[med-svn] [Git][med-team/crac][upstream] New upstream version 2.5.2+dfsg
Andreas Tille
gitlab at salsa.debian.org
Fri Jul 19 19:08:28 BST 2019
Andreas Tille pushed to branch upstream at Debian Med / crac
Commits:
1e946396 by Andreas Tille at 2019-07-19T17:54:34Z
New upstream version 2.5.2+dfsg
- - - - -
30 changed files:
- Makefile.in
- aclocal.m4
- configure
- configure.ac
- man/Makefile.in
- scripts/Makefile.in
- scripts/crac-client
- src/Bitset.h
- src/Makefile.am
- src/Makefile.in
- src/Support.cpp
- src/SupportBreak.cpp
- src/libReadsInfo/Makefile.in
- src/libReadsReader/Makefile.in
- src/libReadsReader/kseq/Makefile.in
- src/libSSA/Makefile.in
- test_f/Makefile.in
- test_f/bug/Makefile.in
- + test_f/bug/bug-17175-2-genome.fa
- + test_f/bug/bug-17175-2-reads.fa
- + test_f/bug/test.fa
- + test_f/bug/test0.fa
- + test_f/bug/tmp-genome.fa
- + test_f/bug/tmp-reads.fa
- test_f/causes/Makefile.in
- test_f/cigar/Makefile.in
- + test_f/cigar/genome2.fasta
- + test_f/cigar/read_c4.fasta
- test_f/splices_adjust/Makefile.in
- + test_f/tmp-genome.fa
Changes:
=====================================
Makefile.in
=====================================
@@ -1,7 +1,7 @@
-# Makefile.in generated by automake 1.14.1 from Makefile.am.
+# Makefile.in generated by automake 1.16.1 from Makefile.am.
# @configure_input@
-# Copyright (C) 1994-2013 Free Software Foundation, Inc.
+# Copyright (C) 1994-2018 Free Software Foundation, Inc.
# This Makefile.in is free software; the Free Software Foundation
# gives unlimited permission to copy and/or distribute it,
@@ -113,7 +113,17 @@
# #
###############################################################################
VPATH = @srcdir@
-am__is_gnu_make = test -n '$(MAKEFILE_LIST)' && test -n '$(MAKELEVEL)'
+am__is_gnu_make = { \
+ if test -z '$(MAKELEVEL)'; then \
+ false; \
+ elif test -n '$(MAKE_HOST)'; then \
+ true; \
+ elif test -n '$(MAKE_VERSION)' && test -n '$(CURDIR)'; then \
+ true; \
+ else \
+ false; \
+ fi; \
+}
am__make_running_with_option = \
case $${target_option-} in \
?) ;; \
@@ -177,18 +187,6 @@ POST_UNINSTALL = :
build_triplet = @build@
host_triplet = @host@
subdir = .
-DIST_COMMON = INSTALL NEWS README AUTHORS ChangeLog \
- $(srcdir)/Makefile.in $(srcdir)/Makefile.am \
- $(top_srcdir)/configure $(am__configure_deps) \
- $(top_srcdir)/config/config.h.in $(srcdir)/control.in \
- $(srcdir)/crac.spec.in COPYING config/compile \
- config/config.guess config/config.sub config/depcomp \
- config/install-sh config/missing config/texinfo.tex \
- config/ltmain.sh $(top_srcdir)/config/compile \
- $(top_srcdir)/config/config.guess \
- $(top_srcdir)/config/config.sub \
- $(top_srcdir)/config/install-sh $(top_srcdir)/config/ltmain.sh \
- $(top_srcdir)/config/missing
ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
am__aclocal_m4_deps = $(top_srcdir)/config/m4/libtool.m4 \
$(top_srcdir)/config/m4/ltoptions.m4 \
@@ -198,6 +196,8 @@ am__aclocal_m4_deps = $(top_srcdir)/config/m4/libtool.m4 \
$(top_srcdir)/configure.ac
am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \
$(ACLOCAL_M4)
+DIST_COMMON = $(srcdir)/Makefile.am $(top_srcdir)/configure \
+ $(am__configure_deps) $(am__DIST_COMMON)
am__CONFIG_DISTCLEAN_FILES = config.status config.cache config.log \
configure.lineno config.status.lineno
mkinstalldirs = $(install_sh) -d
@@ -238,7 +238,7 @@ am__recursive_targets = \
$(RECURSIVE_CLEAN_TARGETS) \
$(am__extra_recursive_targets)
AM_RECURSIVE_TARGETS = $(am__recursive_targets:-recursive=) TAGS CTAGS \
- cscope distdir dist dist-all distcheck
+ cscope distdir distdir-am dist dist-all distcheck
am__tagged_files = $(HEADERS) $(SOURCES) $(TAGS_FILES) $(LISP)
# Read a list of newline-separated strings from the standard input,
# and print each of them once, without duplicates. Input order is
@@ -260,6 +260,16 @@ ETAGS = etags
CTAGS = ctags
CSCOPE = cscope
DIST_SUBDIRS = $(SUBDIRS)
+am__DIST_COMMON = $(srcdir)/Makefile.in $(srcdir)/control.in \
+ $(srcdir)/crac.spec.in $(top_srcdir)/config/compile \
+ $(top_srcdir)/config/config.guess \
+ $(top_srcdir)/config/config.h.in \
+ $(top_srcdir)/config/config.sub \
+ $(top_srcdir)/config/install-sh $(top_srcdir)/config/ltmain.sh \
+ $(top_srcdir)/config/missing AUTHORS COPYING ChangeLog INSTALL \
+ NEWS README config/compile config/config.guess \
+ config/config.sub config/depcomp config/install-sh \
+ config/ltmain.sh config/missing config/texinfo.tex
DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
distdir = $(PACKAGE)-$(VERSION)
top_distdir = $(distdir)
@@ -349,6 +359,7 @@ LIBTOOL = @LIBTOOL@
LIPO = @LIPO@
LN_S = @LN_S@
LTLIBOBJS = @LTLIBOBJS@
+LT_SYS_LIBRARY_PATH = @LT_SYS_LIBRARY_PATH@
MAKEINFO = @MAKEINFO@
MANIFEST_TOOL = @MANIFEST_TOOL@
MKDIR_P = @MKDIR_P@
@@ -419,6 +430,7 @@ pdfdir = @pdfdir@
prefix = @prefix@
program_transform_name = @program_transform_name@
psdir = @psdir@
+runstatedir = @runstatedir@
sbindir = @sbindir@
sharedstatedir = @sharedstatedir@
srcdir = @srcdir@
@@ -457,15 +469,14 @@ $(srcdir)/Makefile.in: $(srcdir)/Makefile.am $(am__configure_deps)
echo ' cd $(top_srcdir) && $(AUTOMAKE) --gnu Makefile'; \
$(am__cd) $(top_srcdir) && \
$(AUTOMAKE) --gnu Makefile
-.PRECIOUS: Makefile
Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status
@case '$?' in \
*config.status*) \
echo ' $(SHELL) ./config.status'; \
$(SHELL) ./config.status;; \
*) \
- echo ' cd $(top_builddir) && $(SHELL) ./config.status $@ $(am__depfiles_maybe)'; \
- cd $(top_builddir) && $(SHELL) ./config.status $@ $(am__depfiles_maybe);; \
+ echo ' cd $(top_builddir) && $(SHELL) ./config.status $@ $(am__maybe_remake_depfiles)'; \
+ cd $(top_builddir) && $(SHELL) ./config.status $@ $(am__maybe_remake_depfiles);; \
esac;
$(top_builddir)/config.status: $(top_srcdir)/configure $(CONFIG_STATUS_DEPENDENCIES)
@@ -611,7 +622,10 @@ distclean-tags:
-rm -f TAGS ID GTAGS GRTAGS GSYMS GPATH tags
-rm -f cscope.out cscope.in.out cscope.po.out cscope.files
-distdir: $(DISTFILES)
+distdir: $(BUILT_SOURCES)
+ $(MAKE) $(AM_MAKEFLAGS) distdir-am
+
+distdir-am: $(DISTFILES)
$(am__remove_distdir)
test -d "$(distdir)" || mkdir "$(distdir)"
@srcdirstrip=`echo "$(srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \
@@ -676,7 +690,7 @@ distdir: $(DISTFILES)
! -type d ! -perm -444 -exec $(install_sh) -c -m a+r {} {} \; \
|| chmod -R a+r "$(distdir)"
dist-gzip: distdir
- tardir=$(distdir) && $(am__tar) | GZIP=$(GZIP_ENV) gzip -c >$(distdir).tar.gz
+ tardir=$(distdir) && $(am__tar) | eval GZIP= gzip $(GZIP_ENV) -c >$(distdir).tar.gz
$(am__post_remove_distdir)
dist-bzip2: distdir
@@ -692,17 +706,17 @@ dist-xz: distdir
$(am__post_remove_distdir)
dist-tarZ: distdir
- @echo WARNING: "Support for shar distribution archives is" \
- "deprecated." >&2
+ @echo WARNING: "Support for distribution archives compressed with" \
+ "legacy program 'compress' is deprecated." >&2
@echo WARNING: "It will be removed altogether in Automake 2.0" >&2
tardir=$(distdir) && $(am__tar) | compress -c >$(distdir).tar.Z
$(am__post_remove_distdir)
dist-shar: distdir
- @echo WARNING: "Support for distribution archives compressed with" \
- "legacy program 'compress' is deprecated." >&2
+ @echo WARNING: "Support for shar distribution archives is" \
+ "deprecated." >&2
@echo WARNING: "It will be removed altogether in Automake 2.0" >&2
- shar $(distdir) | GZIP=$(GZIP_ENV) gzip -c >$(distdir).shar.gz
+ shar $(distdir) | eval GZIP= gzip $(GZIP_ENV) -c >$(distdir).shar.gz
$(am__post_remove_distdir)
dist-zip: distdir
@@ -720,7 +734,7 @@ dist dist-all:
distcheck: dist
case '$(DIST_ARCHIVES)' in \
*.tar.gz*) \
- GZIP=$(GZIP_ENV) gzip -dc $(distdir).tar.gz | $(am__untar) ;;\
+ eval GZIP= gzip $(GZIP_ENV) -dc $(distdir).tar.gz | $(am__untar) ;;\
*.tar.bz2*) \
bzip2 -dc $(distdir).tar.bz2 | $(am__untar) ;;\
*.tar.lz*) \
@@ -730,23 +744,23 @@ distcheck: dist
*.tar.Z*) \
uncompress -c $(distdir).tar.Z | $(am__untar) ;;\
*.shar.gz*) \
- GZIP=$(GZIP_ENV) gzip -dc $(distdir).shar.gz | unshar ;;\
+ eval GZIP= gzip $(GZIP_ENV) -dc $(distdir).shar.gz | unshar ;;\
*.zip*) \
unzip $(distdir).zip ;;\
esac
chmod -R a-w $(distdir)
chmod u+w $(distdir)
- mkdir $(distdir)/_build $(distdir)/_inst
+ mkdir $(distdir)/_build $(distdir)/_build/sub $(distdir)/_inst
chmod a-w $(distdir)
test -d $(distdir)/_build || exit 0; \
dc_install_base=`$(am__cd) $(distdir)/_inst && pwd | sed -e 's,^[^:\\/]:[\\/],/,'` \
&& dc_destdir="$${TMPDIR-/tmp}/am-dc-$$$$/" \
&& am__cwd=`pwd` \
- && $(am__cd) $(distdir)/_build \
- && ../configure \
+ && $(am__cd) $(distdir)/_build/sub \
+ && ../../configure \
$(AM_DISTCHECK_CONFIGURE_FLAGS) \
$(DISTCHECK_CONFIGURE_FLAGS) \
- --srcdir=.. --prefix="$$dc_install_base" \
+ --srcdir=../.. --prefix="$$dc_install_base" \
&& $(MAKE) $(AM_MAKEFLAGS) \
&& $(MAKE) $(AM_MAKEFLAGS) dvi \
&& $(MAKE) $(AM_MAKEFLAGS) check \
@@ -927,6 +941,8 @@ uninstall-am:
mostlyclean-libtool pdf pdf-am ps ps-am tags tags-am uninstall \
uninstall-am
+.PRECIOUS: Makefile
+
# dist-hook:
# rm -rf `find $(distdir) -type d -name .svn`
=====================================
aclocal.m4
=====================================
@@ -1,6 +1,6 @@
-# generated automatically by aclocal 1.14.1 -*- Autoconf -*-
+# generated automatically by aclocal 1.16.1 -*- Autoconf -*-
-# Copyright (C) 1996-2013 Free Software Foundation, Inc.
