLAGS"; then
+                    for libsubdir in $libsubdirs ; do
+                        if ls "$_AX_BOOST_BASE_boost_path/$libsubdir/libboost_"* >/dev/null 2>&1 ; then break; fi
+                    done
+                    BOOST_LDFLAGS="-L$_AX_BOOST_BASE_boost_path/$libsubdir"
+                fi
+            fi
+        else
+            if test "x$cross_compiling" != "xyes" ; then
+                for _AX_BOOST_BASE_boost_path in /usr /usr/local /opt /opt/local ; do
+                    if test -d "$_AX_BOOST_BASE_boost_path" && test -r "$_AX_BOOST_BASE_boost_path" ; then
+                        for i in `ls -d $_AX_BOOST_BASE_boost_path/include/boost-* 2>/dev/null`; do
+                            _version_tmp=`echo $i | sed "s#$_AX_BOOST_BASE_boost_path##" | sed 's/\/include\/boost-//' | sed 's/_/./'`
+                            V_CHECK=`expr $_version_tmp \> $_version`
+                            if test "x$V_CHECK" = "x1" ; then
+                                _version=$_version_tmp
+                                best_path=$_AX_BOOST_BASE_boost_path
+                            fi
+                        done
+                    fi
+                done
+
+                VERSION_UNDERSCORE=`echo $_version | sed 's/\./_/'`
+                BOOST_CPPFLAGS="-I$best_path/include/boost-$VERSION_UNDERSCORE"
+                if test -z "$_AX_BOOST_BASE_boost_lib_path" ; then
+                    for libsubdir in $libsubdirs ; do
+                        if ls "$best_path/$libsubdir/libboost_"* >/dev/null 2>&1 ; then break; fi
+                    done
+                    BOOST_LDFLAGS="-L$best_path/$libsubdir"
+                fi
+            fi
+
+            if test -n "$BOOST_ROOT" ; then
+                for libsubdir in $libsubdirs ; do
+                    if ls "$BOOST_ROOT/stage/$libsubdir/libboost_"* >/dev/null 2>&1 ; then break; fi
+                done
+                if test -d "$BOOST_ROOT" && test -r "$BOOST_ROOT" && test -d "$BOOST_ROOT/stage/$libsubdir" && test -r "$BOOST_ROOT/stage/$libsubdir"; then
+                    version_dir=`expr //$BOOST_ROOT : '.*/\(.*\)'`
+                    stage_version=`echo $version_dir | sed 's/boost_//' | sed 's/_/./g'`
+                        stage_version_shorten=`expr $stage_version : '\([[0-9]]*\.[[0-9]]*\)'`
+                    V_CHECK=`expr $stage_version_shorten \>\= $_version`
+                    if test "x$V_CHECK" = "x1" && test -z "$_AX_BOOST_BASE_boost_lib_path" ; then
+                        AC_MSG_NOTICE(We will use a staged boost library from $BOOST_ROOT)
+                        BOOST_CPPFLAGS="-I$BOOST_ROOT"
+                        BOOST_LDFLAGS="-L$BOOST_ROOT/stage/$libsubdir"
+                    fi
+                fi
+            fi
+        fi
+
+        CPPFLAGS="$CPPFLAGS $BOOST_CPPFLAGS"
+        export CPPFLAGS
+        LDFLAGS="$LDFLAGS $BOOST_LDFLAGS"
+        export LDFLAGS
+
+        AC_LANG_PUSH(C++)
+            AC_COMPILE_IFELSE([_AX_BOOST_BASE_PROGRAM($WANT_BOOST_VERSION)],[
+            AC_MSG_RESULT(yes)
+        succeeded=yes
+        found_system=yes
+            ],[
+            ])
+        AC_LANG_POP([C++])
+    fi
+
+    if test "x$succeeded" != "xyes" ; then
+        if test "x$_version" = "x0" ; then
+            AC_MSG_NOTICE([[We could not detect the boost libraries (version $1 or higher). If you have a staged boost library (still not installed) please specify \$BOOST_ROOT in your environment and do not give a PATH to --with-boost option.  If you are sure you have boost installed, then check your version number looking in <boost/version.hpp>. See http://randspringer.de/boost for more documentation.]])
+        else
+            AC_MSG_NOTICE([Your boost libraries seems to old (version $_version).])
+        fi
+        # execute ACTION-IF-NOT-FOUND (if present):
+        ifelse([$3], , :, [$3])
+    else
+        AC_DEFINE(HAVE_BOOST,,[define if the Boost library is available])
+        # execute ACTION-IF-FOUND (if present):
+        ifelse([$2], , :, [$2])
+    fi
+
+    CPPFLAGS="$CPPFLAGS_SAVED"
+    LDFLAGS="$LDFLAGS_SAVED"
+
+])