Initial commit of Kat... doesn't work yet.

TGAC · Jun 7, 2013 · 4e56ed5 · 4e56ed5
commit 4e56ed5
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diff --git a/.gitignore b/.gitignore
@@ -0,0 +1,12 @@
+/$(top_builddir)/
+/autom4te.cache/
+/INSTALL
+/Makefile
+/Makefile.in
+/aclocal.m4
+/config.log
+/config.status
+/configure
+/depcomp
+/install-sh
+/missing
diff --git a/AUTHORS b/AUTHORS
@@ -0,0 +1,3 @@
+Daniel Mapleson <daniel.mapleson@tgac.ac.u>
+Bernardo Clavijo <bernardo.clavijo@tgac.ac.uk>
+
diff --git a/COPYING b/COPYING
diff --git a/ChangeLog b/ChangeLog
diff --git a/Makefile.am b/Makefile.am
@@ -0,0 +1,19 @@
+AUTOMAKE_OPTIONS = subdir-objects
+ACLOCAL_AMFLAGS = ${ACLOCAL_FLAGS}
+EXTRA_DIST = README COPYING AUTHORS NEWS
+
+AM_LDFLAGS = -pthread
+AM_CPPFLAGS = -Wall -Wno-sign-compare -Wnon-virtual-dtor -I$(top_srcdir)/src/inc
+AM_CXXFLAGS = -g -O3
+
+
+bin_PROGRAMS = $(top_builddir)/bin/kat
+
+__top_builddir__bin_kat_SOURCES = src/sect/sect.hpp src/sect/sect_main.cc \
+					src/kat.cc
+
+__top_builddir__bin_kat_LDADD = lib/libjellyfish-1.1.a lib/libz.a
+
+
+dist_noinst_SCRIPTS = autogen.sh
+
diff --git a/NEWS b/NEWS
diff --git a/README b/README
diff --git a/autogen.sh b/autogen.sh
@@ -0,0 +1,7 @@
+#!/bin/sh -e
+
+test -n "$srcdir" || srcdir=`dirname "$0"`
+test -n "$srcdir" || srcdir=.
+autoreconf --force --install --verbose "$srcdir"
+test -n "$NOCONFIGURE" || "$srcdir/configure" "$@"
+
diff --git a/clean.sh b/clean.sh
@@ -0,0 +1,6 @@
+#!/bin/sh -e
+
+rm -r -f autom4te.cache autoscan.* Makefile.in aclocal.m4 configure depcomp INSTALL install-sh missing config.* *.scan stamp-h1 */*.o
+
+
+
diff --git a/configure.ac b/configure.ac
@@ -0,0 +1,6 @@
+AC_INIT([Kmer Analysis Toolkit (KAT)], [0.1], [daniel.mapleson@tgac.ac.uk], [kat], [http://www.tgac.ac.uk])
+AM_INIT_AUTOMAKE([1.11 -Wall no-define])
+AC_PROG_CXX
+AC_PROG_CC
+AC_PROG_INSTALL
+AC_OUTPUT(Makefile)
diff --git a/lib/libjellyfish-1.1.a b/lib/libjellyfish-1.1.a
diff --git a/lib/libjellyfish-1.1.lai b/lib/libjellyfish-1.1.lai
@@ -0,0 +1,41 @@
+# libjellyfish-1.1.la - a libtool library file
+# Generated by libtool (GNU libtool) 2.4.2 Debian-2.4.2-1.1
+#
+# Please DO NOT delete this file!
+# It is necessary for linking the library.
+
+# The name that we can dlopen(3).
+dlname='libjellyfish-1.1.so.1'
+
+# Names of this library.
+library_names='libjellyfish-1.1.so.1.0.1 libjellyfish-1.1.so.1 libjellyfish-1.1.so'
+
+# The name of the static archive.
+old_library='libjellyfish-1.1.a'
+
+# Linker flags that can not go in dependency_libs.
+inherited_linker_flags=''
+
+# Libraries that this one depends upon.
+dependency_libs=''
+
+# Names of additional weak libraries provided by this library
+weak_library_names=''
+
+# Version information for libjellyfish-1.1.
+current=1
+age=0
+revision=1
+
+# Is this an already installed library?
+installed=yes
+
+# Should we warn about portability when linking against -modules?
+shouldnotlink=no
+
+# Files to dlopen/dlpreopen
+dlopen=''
+dlpreopen=''
+
+# Directory that this library needs to be installed in:
+libdir='/usr/local/lib'
diff --git a/lib/libjellyfish-1.1.so.1.0.1 b/lib/libjellyfish-1.1.so.1.0.1
diff --git a/lib/libz.a b/lib/libz.a
diff --git a/lib/libz.so.1.2.8 b/lib/libz.so.1.2.8
diff --git a/src/.deps/.gitignore b/src/.deps/.gitignore
@@ -0,0 +1,3 @@
+/*.dirstamp
+/*.Po
+/*.Tpo
diff --git a/src/.gitignore b/src/.gitignore
@@ -0,0 +1,3 @@
+/*.dirstamp
+/*.o
+/*~