+# Copyright (C) 1996-2018 Free Software Foundation, Inc.
# This file is free software; the Free Software Foundation
# gives unlimited permission to copy and/or distribute it,
@@ -20,7 +20,7 @@ You have another version of autoconf. It may work, but is not guaranteed to.
If you have problems, you may need to regenerate the build system entirely.
To do so, use the procedure documented by the package, typically 'autoreconf'.])])
-# Copyright (C) 2002-2013 Free Software Foundation, Inc.
+# Copyright (C) 2002-2018 Free Software Foundation, Inc.
#
# This file is free software; the Free Software Foundation
# gives unlimited permission to copy and/or distribute it,
@@ -32,10 +32,10 @@ To do so, use the procedure documented by the package, typically 'autoreconf'.])
# generated from the m4 files accompanying Automake X.Y.
# (This private macro should not be called outside this file.)
AC_DEFUN([AM_AUTOMAKE_VERSION],
-[am__api_version='1.14'
+[am__api_version='1.16'
dnl Some users find AM_AUTOMAKE_VERSION and mistake it for a way to
dnl require some minimum version. Point them to the right macro.
-m4_if([$1], [1.14.1], [],
+m4_if([$1], [1.16.1], [],
[AC_FATAL([Do not call $0, use AM_INIT_AUTOMAKE([$1]).])])dnl
])
@@ -51,14 +51,14 @@ m4_define([_AM_AUTOCONF_VERSION], [])
# Call AM_AUTOMAKE_VERSION and AM_AUTOMAKE_VERSION so they can be traced.
# This function is AC_REQUIREd by AM_INIT_AUTOMAKE.
AC_DEFUN([AM_SET_CURRENT_AUTOMAKE_VERSION],
-[AM_AUTOMAKE_VERSION([1.14.1])dnl
+[AM_AUTOMAKE_VERSION([1.16.1])dnl
m4_ifndef([AC_AUTOCONF_VERSION],
[m4_copy([m4_PACKAGE_VERSION], [AC_AUTOCONF_VERSION])])dnl
_AM_AUTOCONF_VERSION(m4_defn([AC_AUTOCONF_VERSION]))])
# AM_AUX_DIR_EXPAND -*- Autoconf -*-
-# Copyright (C) 2001-2013 Free Software Foundation, Inc.
+# Copyright (C) 2001-2018 Free Software Foundation, Inc.
#
# This file is free software; the Free Software Foundation
# gives unlimited permission to copy and/or distribute it,
@@ -110,7 +110,7 @@ am_aux_dir=`cd "$ac_aux_dir" && pwd`
# AM_CONDITIONAL -*- Autoconf -*-
-# Copyright (C) 1997-2013 Free Software Foundation, Inc.
+# Copyright (C) 1997-2018 Free Software Foundation, Inc.
#
# This file is free software; the Free Software Foundation
# gives unlimited permission to copy and/or distribute it,
@@ -141,7 +141,7 @@ AC_CONFIG_COMMANDS_PRE(
Usually this means the macro was only invoked conditionally.]])
fi])])
-# Copyright (C) 1999-2013 Free Software Foundation, Inc.
+# Copyright (C) 1999-2018 Free Software Foundation, Inc.
#
# This file is free software; the Free Software Foundation
# gives unlimited permission to copy and/or distribute it,
@@ -332,13 +332,12 @@ _AM_SUBST_NOTMAKE([am__nodep])dnl
# Generate code to set up dependency tracking. -*- Autoconf -*-
-# Copyright (C) 1999-2013 Free Software Foundation, Inc.
+# Copyright (C) 1999-2018 Free Software Foundation, Inc.
#
# This file is free software; the Free Software Foundation
# gives unlimited permission to copy and/or distribute it,
# with or without modifications, as long as this notice is preserved.
-
# _AM_OUTPUT_DEPENDENCY_COMMANDS
# ------------------------------
AC_DEFUN([_AM_OUTPUT_DEPENDENCY_COMMANDS],
@@ -346,49 +345,41 @@ AC_DEFUN([_AM_OUTPUT_DEPENDENCY_COMMANDS],
# Older Autoconf quotes --file arguments for eval, but not when files
# are listed without --file. Let's play safe and only enable the eval
# if we detect the quoting.
- case $CONFIG_FILES in
- *\'*) eval set x "$CONFIG_FILES" ;;
- *) set x $CONFIG_FILES ;;
- esac
+ # TODO: see whether this extra hack can be removed once we start
+ # requiring Autoconf 2.70 or later.
+ AS_CASE([$CONFIG_FILES],
+ [*\'*], [eval set x "$CONFIG_FILES"],
+ [*], [set x $CONFIG_FILES])
shift
- for mf
+ # Used to flag and report bootstrapping failures.
+ am_rc=0
+ for am_mf
do
# Strip MF so we end up with the name of the file.
- mf=`echo "$mf" | sed -e 's/:.*$//'`
- # Check whether this is an Automake generated Makefile or not.
- # We used to match only the files named 'Makefile.in', but
- # some people rename them; so instead we look at the file content.
- # Grep'ing the first line is not enough: some people post-process
- # each Makefile.in and add a new line on top of each file to say so.
- # Grep'ing the whole file is not good either: AIX grep has a line
+ am_mf=`AS_ECHO(["$am_mf"]) | sed -e 's/:.*$//'`
+ # Check whether this is an Automake generated Makefile which includes
+ # dependency-tracking related rules and includes.
+ # Grep'ing the whole file directly is not great: AIX grep has a line
# limit of 2048, but all sed's we know have understand at least 4000.
- if sed -n 's,^#.*generated by automake.*,X,p' "$mf" | grep X >/dev/null 2>&1; then
- dirpart=`AS_DIRNAME("$mf")`
- else
- continue
- fi
- # Extract the definition of DEPDIR, am__include, and am__quote
- # from the Makefile without running 'make'.
- DEPDIR=`sed -n 's/^DEPDIR = //p' < "$mf"`
- test -z "$DEPDIR" && continue
- am__include=`sed -n 's/^am__include = //p' < "$mf"`
- test -z "$am__include" && continue
- am__quote=`sed -n 's/^am__quote = //p' < "$mf"`
- # Find all dependency output files, they are included files with
- # $(DEPDIR) in their names. We invoke sed twice because it is the
- # simplest approach to changing $(DEPDIR) to its actual value in the
- # expansion.
- for file in `sed -n "
- s/^$am__include $am__quote\(.*(DEPDIR).*\)$am__quote"'$/\1/p' <"$mf" | \
- sed -e 's/\$(DEPDIR)/'"$DEPDIR"'/g'`; do
- # Make sure the directory exists.
- test -f "$dirpart/$file" && continue
- fdir=`AS_DIRNAME(["$file"])`
- AS_MKDIR_P([$dirpart/$fdir])
- # echo "creating $dirpart/$file"
- echo '# dummy' > "$dirpart/$file"
- done
+ sed -n 's,^am--depfiles:.*,X,p' "$am_mf" | grep X >/dev/null 2>&1 \
+ || continue
+ am_dirpart=`AS_DIRNAME(["$am_mf"])`
+ am_filepart=`AS_BASENAME(["$am_mf"])`
+ AM_RUN_LOG([cd "$am_dirpart" \
+ && sed -e '/# am--include-marker/d' "$am_filepart" \
+ | $MAKE -f - am--depfiles]) || am_rc=$?
done
+ if test $am_rc -ne 0; then
+ AC_MSG_FAILURE([Something went wrong bootstrapping makefile fragments
+ for automatic dependency tracking. Try re-running configure with the
+ '--disable-dependency-tracking' option to at least be able to build
+ the package (albeit without support for automatic dependency tracking).])
+ fi
+ AS_UNSET([am_dirpart])
+ AS_UNSET([am_filepart])
+ AS_UNSET([am_mf])
+ AS_UNSET([am_rc])
+ rm -f conftest-deps.mk
}
])# _AM_OUTPUT_DEPENDENCY_COMMANDS
@@ -397,18 +388,17 @@ AC_DEFUN([_AM_OUTPUT_DEPENDENCY_COMMANDS],
# -----------------------------
# This macro should only be invoked once -- use via AC_REQUIRE.
#
-# This code is only required when automatic dependency tracking
-# is enabled. FIXME. This creates each '.P' file that we will
-# need in order to bootstrap the dependency handling code.
+# This code is only required when automatic dependency tracking is enabled.
+# This creates each '.Po' and '.Plo' makefile fragment that we'll need in
+# order to bootstrap the dependency handling code.
AC_DEFUN([AM_OUTPUT_DEPENDENCY_COMMANDS],
[AC_CONFIG_COMMANDS([depfiles],
[test x"$AMDEP_TRUE" != x"" || _AM_OUTPUT_DEPENDENCY_COMMANDS],
- [AMDEP_TRUE="$AMDEP_TRUE" ac_aux_dir="$ac_aux_dir"])
-])
+ [AMDEP_TRUE="$AMDEP_TRUE" MAKE="${MAKE-make}"])])
# Do all the work for Automake. -*- Autoconf -*-
-# Copyright (C) 1996-2013 Free Software Foundation, Inc.
+# Copyright (C) 1996-2018 Free Software Foundation, Inc.
#
# This file is free software; the Free Software Foundation
# gives unlimited permission to copy and/or distribute it,
@@ -495,11 +485,11 @@ AC_REQUIRE([AM_PROG_INSTALL_STRIP])dnl
AC_REQUIRE([AC_PROG_MKDIR_P])dnl
# For better backward compatibility. To be removed once Automake 1.9.x
# dies out for good. For more background, see:
-# <http://lists.gnu.org/archive/html/automake/2012-07/msg00001.html>
-# <http://lists.gnu.org/archive/html/automake/2012-07/msg00014.html>
+# <https://lists.gnu.org/archive/html/automake/2012-07/msg00001.html>
+# <https://lists.gnu.org/archive/html/automake/2012-07/msg00014.html>
AC_SUBST([mkdir_p], ['$(MKDIR_P)'])
-# We need awk for the "check" target. The system "awk" is bad on
-# some platforms.
+# We need awk for the "check" target (and possibly the TAP driver). The
+# system "awk" is bad on some platforms.
AC_REQUIRE([AC_PROG_AWK])dnl
AC_REQUIRE([AC_PROG_MAKE_SET])dnl
AC_REQUIRE([AM_SET_LEADING_DOT])dnl
@@ -563,7 +553,7 @@ END
Aborting the configuration process, to ensure you take notice of the issue.
You can download and install GNU coreutils to get an 'rm' implementation
-that behaves properly: <http://www.gnu.org/software/coreutils/>.
+that behaves properly: <https://www.gnu.org/software/coreutils/>.
If you want to complete the configuration process using your problematic
'rm' anyway, export the environment variable ACCEPT_INFERIOR_RM_PROGRAM
@@ -573,6 +563,9 @@ END
AC_MSG_ERROR([Your 'rm' program is bad, sorry.])
fi
fi
+dnl The trailing newline in this macro's definition is deliberate, for
+dnl backward compatibility and to allow trailing 'dnl'-style comments
+dnl after the AM_INIT_AUTOMAKE invocation. See automake bug#16841.
])
dnl Hook into '_AC_COMPILER_EXEEXT' early to learn its expansion. Do not
@@ -602,7 +595,7 @@ for _am_header in $config_headers :; do
done
echo "timestamp for $_am_arg" >`AS_DIRNAME(["$_am_arg"])`/stamp-h[]$_am_stamp_count])
-# Copyright (C) 2001-2013 Free Software Foundation, Inc.
+# Copyright (C) 2001-2018 Free Software Foundation, Inc.
#
# This file is free software; the Free Software Foundation
# gives unlimited permission to copy and/or distribute it,
@@ -613,7 +606,7 @@ echo "timestamp for $_am_arg" >`AS_DIRNAME(["$_am_arg"])`/stamp-h[]$_am_stamp_co
# Define $install_sh.
AC_DEFUN([AM_PROG_INSTALL_SH],
[AC_REQUIRE([AM_AUX_DIR_EXPAND])dnl
-if test x"${install_sh}" != xset; then
+if test x"${install_sh+set}" != xset; then
case $am_aux_dir in
*\ * | *\ *)
install_sh="\${SHELL} '$am_aux_dir/install-sh'" ;;
@@ -623,7 +616,7 @@ if test x"${install_sh}" != xset; then
fi
AC_SUBST([install_sh])])
-# Copyright (C) 2003-2013 Free Software Foundation, Inc.
+# Copyright (C) 2003-2018 Free Software Foundation, Inc.
#
# This file is free software; the Free Software Foundation
# gives unlimited permission to copy and/or distribute it,
@@ -644,7 +637,7 @@ AC_SUBST([am__leading_dot])])
# Check to see how 'make' treats includes. -*- Autoconf -*-
-# Copyright (C) 2001-2013 Free Software Foundation, Inc.
+# Copyright (C) 2001-2018 Free Software Foundation, Inc.
#
# This file is free software; the Free Software Foundation
# gives unlimited permission to copy and/or distribute it,
@@ -652,49 +645,42 @@ AC_SUBST([am__leading_dot])])
# AM_MAKE_INCLUDE()
# -----------------
-# Check to see how make treats includes.
+# Check whether make has an 'include' directive that can support all
+# the idioms we need for our automatic dependency tracking code.
AC_DEFUN([AM_MAKE_INCLUDE],
-[am_make=${MAKE-make}
-cat > confinc << 'END'
+[AC_MSG_CHECKING([whether ${MAKE-make} supports the include directive])
+cat > confinc.mk << 'END'
am__doit:
- @echo this is the am__doit target
+ @echo this is the am__doit target >confinc.out
.PHONY: am__doit
END
-# If we don't find an include directive, just comment out the code.
-AC_MSG_CHECKING([for style of include used by $am_make])
am__include="#"
am__quote=
-_am_result=none
-# First try GNU make style include.
-echo "include confinc" > confmf
-# Ignore all kinds of additional output from 'make'.
-case `$am_make -s -f confmf 2> /dev/null` in #(
-*the\ am__doit\ target*)
- am__include=include
- am__quote=
- _am_result=GNU
- ;;
-esac
-# Now try BSD make style include.
-if test "$am__include" = "#"; then
- echo '.include "confinc"' > confmf
- case `$am_make -s -f confmf 2> /dev/null` in #(
- *the\ am__doit\ target*)
- am__include=.include
- am__quote="\""
- _am_result=BSD
- ;;
- esac
-fi
-AC_SUBST([am__include])
-AC_SUBST([am__quote])
-AC_MSG_RESULT([$_am_result])
-rm -f confinc confmf
-])
+# BSD make does it like this.
+echo '.include "confinc.mk" # ignored' > confmf.BSD
+# Other make implementations (GNU, Solaris 10, AIX) do it like this.
+echo 'include confinc.mk # ignored' > confmf.GNU
+_am_result=no
+for s in GNU BSD; do
+ AM_RUN_LOG([${MAKE-make} -f confmf.$s && cat confinc.out])
+ AS_CASE([$?:`cat confinc.out 2>/dev/null`],
+ ['0:this is the am__doit target'],
+ [AS_CASE([$s],
+ [BSD], [am__include='.include' am__quote='"'],
+ [am__include='include' am__quote=''])])
+ if test "$am__include" != "#"; then
+ _am_result="yes ($s style)"
+ break
+ fi
+done
+rm -f confinc.* confmf.*
+AC_MSG_RESULT([${_am_result}])
+AC_SUBST([am__include])])
+AC_SUBST([am__quote])])
# Fake the existence of programs that GNU maintainers use. -*- Autoconf -*-
-# Copyright (C) 1997-2013 Free Software Foundation, Inc.
+# Copyright (C) 1997-2018 Free Software Foundation, Inc.
#
# This file is free software; the Free Software Foundation
# gives unlimited permission to copy and/or distribute it,
@@ -733,7 +719,7 @@ fi
# Helper functions for option handling. -*- Autoconf -*-
-# Copyright (C) 2001-2013 Free Software Foundation, Inc.
+# Copyright (C) 2001-2018 Free Software Foundation, Inc.
#
# This file is free software; the Free Software Foundation
# gives unlimited permission to copy and/or distribute it,
@@ -762,7 +748,7 @@ AC_DEFUN([_AM_SET_OPTIONS],
AC_DEFUN([_AM_IF_OPTION],
[m4_ifset(_AM_MANGLE_OPTION([$1]), [$2], [$3])])
-# Copyright (C) 1999-2013 Free Software Foundation, Inc.
+# Copyright (C) 1999-2018 Free Software Foundation, Inc.
#
# This file is free software; the Free Software Foundation
# gives unlimited permission to copy and/or distribute it,
@@ -809,7 +795,7 @@ AC_LANG_POP([C])])
# For backward compatibility.
AC_DEFUN_ONCE([AM_PROG_CC_C_O], [AC_REQUIRE([AC_PROG_CC])])
-# Copyright (C) 2001-2013 Free Software Foundation, Inc.
+# Copyright (C) 2001-2018 Free Software Foundation, Inc.
#
# This file is free software; the Free Software Foundation
# gives unlimited permission to copy and/or distribute it,
@@ -828,7 +814,7 @@ AC_DEFUN([AM_RUN_LOG],
# Check to make sure that the build environment is sane. -*- Autoconf -*-
-# Copyright (C) 1996-2013 Free Software Foundation, Inc.
+# Copyright (C) 1996-2018 Free Software Foundation, Inc.
#
# This file is free software; the Free Software Foundation
# gives unlimited permission to copy and/or distribute it,
@@ -909,7 +895,7 @@ AC_CONFIG_COMMANDS_PRE(
rm -f conftest.file
])
-# Copyright (C) 2009-2013 Free Software Foundation, Inc.
+# Copyright (C) 2009-2018 Free Software Foundation, Inc.
#
# This file is free software; the Free Software Foundation
# gives unlimited permission to copy and/or distribute it,
@@ -969,7 +955,7 @@ AC_SUBST([AM_BACKSLASH])dnl
_AM_SUBST_NOTMAKE([AM_BACKSLASH])dnl
])
-# Copyright (C) 2001-2013 Free Software Foundation, Inc.
+# Copyright (C) 2001-2018 Free Software Foundation, Inc.
#
# This file is free software; the Free Software Foundation
# gives unlimited permission to copy and/or distribute it,
@@ -997,7 +983,7 @@ fi
INSTALL_STRIP_PROGRAM="\$(install_sh) -c -s"
AC_SUBST([INSTALL_STRIP_PROGRAM])])
-# Copyright (C) 2006-2013 Free Software Foundation, Inc.
+# Copyright (C) 2006-2018 Free Software Foundation, Inc.
#
# This file is free software; the Free Software Foundation
# gives unlimited permission to copy and/or distribute it,
@@ -1016,7 +1002,7 @@ AC_DEFUN([AM_SUBST_NOTMAKE], [_AM_SUBST_NOTMAKE($@)])
# Check how to create a tarball. -*- Autoconf -*-
-# Copyright (C) 2004-2013 Free Software Foundation, Inc.
+# Copyright (C) 2004-2018 Free Software Foundation, Inc.
#
# This file is free software; the Free Software Foundation
# gives unlimited permission to copy and/or distribute it,
=====================================
configure
=====================================
The diff for this file was not included because it is too large.
=====================================
configure.ac
=====================================
@@ -56,7 +56,7 @@ dnl Process this file with autoconf to produce a configure script.
AC_PREREQ([2.64])
m4_define([V_MAJOR], [2])
m4_define([V_MINOR], [5])
-m4_define([V_MICRO], [0])
+m4_define([V_MICRO], [2])
AC_INIT(
[crac],
@@ -153,7 +153,8 @@ AC_PROG_LN_S
AC_SUBST([VERSION])
dnl Disable shared library construction by default (must appear before LT_INIT)
-AC_DISABLE_SHARED
+AC_ENABLE_SHARED
+AC_DISABLE_STATIC
LT_INIT
LT_PATH_LD
@@ -307,7 +308,7 @@ AM_CONDITIONAL([INCLUDED_PROGRESSBAR], [test "x$with_included_ProgressBar" == "x
AC_CHECK_LIB([z], [gzread], ,
[AC_MSG_ERROR([zlib not found, see http://www.zlib.net])])
-AC_CHECK_LIB([hts], [hts_open], ,
+AC_CHECK_LIB([hts], [hts_hopen], ,
[AC_MSG_ERROR([htslib not found, see http://www.htslib.org/])])
GK_OK=1
@@ -359,7 +360,8 @@ AS_IF([test "x$enable_shared" == "xyes" ],
[AS_VAR_APPEND([ac_configure_args], [" --enable-shared"])],
[AS_VAR_APPEND([ac_configure_args], [" --disable-shared"])])
AS_IF([test "x$enable_static" == "xyes" ],
- [AS_VAR_APPEND([ac_configure_args], [" --enable-static"])],
+ [LDFLAGS="$LDFLAGS -all-static"
+ AS_VAR_APPEND([ac_configure_args], [" --enable-static"])],
[AS_VAR_APPEND([ac_configure_args], [" --disable-static"])])
dnl Forward FLAGS to libGkArrays/libProgressBar configure scripts if needed
=====================================
man/Makefile.in
=====================================
@@ -1,7 +1,7 @@
-# Makefile.in generated by automake 1.14.1 from Makefile.am.
+# Makefile.in generated by automake 1.16.1 from Makefile.am.
# @configure_input@
-# Copyright (C) 1994-2013 Free Software Foundation, Inc.
+# Copyright (C) 1994-2018 Free Software Foundation, Inc.
# This Makefile.in is free software; the Free Software Foundation
# gives unlimited permission to copy and/or distribute it,
@@ -113,7 +113,17 @@
# #
###############################################################################
VPATH = @srcdir@
-am__is_gnu_make = test -n '$(MAKEFILE_LIST)' && test -n '$(MAKELEVEL)'
+am__is_gnu_make = { \
+ if test -z '$(MAKELEVEL)'; then \
+ false; \
+ elif test -n '$(MAKE_HOST)'; then \
+ true; \
+ elif test -n '$(MAKE_VERSION)' && test -n '$(CURDIR)'; then \
+ true; \
+ else \
+ false; \
+ fi; \
+}
am__make_running_with_option = \
case $${target_option-} in \
?) ;; \
@@ -177,8 +187,6 @@ POST_UNINSTALL = :
build_triplet = @build@
host_triplet = @host@
subdir = man
-DIST_COMMON = $(srcdir)/Makefile.in $(srcdir)/Makefile.am \
- $(srcdir)/crac.1.in
ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
am__aclocal_m4_deps = $(top_srcdir)/config/m4/libtool.m4 \
$(top_srcdir)/config/m4/ltoptions.m4 \
@@ -188,6 +196,7 @@ am__aclocal_m4_deps = $(top_srcdir)/config/m4/libtool.m4 \
$(top_srcdir)/configure.ac
am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \
$(ACLOCAL_M4)
+DIST_COMMON = $(srcdir)/Makefile.am $(am__DIST_COMMON)
mkinstalldirs = $(install_sh) -d
CONFIG_HEADER = $(top_builddir)/config/config.h
CONFIG_CLEAN_FILES = crac.1
@@ -243,6 +252,7 @@ am__installdirs = "$(DESTDIR)$(man1dir)"
NROFF = nroff
MANS = $(man_MANS)
am__tagged_files = $(HEADERS) $(SOURCES) $(TAGS_FILES) $(LISP)
+am__DIST_COMMON = $(srcdir)/Makefile.in $(srcdir)/crac.1.in
DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
ACLOCAL = @ACLOCAL@
ALLOCA = @ALLOCA@
@@ -291,6 +301,7 @@ LIBTOOL = @LIBTOOL@
LIPO = @LIPO@
LN_S = @LN_S@
LTLIBOBJS = @LTLIBOBJS@
+LT_SYS_LIBRARY_PATH = @LT_SYS_LIBRARY_PATH@
MAKEINFO = @MAKEINFO@
MANIFEST_TOOL = @MANIFEST_TOOL@
MKDIR_P = @MKDIR_P@
@@ -361,6 +372,7 @@ pdfdir = @pdfdir@
prefix = @prefix@
program_transform_name = @program_transform_name@
psdir = @psdir@
+runstatedir = @runstatedir@
sbindir = @sbindir@
sharedstatedir = @sharedstatedir@
srcdir = @srcdir@
@@ -396,14 +408,13 @@ $(srcdir)/Makefile.in: $(srcdir)/Makefile.am $(am__configure_deps)
echo ' cd $(top_srcdir) && $(AUTOMAKE) --gnu man/Makefile'; \
$(am__cd) $(top_srcdir) && \
$(AUTOMAKE) --gnu man/Makefile
-.PRECIOUS: Makefile
Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status
@case '$?' in \
*config.status*) \
cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh;; \
*) \
- echo ' cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__depfiles_maybe)'; \
- cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__depfiles_maybe);; \
+ echo ' cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__maybe_remake_depfiles)'; \
+ cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__maybe_remake_depfiles);; \
esac;
$(top_builddir)/config.status: $(top_srcdir)/configure $(CONFIG_STATUS_DEPENDENCIES)
@@ -472,7 +483,10 @@ ctags CTAGS:
cscope cscopelist:
-distdir: $(DISTFILES)
+distdir: $(BUILT_SOURCES)
+ $(MAKE) $(AM_MAKEFLAGS) distdir-am
+
+distdir-am: $(DISTFILES)
@srcdirstrip=`echo "$(srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \
topsrcdirstrip=`echo "$(top_srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \
list='$(DISTFILES)'; \
@@ -626,6 +640,8 @@ uninstall-man: uninstall-man1
ps ps-am tags-am uninstall uninstall-am uninstall-man \
uninstall-man1
+.PRECIOUS: Makefile
+
# Tell versions [3.59,3.63) of GNU make to not export all variables.
# Otherwise a system limit (for SysV at least) may be exceeded.
=====================================
scripts/Makefile.in
=====================================
@@ -1,7 +1,7 @@
-# Makefile.in generated by automake 1.14.1 from Makefile.am.
+# Makefile.in generated by automake 1.16.1 from Makefile.am.
# @configure_input@
-# Copyright (C) 1994-2013 Free Software Foundation, Inc.
+# Copyright (C) 1994-2018 Free Software Foundation, Inc.
# This Makefile.in is free software; the Free Software Foundation
# gives unlimited permission to copy and/or distribute it,
@@ -100,7 +100,17 @@
###############################################################################
VPATH = @srcdir@
-am__is_gnu_make = test -n '$(MAKEFILE_LIST)' && test -n '$(MAKELEVEL)'
+am__is_gnu_make = { \
+ if test -z '$(MAKELEVEL)'; then \
+ false; \
+ elif test -n '$(MAKE_HOST)'; then \
+ true; \
+ elif test -n '$(MAKE_VERSION)' && test -n '$(CURDIR)'; then \
+ true; \
+ else \
+ false; \
+ fi; \
+}
am__make_running_with_option = \
case $${target_option-} in \
?) ;; \
@@ -164,8 +174,6 @@ POST_UNINSTALL = :
build_triplet = @build@
host_triplet = @host@
subdir = scripts
-DIST_COMMON = $(srcdir)/Makefile.in $(srcdir)/Makefile.am \
- $(srcdir)/crac-client.in $(dist_bin_SCRIPTS)
ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
am__aclocal_m4_deps = $(top_srcdir)/config/m4/libtool.m4 \
$(top_srcdir)/config/m4/ltoptions.m4 \
@@ -175,6 +183,8 @@ am__aclocal_m4_deps = $(top_srcdir)/config/m4/libtool.m4 \
$(top_srcdir)/configure.ac
am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \
$(ACLOCAL_M4)
+DIST_COMMON = $(srcdir)/Makefile.am $(dist_bin_SCRIPTS) \
+ $(am__DIST_COMMON)
mkinstalldirs = $(install_sh) -d
CONFIG_HEADER = $(top_builddir)/config/config.h
CONFIG_CLEAN_FILES = crac-client
@@ -228,6 +238,7 @@ am__can_run_installinfo = \
*) (install-info --version) >/dev/null 2>&1;; \
esac
am__tagged_files = $(HEADERS) $(SOURCES) $(TAGS_FILES) $(LISP)
+am__DIST_COMMON = $(srcdir)/Makefile.in $(srcdir)/crac-client.in
DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
ACLOCAL = @ACLOCAL@
ALLOCA = @ALLOCA@
@@ -276,6 +287,7 @@ LIBTOOL = @LIBTOOL@
LIPO = @LIPO@
LN_S = @LN_S@
LTLIBOBJS = @LTLIBOBJS@
+LT_SYS_LIBRARY_PATH = @LT_SYS_LIBRARY_PATH@
MAKEINFO = @MAKEINFO@
MANIFEST_TOOL = @MANIFEST_TOOL@
MKDIR_P = @MKDIR_P@
@@ -346,6 +358,7 @@ pdfdir = @pdfdir@
prefix = @prefix@
program_transform_name = @program_transform_name@
psdir = @psdir@
+runstatedir = @runstatedir@
sbindir = @sbindir@
sharedstatedir = @sharedstatedir@
srcdir = @srcdir@
@@ -375,14 +388,13 @@ $(srcdir)/Makefile.in: $(srcdir)/Makefile.am $(am__configure_deps)
echo ' cd $(top_srcdir) && $(AUTOMAKE) --gnu scripts/Makefile'; \
$(am__cd) $(top_srcdir) && \
$(AUTOMAKE) --gnu scripts/Makefile
-.PRECIOUS: Makefile
Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status
@case '$?' in \
*config.status*) \
cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh;; \
*) \
- echo ' cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__depfiles_maybe)'; \
- cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__depfiles_maybe);; \
+ echo ' cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__maybe_remake_depfiles)'; \
+ cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__maybe_remake_depfiles);; \
esac;
$(top_builddir)/config.status: $(top_srcdir)/configure $(CONFIG_STATUS_DEPENDENCIES)
@@ -443,7 +455,10 @@ ctags CTAGS:
cscope cscopelist:
-distdir: $(DISTFILES)
+distdir: $(BUILT_SOURCES)
+ $(MAKE) $(AM_MAKEFLAGS) distdir-am
+
+distdir-am: $(DISTFILES)
@srcdirstrip=`echo "$(srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \
topsrcdirstrip=`echo "$(top_srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \
list='$(DISTFILES)'; \
@@ -595,6 +610,8 @@ uninstall-am: uninstall-dist_binSCRIPTS
mostlyclean-libtool pdf pdf-am ps ps-am tags-am uninstall \
uninstall-am uninstall-dist_binSCRIPTS
+.PRECIOUS: Makefile
+
# Tell versions [3.59,3.63) of GNU make to not export all variables.
# Otherwise a system limit (for SysV at least) may be exceeded.
=====================================
scripts/crac-client
=====================================
@@ -113,7 +113,7 @@ do
done
if [ $QUIET -eq 0 ]; then
- echo "This is the client of crac v. 2.5.0";
+ echo "This is the client of crac v. 2.5.2";
fi
[ -p $PIPE ] || PIPE=${PIPE/`dirname $0`/$PWD}
=====================================
src/Bitset.h
=====================================
@@ -53,6 +53,7 @@
#include <cstdlib> // for uint
#include <vector> // std::vector
+#include "types.h"
class Bitset {
public:
=====================================
src/Makefile.am
=====================================
@@ -98,6 +98,8 @@
###############################################################################
+AUTOMAKE_OPTIONS = subdir-objects
+
bin_PROGRAMS=crac
CRAC_LINKS = crac-index
=====================================
src/Makefile.in
=====================================
@@ -1,7 +1,7 @@
-# Makefile.in generated by automake 1.14.1 from Makefile.am.
+# Makefile.in generated by automake 1.16.1 from Makefile.am.
# @configure_input@
-# Copyright (C) 1994-2013 Free Software Foundation, Inc.
+# Copyright (C) 1994-2018 Free Software Foundation, Inc.
# This Makefile.in is free software; the Free Software Foundation
# gives unlimited permission to copy and/or distribute it,
@@ -114,7 +114,17 @@
###############################################################################
VPATH = @srcdir@
-am__is_gnu_make = test -n '$(MAKEFILE_LIST)' && test -n '$(MAKELEVEL)'
+am__is_gnu_make = { \
+ if test -z '$(MAKELEVEL)'; then \
+ false; \
+ elif test -n '$(MAKE_HOST)'; then \
+ true; \
+ elif test -n '$(MAKE_VERSION)' && test -n '$(CURDIR)'; then \
+ true; \
+ else \
+ false; \
+ fi; \
+}
am__make_running_with_option = \
case $${target_option-} in \
?) ;; \
@@ -189,8 +199,6 @@ bin_PROGRAMS = crac$(EXEEXT)
@HAVE_LIBGKARRAYS_TRUE at am__append_9 = -lGkArrays
@HAVE_LIBJELLYFISH_TRUE at am__append_10 = -ljellyfish-2.0
subdir = src
-DIST_COMMON = $(srcdir)/Makefile.in $(srcdir)/Makefile.am \
- $(top_srcdir)/config/depcomp
ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
am__aclocal_m4_deps = $(top_srcdir)/config/m4/libtool.m4 \
$(top_srcdir)/config/m4/ltoptions.m4 \
@@ -200,6 +208,7 @@ am__aclocal_m4_deps = $(top_srcdir)/config/m4/libtool.m4 \
$(top_srcdir)/configure.ac
am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \
$(ACLOCAL_M4)
+DIST_COMMON = $(srcdir)/Makefile.am $(am__DIST_COMMON)
mkinstalldirs = $(install_sh) -d
CONFIG_HEADER = $(top_builddir)/config/config.h
CONFIG_CLEAN_FILES =
@@ -237,7 +246,14 @@ am__v_at_0 = @
am__v_at_1 =
DEFAULT_INCLUDES = -I. at am__isrc@ -I$(top_builddir)/config
depcomp = $(SHELL) $(top_srcdir)/config/depcomp
-am__depfiles_maybe = depfiles
+am__maybe_remake_depfiles = depfiles
+am__depfiles_remade = ./$(DEPDIR)/Bitset.Po ./$(DEPDIR)/BreakList.Po \
+ ./$(DEPDIR)/CandidatBreak.Po ./$(DEPDIR)/Classifier.Po \
+ ./$(DEPDIR)/GkReadIndex.Po ./$(DEPDIR)/JellyReadIndex.Po \
+ ./$(DEPDIR)/Parameters.Po ./$(DEPDIR)/Support.Po \
+ ./$(DEPDIR)/SupportBreak.Po ./$(DEPDIR)/classifyTags.Po \
+ ./$(DEPDIR)/crac.Po ./$(DEPDIR)/locateServer.Po \
+ ./$(DEPDIR)/utils.Po
am__mv = mv -f
CXXCOMPILE = $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) \
$(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS)
@@ -297,7 +313,7 @@ am__recursive_targets = \
$(RECURSIVE_CLEAN_TARGETS) \
$(am__extra_recursive_targets)
AM_RECURSIVE_TARGETS = $(am__recursive_targets:-recursive=) TAGS CTAGS \
- distdir
+ distdir distdir-am
am__tagged_files = $(HEADERS) $(SOURCES) $(TAGS_FILES) $(LISP)
# Read a list of newline-separated strings from the standard input,
# and print each of them once, without duplicates. Input order is
@@ -319,6 +335,7 @@ ETAGS = etags
CTAGS = ctags
DIST_SUBDIRS = libReadsInfo libSSA libgzstream libReadsReader \
libGkArrays libJellyfish-2.0
+am__DIST_COMMON = $(srcdir)/Makefile.in $(top_srcdir)/config/depcomp
DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
am__relativize = \
dir0=`pwd`; \
@@ -392,6 +409,7 @@ LIBTOOL = @LIBTOOL@
LIPO = @LIPO@
LN_S = @LN_S@
LTLIBOBJS = @LTLIBOBJS@
+LT_SYS_LIBRARY_PATH = @LT_SYS_LIBRARY_PATH@
MAKEINFO = @MAKEINFO@
MANIFEST_TOOL = @MANIFEST_TOOL@
MKDIR_P = @MKDIR_P@
@@ -462,6 +480,7 @@ pdfdir = @pdfdir@
prefix = @prefix@
program_transform_name = @program_transform_name@
psdir = @psdir@
+runstatedir = @runstatedir@
sbindir = @sbindir@
sharedstatedir = @sharedstatedir@
srcdir = @srcdir@
@@ -471,6 +490,7 @@ target_alias = @target_alias@
top_build_prefix = @top_build_prefix@
top_builddir = @top_builddir@
top_srcdir = @top_srcdir@
+AUTOMAKE_OPTIONS = subdir-objects
CRAC_LINKS = crac-index
SUBDIRS = libReadsInfo libSSA libgzstream libReadsReader \
$(am__append_1) $(am__append_2)
@@ -525,14 +545,13 @@ $(srcdir)/Makefile.in: $(srcdir)/Makefile.am $(am__configure_deps)
echo ' cd $(top_srcdir) && $(AUTOMAKE) --gnu src/Makefile'; \
$(am__cd) $(top_srcdir) && \
$(AUTOMAKE) --gnu src/Makefile
-.PRECIOUS: Makefile
Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status
@case '$?' in \
*config.status*) \
cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh;; \
*) \
- echo ' cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__depfiles_maybe)'; \
- cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__depfiles_maybe);; \
+ echo ' cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__maybe_remake_depfiles)'; \
+ cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__maybe_remake_depfiles);; \
esac;
$(top_builddir)/config.status: $(top_srcdir)/configure $(CONFIG_STATUS_DEPENDENCIES)
@@ -603,37 +622,46 @@ mostlyclean-compile:
distclean-compile:
-rm -f *.tab.c
- at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/Bitset.Po at am__quote@
- at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/BreakList.Po at am__quote@
- at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/CandidatBreak.Po at am__quote@
- at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/Classifier.Po at am__quote@
- at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/GkReadIndex.Po at am__quote@
- at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/JellyReadIndex.Po at am__quote@
- at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/Parameters.Po at am__quote@
- at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/Support.Po at am__quote@
- at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/SupportBreak.Po at am__quote@
- at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/classifyTags.Po at am__quote@
- at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/crac.Po at am__quote@
- at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/locateServer.Po at am__quote@
- at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/utils.Po at am__quote@
+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/Bitset.Po at am__quote@ # am--include-marker
+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/BreakList.Po at am__quote@ # am--include-marker
+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/CandidatBreak.Po at am__quote@ # am--include-marker
+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/Classifier.Po at am__quote@ # am--include-marker
+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/GkReadIndex.Po at am__quote@ # am--include-marker
+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/JellyReadIndex.Po at am__quote@ # am--include-marker
+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/Parameters.Po at am__quote@ # am--include-marker
+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/Support.Po at am__quote@ # am--include-marker
+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/SupportBreak.Po at am__quote@ # am--include-marker
+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/classifyTags.Po at am__quote@ # am--include-marker
+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/crac.Po at am__quote@ # am--include-marker
+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/locateServer.Po at am__quote@ # am--include-marker
+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/utils.Po at am__quote@ # am--include-marker
+
+$(am__depfiles_remade):
+ @$(MKDIR_P) $(@D)
+ @echo '# dummy' >$@-t && $(am__mv) $@-t $@
+
+am--depfiles: $(am__depfiles_remade)
.cpp.o:
- at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXXCOMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ $<
- at am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po
+ at am__fastdepCXX_TRUE@ $(AM_V_CXX)depbase=`echo $@ | sed 's|[^/]*$$|$(DEPDIR)/&|;s|\.o$$||'`;\
+ at am__fastdepCXX_TRUE@ $(CXXCOMPILE) -MT $@ -MD -MP -MF $$depbase.Tpo -c -o $@ $< &&\
+ at am__fastdepCXX_TRUE@ $(am__mv) $$depbase.Tpo $$depbase.Po
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ $(AM_V_CXX)source='$<' object='$@' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXXCOMPILE) -c -o $@ $<
.cpp.obj:
- at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXXCOMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ `$(CYGPATH_W) '$<'`
- at am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po
+ at am__fastdepCXX_TRUE@ $(AM_V_CXX)depbase=`echo $@ | sed 's|[^/]*$$|$(DEPDIR)/&|;s|\.obj$$||'`;\
+ at am__fastdepCXX_TRUE@ $(CXXCOMPILE) -MT $@ -MD -MP -MF $$depbase.Tpo -c -o $@ `$(CYGPATH_W) '$<'` &&\
+ at am__fastdepCXX_TRUE@ $(am__mv) $$depbase.Tpo $$depbase.Po
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ $(AM_V_CXX)source='$<' object='$@' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXXCOMPILE) -c -o $@ `$(CYGPATH_W) '$<'`
.cpp.lo:
- at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(LTCXXCOMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ $<
- at am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Plo
+ at am__fastdepCXX_TRUE@ $(AM_V_CXX)depbase=`echo $@ | sed 's|[^/]*$$|$(DEPDIR)/&|;s|\.lo$$||'`;\
+ at am__fastdepCXX_TRUE@ $(LTCXXCOMPILE) -MT $@ -MD -MP -MF $$depbase.Tpo -c -o $@ $< &&\
+ at am__fastdepCXX_TRUE@ $(am__mv) $$depbase.Tpo $$depbase.Plo
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ $(AM_V_CXX)source='$<' object='$@' libtool=yes @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(LTCXXCOMPILE) -c -o $@ $<
@@ -743,7 +771,10 @@ cscopelist-am: $(am__tagged_files)
distclean-tags:
-rm -f TAGS ID GTAGS GRTAGS GSYMS GPATH tags
-distdir: $(DISTFILES)
+distdir: $(BUILT_SOURCES)
+ $(MAKE) $(AM_MAKEFLAGS) distdir-am
+
+distdir-am: $(DISTFILES)
@srcdirstrip=`echo "$(srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \
topsrcdirstrip=`echo "$(top_srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \
list='$(DISTFILES)'; \
@@ -845,7 +876,19 @@ clean: clean-recursive
clean-am: clean-binPROGRAMS clean-generic clean-libtool mostlyclean-am
distclean: distclean-recursive
- -rm -rf ./$(DEPDIR)
+ -rm -f ./$(DEPDIR)/Bitset.Po
+ -rm -f ./$(DEPDIR)/BreakList.Po
+ -rm -f ./$(DEPDIR)/CandidatBreak.Po
+ -rm -f ./$(DEPDIR)/Classifier.Po
+ -rm -f ./$(DEPDIR)/GkReadIndex.Po
+ -rm -f ./$(DEPDIR)/JellyReadIndex.Po
+ -rm -f ./$(DEPDIR)/Parameters.Po
+ -rm -f ./$(DEPDIR)/Support.Po
+ -rm -f ./$(DEPDIR)/SupportBreak.Po
+ -rm -f ./$(DEPDIR)/classifyTags.Po
+ -rm -f ./$(DEPDIR)/crac.Po
+ -rm -f ./$(DEPDIR)/locateServer.Po
+ -rm -f ./$(DEPDIR)/utils.Po
-rm -f Makefile
distclean-am: clean-am distclean-compile distclean-generic \
distclean-tags
@@ -891,7 +934,19 @@ install-ps-am:
installcheck-am:
maintainer-clean: maintainer-clean-recursive
- -rm -rf ./$(DEPDIR)
+ -rm -f ./$(DEPDIR)/Bitset.Po
+ -rm -f ./$(DEPDIR)/BreakList.Po
+ -rm -f ./$(DEPDIR)/CandidatBreak.Po
+ -rm -f ./$(DEPDIR)/Classifier.Po
+ -rm -f ./$(DEPDIR)/GkReadIndex.Po
+ -rm -f ./$(DEPDIR)/JellyReadIndex.Po
+ -rm -f ./$(DEPDIR)/Parameters.Po
+ -rm -f ./$(DEPDIR)/Support.Po
+ -rm -f ./$(DEPDIR)/SupportBreak.Po
+ -rm -f ./$(DEPDIR)/classifyTags.Po
+ -rm -f ./$(DEPDIR)/crac.Po
+ -rm -f ./$(DEPDIR)/locateServer.Po
+ -rm -f ./$(DEPDIR)/utils.Po
-rm -f Makefile
maintainer-clean-am: distclean-am maintainer-clean-generic
@@ -913,19 +968,22 @@ uninstall-am: uninstall-binPROGRAMS
.MAKE: $(am__recursive_targets) install-am install-strip
.PHONY: $(am__recursive_targets) CTAGS GTAGS TAGS all all-am all-local \
- check check-am clean clean-binPROGRAMS clean-generic \
- clean-libtool cscopelist-am ctags ctags-am distclean \
- distclean-compile distclean-generic distclean-libtool \
- distclean-tags distdir dvi dvi-am html html-am info info-am \
- install install-am install-binPROGRAMS install-data \
- install-data-am install-dvi install-dvi-am install-exec \
- install-exec-am install-html install-html-am install-info \
- install-info-am install-man install-pdf install-pdf-am \
- install-ps install-ps-am install-strip installcheck \
- installcheck-am installdirs installdirs-am maintainer-clean \
- maintainer-clean-generic mostlyclean mostlyclean-compile \
- mostlyclean-generic mostlyclean-libtool pdf pdf-am ps ps-am \
- tags tags-am uninstall uninstall-am uninstall-binPROGRAMS
+ am--depfiles check check-am clean clean-binPROGRAMS \
+ clean-generic clean-libtool cscopelist-am ctags ctags-am \
+ distclean distclean-compile distclean-generic \
+ distclean-libtool distclean-tags distdir dvi dvi-am html \
+ html-am info info-am install install-am install-binPROGRAMS \
+ install-data install-data-am install-dvi install-dvi-am \
+ install-exec install-exec-am install-html install-html-am \
+ install-info install-info-am install-man install-pdf \
+ install-pdf-am install-ps install-ps-am install-strip \
+ installcheck installcheck-am installdirs installdirs-am \
+ maintainer-clean maintainer-clean-generic mostlyclean \
+ mostlyclean-compile mostlyclean-generic mostlyclean-libtool \
+ pdf pdf-am ps ps-am tags tags-am uninstall uninstall-am \
+ uninstall-binPROGRAMS
+
+.PRECIOUS: Makefile
all-local: $(bin_PROGRAMS) $(CRAC_LINKS)
=====================================
src/Support.cpp
=====================================
@@ -53,6 +53,7 @@
#include <utility>
#include <vector>
#include <algorithm>
+#include <cmath>
#include "Support.h"
#include "BreakList.h"
#include "utils.h"
=====================================
src/SupportBreak.cpp
=====================================
@@ -177,16 +177,20 @@ CandidatBreak *SupportBreak::getCandidatChosen(){
}
int SupportBreak::getChimeraClass(){
- if (getTagBreakLength() < getThreshold() && hasLongEnoughTagBreak()){
+ if (hasLongEnoughTagBreak()){
+ int insert_in_fusion = 0;
+ if (getTagBreakLength() >= getThreshold())
+ insert_in_fusion = 5;
+
if (getChrId(START_BREAK) != getChrId(END_BREAK))
- return 1;
+ return 1+insert_in_fusion;
if (getStrandLocation(START_BREAK) != getStrandLocation(END_BREAK))
- return 4;
+ return 4+insert_in_fusion;
if (getGenomeGapLength() < 0)
- return 3;
+ return 3+insert_in_fusion;
if (labs(getGenomeGapLength()) > parameters->max_splice_length)
- return 2;
- }
+ return 2+insert_in_fusion;
+ }
return 0;
}
=====================================
src/libReadsInfo/Makefile.in
=====================================
@@ -1,7 +1,7 @@
-# Makefile.in generated by automake 1.14.1 from Makefile.am.
+# Makefile.in generated by automake 1.16.1 from Makefile.am.
# @configure_input@
-# Copyright (C) 1994-2013 Free Software Foundation, Inc.
+# Copyright (C) 1994-2018 Free Software Foundation, Inc.
# This Makefile.in is free software; the Free Software Foundation
# gives unlimited permission to copy and/or distribute it,
@@ -114,7 +114,17 @@
###############################################################################
VPATH = @srcdir@
-am__is_gnu_make = test -n '$(MAKEFILE_LIST)' && test -n '$(MAKELEVEL)'
+am__is_gnu_make = { \
+ if test -z '$(MAKELEVEL)'; then \
+ false; \
+ elif test -n '$(MAKE_HOST)'; then \
+ true; \
+ elif test -n '$(MAKE_VERSION)' && test -n '$(CURDIR)'; then \
+ true; \
+ else \
+ false; \
+ fi; \
+}
am__make_running_with_option = \
case $${target_option-} in \
?) ;; \
@@ -179,8 +189,6 @@ build_triplet = @build@
host_triplet = @host@
@INCLUDED_GKARRAYS_TRUE at am__append_1 = -I at abs_srcdir@/../libGkArrays/src/
subdir = src/libReadsInfo
-DIST_COMMON = $(srcdir)/Makefile.in $(srcdir)/Makefile.am \
- $(top_srcdir)/config/depcomp
ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
am__aclocal_m4_deps = $(top_srcdir)/config/m4/libtool.m4 \
$(top_srcdir)/config/m4/ltoptions.m4 \
@@ -190,6 +198,7 @@ am__aclocal_m4_deps = $(top_srcdir)/config/m4/libtool.m4 \
$(top_srcdir)/configure.ac
am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \
$(ACLOCAL_M4)
+DIST_COMMON = $(srcdir)/Makefile.am $(am__DIST_COMMON)
mkinstalldirs = $(install_sh) -d
CONFIG_HEADER = $(top_builddir)/config/config.h
CONFIG_CLEAN_FILES =
@@ -237,7 +246,27 @@ am__v_at_0 = @
am__v_at_1 =
DEFAULT_INCLUDES = -I. at am__isrc@ -I$(top_builddir)/config
depcomp = $(SHELL) $(top_srcdir)/config/depcomp
-am__depfiles_maybe = depfiles
+am__maybe_remake_depfiles = depfiles
+am__depfiles_remade = ./$(DEPDIR)/libReadsInfo_a-BioTagIndelInfo.Po \
+ ./$(DEPDIR)/libReadsInfo_a-BioUndeterminedInfo.Po \
+ ./$(DEPDIR)/libReadsInfo_a-Cigar.Po \
+ ./$(DEPDIR)/libReadsInfo_a-DuplicationInfo.Po \
+ ./$(DEPDIR)/libReadsInfo_a-IndelInfo.Po \
+ ./$(DEPDIR)/libReadsInfo_a-SNPInfo.Po \
+ ./$(DEPDIR)/libReadsInfo_a-SeqErrInfo.Po \
+ ./$(DEPDIR)/libReadsInfo_a-SpliceInfo.Po \
+ ./$(DEPDIR)/libReadsInfo_a-SpliceInterInfo.Po \
+ ./$(DEPDIR)/libReadsInfo_a-SpliceIntraInfo.Po \
+ ./$(DEPDIR)/libReadsInfo_a-SpliceNoCoverInfo.Po \
+ ./$(DEPDIR)/libReadsInfo_a-SplicingInfo.Po \
+ ./$(DEPDIR)/libReadsInfo_a-bamUtils.Po \
+ ./$(DEPDIR)/libReadsInfo_a-cigarTypes.Po \
+ ./$(DEPDIR)/libReadsInfo_a-genericInfo.Po \
+ ./$(DEPDIR)/libReadsInfo_a-repetitionInfo.Po \
+ ./$(DEPDIR)/libReadsInfo_a-samHeader.Po \
+ ./$(DEPDIR)/libReadsInfo_a-samLine.Po \
+ ./$(DEPDIR)/libReadsInfo_a-tagInfo.Po \
+ ./$(DEPDIR)/libReadsInfo_a-undeterminedErrorInfo.Po
am__mv = mv -f
AM_V_lt = $(am__v_lt_ at AM_V@)
am__v_lt_ = $(am__v_lt_ at AM_DEFAULT_V@)
@@ -305,6 +334,7 @@ am__define_uniq_tagged_files = \
done | $(am__uniquify_input)`
ETAGS = etags
CTAGS = ctags
+am__DIST_COMMON = $(srcdir)/Makefile.in $(top_srcdir)/config/depcomp
DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
ACLOCAL = @ACLOCAL@
ALLOCA = @ALLOCA@
@@ -353,6 +383,7 @@ LIBTOOL = @LIBTOOL@
LIPO = @LIPO@
LN_S = @LN_S@
LTLIBOBJS = @LTLIBOBJS@
+LT_SYS_LIBRARY_PATH = @LT_SYS_LIBRARY_PATH@
MAKEINFO = @MAKEINFO@
MANIFEST_TOOL = @MANIFEST_TOOL@
MKDIR_P = @MKDIR_P@
@@ -423,6 +454,7 @@ pdfdir = @pdfdir@
prefix = @prefix@
program_transform_name = @program_transform_name@
psdir = @psdir@
+runstatedir = @runstatedir@
sbindir = @sbindir@
sharedstatedir = @sharedstatedir@
srcdir = @srcdir@
@@ -477,14 +509,13 @@ $(srcdir)/Makefile.in: $(srcdir)/Makefile.am $(am__configure_deps)
echo ' cd $(top_srcdir) && $(AUTOMAKE) --gnu src/libReadsInfo/Makefile'; \
$(am__cd) $(top_srcdir) && \
$(AUTOMAKE) --gnu src/libReadsInfo/Makefile
-.PRECIOUS: Makefile
Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status
@case '$?' in \
*config.status*) \
cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh;; \
*) \
- echo ' cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__depfiles_maybe)'; \
- cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__depfiles_maybe);; \
+ echo ' cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__maybe_remake_depfiles)'; \
+ cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__maybe_remake_depfiles);; \
esac;
$(top_builddir)/config.status: $(top_srcdir)/configure $(CONFIG_STATUS_DEPENDENCIES)
@@ -510,26 +541,32 @@ mostlyclean-compile:
distclean-compile:
-rm -f *.tab.c
- at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/libReadsInfo_a-BioTagIndelInfo.Po at am__quote@
- at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/libReadsInfo_a-BioUndeterminedInfo.Po at am__quote@
- at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/libReadsInfo_a-Cigar.Po at am__quote@
- at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/libReadsInfo_a-DuplicationInfo.Po at am__quote@
- at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/libReadsInfo_a-IndelInfo.Po at am__quote@
- at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/libReadsInfo_a-SNPInfo.Po at am__quote@
- at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/libReadsInfo_a-SeqErrInfo.Po at am__quote@
- at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/libReadsInfo_a-SpliceInfo.Po at am__quote@
- at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/libReadsInfo_a-SpliceInterInfo.Po at am__quote@
- at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/libReadsInfo_a-SpliceIntraInfo.Po at am__quote@
- at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/libReadsInfo_a-SpliceNoCoverInfo.Po at am__quote@
- at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/libReadsInfo_a-SplicingInfo.Po at am__quote@
- at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/libReadsInfo_a-bamUtils.Po at am__quote@
- at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/libReadsInfo_a-cigarTypes.Po at am__quote@
- at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/libReadsInfo_a-genericInfo.Po at am__quote@
- at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/libReadsInfo_a-repetitionInfo.Po at am__quote@
- at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/libReadsInfo_a-samHeader.Po at am__quote@
- at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/libReadsInfo_a-samLine.Po at am__quote@
- at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/libReadsInfo_a-tagInfo.Po at am__quote@
- at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/libReadsInfo_a-undeterminedErrorInfo.Po at am__quote@
+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/libReadsInfo_a-BioTagIndelInfo.Po at am__quote@ # am--include-marker
+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/libReadsInfo_a-BioUndeterminedInfo.Po at am__quote@ # am--include-marker
+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/libReadsInfo_a-Cigar.Po at am__quote@ # am--include-marker
+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/libReadsInfo_a-DuplicationInfo.Po at am__quote@ # am--include-marker
+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/libReadsInfo_a-IndelInfo.Po at am__quote@ # am--include-marker
+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/libReadsInfo_a-SNPInfo.Po at am__quote@ # am--include-marker
+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/libReadsInfo_a-SeqErrInfo.Po at am__quote@ # am--include-marker
+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/libReadsInfo_a-SpliceInfo.Po at am__quote@ # am--include-marker
+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/libReadsInfo_a-SpliceInterInfo.Po at am__quote@ # am--include-marker
+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/libReadsInfo_a-SpliceIntraInfo.Po at am__quote@ # am--include-marker
+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/libReadsInfo_a-SpliceNoCoverInfo.Po at am__quote@ # am--include-marker
+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/libReadsInfo_a-SplicingInfo.Po at am__quote@ # am--include-marker
+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/libReadsInfo_a-bamUtils.Po at am__quote@ # am--include-marker
+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/libReadsInfo_a-cigarTypes.Po at am__quote@ # am--include-marker
+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/libReadsInfo_a-genericInfo.Po at am__quote@ # am--include-marker
+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/libReadsInfo_a-repetitionInfo.Po at am__quote@ # am--include-marker
+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/libReadsInfo_a-samHeader.Po at am__quote@ # am--include-marker
+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/libReadsInfo_a-samLine.Po at am__quote@ # am--include-marker
+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/libReadsInfo_a-tagInfo.Po at am__quote@ # am--include-marker
+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/libReadsInfo_a-undeterminedErrorInfo.Po at am__quote@ # am--include-marker
+
+$(am__depfiles_remade):
+ @$(MKDIR_P) $(@D)
+ @echo '# dummy' >$@-t && $(am__mv) $@-t $@
+
+am--depfiles: $(am__depfiles_remade)
.cpp.o:
@am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXXCOMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ $<
@@ -890,7 +927,10 @@ cscopelist-am: $(am__tagged_files)
distclean-tags:
-rm -f TAGS ID GTAGS GRTAGS GSYMS GPATH tags
-distdir: $(DISTFILES)
+distdir: $(BUILT_SOURCES)
+ $(MAKE) $(AM_MAKEFLAGS) distdir-am
+
+distdir-am: $(DISTFILES)
@srcdirstrip=`echo "$(srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \
topsrcdirstrip=`echo "$(top_srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \
list='$(DISTFILES)'; \
@@ -964,7 +1004,26 @@ clean-am: clean-generic clean-libtool clean-noinstLIBRARIES \
mostlyclean-am
distclean: distclean-am
- -rm -rf ./$(DEPDIR)
+ -rm -f ./$(DEPDIR)/libReadsInfo_a-BioTagIndelInfo.Po
+ -rm -f ./$(DEPDIR)/libReadsInfo_a-BioUndeterminedInfo.Po
+ -rm -f ./$(DEPDIR)/libReadsInfo_a-Cigar.Po
+ -rm -f ./$(DEPDIR)/libReadsInfo_a-DuplicationInfo.Po
+ -rm -f ./$(DEPDIR)/libReadsInfo_a-IndelInfo.Po
+ -rm -f ./$(DEPDIR)/libReadsInfo_a-SNPInfo.Po
+ -rm -f ./$(DEPDIR)/libReadsInfo_a-SeqErrInfo.Po
+ -rm -f ./$(DEPDIR)/libReadsInfo_a-SpliceInfo.Po
+ -rm -f ./$(DEPDIR)/libReadsInfo_a-SpliceInterInfo.Po
+ -rm -f ./$(DEPDIR)/libReadsInfo_a-SpliceIntraInfo.Po
+ -rm -f ./$(DEPDIR)/libReadsInfo_a-SpliceNoCoverInfo.Po
+ -rm -f ./$(DEPDIR)/libReadsInfo_a-SplicingInfo.Po
+ -rm -f ./$(DEPDIR)/libReadsInfo_a-bamUtils.Po
+ -rm -f ./$(DEPDIR)/libReadsInfo_a-cigarTypes.Po
+ -rm -f ./$(DEPDIR)/libReadsInfo_a-genericInfo.Po
+ -rm -f ./$(DEPDIR)/libReadsInfo_a-repetitionInfo.Po
+ -rm -f ./$(DEPDIR)/libReadsInfo_a-samHeader.Po
+ -rm -f ./$(DEPDIR)/libReadsInfo_a-samLine.Po
+ -rm -f ./$(DEPDIR)/libReadsInfo_a-tagInfo.Po
+ -rm -f ./$(DEPDIR)/libReadsInfo_a-undeterminedErrorInfo.Po
-rm -f Makefile
distclean-am: clean-am distclean-compile distclean-generic \
distclean-tags
@@ -1010,7 +1069,26 @@ install-ps-am:
installcheck-am:
maintainer-clean: maintainer-clean-am
- -rm -rf ./$(DEPDIR)
+ -rm -f ./$(DEPDIR)/libReadsInfo_a-BioTagIndelInfo.Po
+ -rm -f ./$(DEPDIR)/libReadsInfo_a-BioUndeterminedInfo.Po
+ -rm -f ./$(DEPDIR)/libReadsInfo_a-Cigar.Po
+ -rm -f ./$(DEPDIR)/libReadsInfo_a-DuplicationInfo.Po
+ -rm -f ./$(DEPDIR)/libReadsInfo_a-IndelInfo.Po
+ -rm -f ./$(DEPDIR)/libReadsInfo_a-SNPInfo.Po
+ -rm -f ./$(DEPDIR)/libReadsInfo_a-SeqErrInfo.Po
+ -rm -f ./$(DEPDIR)/libReadsInfo_a-SpliceInfo.Po
+ -rm -f ./$(DEPDIR)/libReadsInfo_a-SpliceInterInfo.Po
+ -rm -f ./$(DEPDIR)/libReadsInfo_a-SpliceIntraInfo.Po
+ -rm -f ./$(DEPDIR)/libReadsInfo_a-SpliceNoCoverInfo.Po
+ -rm -f ./$(DEPDIR)/libReadsInfo_a-SplicingInfo.Po
+ -rm -f ./$(DEPDIR)/libReadsInfo_a-bamUtils.Po
+ -rm -f ./$(DEPDIR)/libReadsInfo_a-cigarTypes.Po
+ -rm -f ./$(DEPDIR)/libReadsInfo_a-genericInfo.Po
+ -rm -f ./$(DEPDIR)/libReadsInfo_a-repetitionInfo.Po
+ -rm -f ./$(DEPDIR)/libReadsInfo_a-samHeader.Po
+ -rm -f ./$(DEPDIR)/libReadsInfo_a-samLine.Po
+ -rm -f ./$(DEPDIR)/libReadsInfo_a-tagInfo.Po
+ -rm -f ./$(DEPDIR)/libReadsInfo_a-undeterminedErrorInfo.Po
-rm -f Makefile
maintainer-clean-am: distclean-am maintainer-clean-generic
@@ -1031,20 +1109,22 @@ uninstall-am:
.MAKE: install-am install-strip
-.PHONY: CTAGS GTAGS TAGS all all-am check check-am clean clean-generic \
- clean-libtool clean-noinstLIBRARIES cscopelist-am ctags \
- ctags-am distclean distclean-compile distclean-generic \
- distclean-libtool distclean-tags distdir dvi dvi-am html \
- html-am info info-am install install-am install-data \
- install-data-am install-dvi install-dvi-am install-exec \
- install-exec-am install-html install-html-am install-info \
- install-info-am install-man install-pdf install-pdf-am \
- install-ps install-ps-am install-strip installcheck \
- installcheck-am installdirs maintainer-clean \
+.PHONY: CTAGS GTAGS TAGS all all-am am--depfiles check check-am clean \
+ clean-generic clean-libtool clean-noinstLIBRARIES \
+ cscopelist-am ctags ctags-am distclean distclean-compile \
+ distclean-generic distclean-libtool distclean-tags distdir dvi \
+ dvi-am html html-am info info-am install install-am \
+ install-data install-data-am install-dvi install-dvi-am \
+ install-exec install-exec-am install-html install-html-am \
+ install-info install-info-am install-man install-pdf \
+ install-pdf-am install-ps install-ps-am install-strip \
+ installcheck installcheck-am installdirs maintainer-clean \
maintainer-clean-generic mostlyclean mostlyclean-compile \
mostlyclean-generic mostlyclean-libtool pdf pdf-am ps ps-am \
tags tags-am uninstall uninstall-am
+.PRECIOUS: Makefile
+
# Tell versions [3.59,3.63) of GNU make to not export all variables.
# Otherwise a system limit (for SysV at least) may be exceeded.
=====================================
src/libReadsReader/Makefile.in
=====================================
@@ -1,7 +1,7 @@
-# Makefile.in generated by automake 1.14.1 from Makefile.am.
+# Makefile.in generated by automake 1.16.1 from Makefile.am.
# @configure_input@
-# Copyright (C) 1994-2013 Free Software Foundation, Inc.
+# Copyright (C) 1994-2018 Free Software Foundation, Inc.
# This Makefile.in is free software; the Free Software Foundation
# gives unlimited permission to copy and/or distribute it,
@@ -115,7 +115,17 @@
VPATH = @srcdir@
-am__is_gnu_make = test -n '$(MAKEFILE_LIST)' && test -n '$(MAKELEVEL)'
+am__is_gnu_make = { \
+ if test -z '$(MAKELEVEL)'; then \
+ false; \
+ elif test -n '$(MAKE_HOST)'; then \
+ true; \
+ elif test -n '$(MAKE_VERSION)' && test -n '$(CURDIR)'; then \
+ true; \
+ else \
+ false; \
+ fi; \
+}
am__make_running_with_option = \
case $${target_option-} in \
?) ;; \
@@ -179,8 +189,6 @@ POST_UNINSTALL = :
build_triplet = @build@
host_triplet = @host@
subdir = src/libReadsReader
-DIST_COMMON = $(srcdir)/Makefile.in $(srcdir)/Makefile.am \
- $(top_srcdir)/config/depcomp $(noinst_HEADERS)
ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
am__aclocal_m4_deps = $(top_srcdir)/config/m4/libtool.m4 \
$(top_srcdir)/config/m4/ltoptions.m4 \
@@ -190,6 +198,8 @@ am__aclocal_m4_deps = $(top_srcdir)/config/m4/libtool.m4 \
$(top_srcdir)/configure.ac
am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \
$(ACLOCAL_M4)
+DIST_COMMON = $(srcdir)/Makefile.am $(noinst_HEADERS) \
+ $(am__DIST_COMMON)
mkinstalldirs = $(install_sh) -d
CONFIG_HEADER = $(top_builddir)/config/config.h
CONFIG_CLEAN_FILES =
@@ -220,7 +230,8 @@ am__v_at_0 = @
am__v_at_1 =
DEFAULT_INCLUDES = -I. at am__isrc@ -I$(top_builddir)/config
depcomp = $(SHELL) $(top_srcdir)/config/depcomp
-am__depfiles_maybe = depfiles
+am__maybe_remake_depfiles = depfiles
+am__depfiles_remade = ./$(DEPDIR)/libReadsReader_a-readsReader.Po
am__mv = mv -f
AM_V_lt = $(am__v_lt_ at AM_V@)
am__v_lt_ = $(am__v_lt_ at AM_DEFAULT_V@)
@@ -285,7 +296,7 @@ am__recursive_targets = \
$(RECURSIVE_CLEAN_TARGETS) \
$(am__extra_recursive_targets)
AM_RECURSIVE_TARGETS = $(am__recursive_targets:-recursive=) TAGS CTAGS \
- distdir
+ distdir distdir-am
am__tagged_files = $(HEADERS) $(SOURCES) $(TAGS_FILES) $(LISP)
# Read a list of newline-separated strings from the standard input,
# and print each of them once, without duplicates. Input order is
@@ -306,6 +317,7 @@ am__define_uniq_tagged_files = \
ETAGS = etags
CTAGS = ctags
DIST_SUBDIRS = $(SUBDIRS)
+am__DIST_COMMON = $(srcdir)/Makefile.in $(top_srcdir)/config/depcomp
DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
am__relativize = \
dir0=`pwd`; \
@@ -379,6 +391,7 @@ LIBTOOL = @LIBTOOL@
LIPO = @LIPO@
LN_S = @LN_S@
LTLIBOBJS = @LTLIBOBJS@
+LT_SYS_LIBRARY_PATH = @LT_SYS_LIBRARY_PATH@
MAKEINFO = @MAKEINFO@
MANIFEST_TOOL = @MANIFEST_TOOL@
MKDIR_P = @MKDIR_P@
@@ -449,6 +462,7 @@ pdfdir = @pdfdir@
prefix = @prefix@
program_transform_name = @program_transform_name@
psdir = @psdir@
+runstatedir = @runstatedir@
sbindir = @sbindir@
sharedstatedir = @sharedstatedir@
srcdir = @srcdir@
@@ -485,14 +499,13 @@ $(srcdir)/Makefile.in: $(srcdir)/Makefile.am $(am__configure_deps)
echo ' cd $(top_srcdir) && $(AUTOMAKE) --gnu src/libReadsReader/Makefile'; \
$(am__cd) $(top_srcdir) && \
$(AUTOMAKE) --gnu src/libReadsReader/Makefile
-.PRECIOUS: Makefile
Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status
@case '$?' in \
*config.status*) \
cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh;; \
*) \
- echo ' cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__depfiles_maybe)'; \
- cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__depfiles_maybe);; \
+ echo ' cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__maybe_remake_depfiles)'; \
+ cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__maybe_remake_depfiles);; \
esac;
$(top_builddir)/config.status: $(top_srcdir)/configure $(CONFIG_STATUS_DEPENDENCIES)
@@ -518,7 +531,13 @@ mostlyclean-compile:
distclean-compile:
-rm -f *.tab.c
- at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/libReadsReader_a-readsReader.Po at am__quote@
+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/libReadsReader_a-readsReader.Po at am__quote@ # am--include-marker
+
+$(am__depfiles_remade):
+ @$(MKDIR_P) $(@D)
+ @echo '# dummy' >$@-t && $(am__mv) $@-t $@
+
+am--depfiles: $(am__depfiles_remade)
.cpp.o:
@am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXXCOMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ $<
@@ -660,7 +679,10 @@ cscopelist-am: $(am__tagged_files)
distclean-tags:
-rm -f TAGS ID GTAGS GRTAGS GSYMS GPATH tags
-distdir: $(DISTFILES)
+distdir: $(BUILT_SOURCES)
+ $(MAKE) $(AM_MAKEFLAGS) distdir-am
+
+distdir-am: $(DISTFILES)
@srcdirstrip=`echo "$(srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \
topsrcdirstrip=`echo "$(top_srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \
list='$(DISTFILES)'; \
@@ -760,7 +782,7 @@ clean-am: clean-generic clean-libtool clean-noinstLIBRARIES \
mostlyclean-am
distclean: distclean-recursive
- -rm -rf ./$(DEPDIR)
+ -rm -f ./$(DEPDIR)/libReadsReader_a-readsReader.Po
-rm -f Makefile
distclean-am: clean-am distclean-compile distclean-generic \
distclean-tags
@@ -806,7 +828,7 @@ install-ps-am:
installcheck-am:
maintainer-clean: maintainer-clean-recursive
- -rm -rf ./$(DEPDIR)
+ -rm -f ./$(DEPDIR)/libReadsReader_a-readsReader.Po
-rm -f Makefile
maintainer-clean-am: distclean-am maintainer-clean-generic
@@ -827,8 +849,8 @@ uninstall-am:
.MAKE: $(am__recursive_targets) install-am install-strip
-.PHONY: $(am__recursive_targets) CTAGS GTAGS TAGS all all-am check \
- check-am clean clean-generic clean-libtool \
+.PHONY: $(am__recursive_targets) CTAGS GTAGS TAGS all all-am \
+ am--depfiles check check-am clean clean-generic clean-libtool \
clean-noinstLIBRARIES cscopelist-am ctags ctags-am distclean \
distclean-compile distclean-generic distclean-libtool \
distclean-tags distdir dvi dvi-am html html-am info info-am \
@@ -842,6 +864,8 @@ uninstall-am:
mostlyclean-libtool pdf pdf-am ps ps-am tags tags-am uninstall \
uninstall-am
+.PRECIOUS: Makefile
+
# Tell versions [3.59,3.63) of GNU make to not export all variables.
# Otherwise a system limit (for SysV at least) may be exceeded.
=====================================
src/libReadsReader/kseq/Makefile.in
=====================================
@@ -1,7 +1,7 @@
-# Makefile.in generated by automake 1.14.1 from Makefile.am.
+# Makefile.in generated by automake 1.16.1 from Makefile.am.
# @configure_input@
-# Copyright (C) 1994-2013 Free Software Foundation, Inc.
+# Copyright (C) 1994-2018 Free Software Foundation, Inc.
# This Makefile.in is free software; the Free Software Foundation
# gives unlimited permission to copy and/or distribute it,
@@ -120,7 +120,17 @@
###############################################################################
VPATH = @srcdir@
-am__is_gnu_make = test -n '$(MAKEFILE_LIST)' && test -n '$(MAKELEVEL)'
+am__is_gnu_make = { \
+ if test -z '$(MAKELEVEL)'; then \
+ false; \
+ elif test -n '$(MAKE_HOST)'; then \
+ true; \
+ elif test -n '$(MAKE_VERSION)' && test -n '$(CURDIR)'; then \
+ true; \
+ else \
+ false; \
+ fi; \
+}
am__make_running_with_option = \
case $${target_option-} in \
?) ;; \
@@ -184,8 +194,6 @@ POST_UNINSTALL = :
build_triplet = @build@
host_triplet = @host@
subdir = src/libReadsReader/kseq
-DIST_COMMON = $(srcdir)/Makefile.in $(srcdir)/Makefile.am \
- $(kseq_HEADERS)
ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
am__aclocal_m4_deps = $(top_srcdir)/config/m4/libtool.m4 \
$(top_srcdir)/config/m4/ltoptions.m4 \
@@ -195,6 +203,7 @@ am__aclocal_m4_deps = $(top_srcdir)/config/m4/libtool.m4 \
$(top_srcdir)/configure.ac
am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \
$(ACLOCAL_M4)
+DIST_COMMON = $(srcdir)/Makefile.am $(kseq_HEADERS) $(am__DIST_COMMON)
mkinstalldirs = $(install_sh) -d
CONFIG_HEADER = $(top_builddir)/config/config.h
CONFIG_CLEAN_FILES =
@@ -266,6 +275,7 @@ am__define_uniq_tagged_files = \
done | $(am__uniquify_input)`
ETAGS = etags
CTAGS = ctags
+am__DIST_COMMON = $(srcdir)/Makefile.in
DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
ACLOCAL = @ACLOCAL@
ALLOCA = @ALLOCA@
@@ -314,6 +324,7 @@ LIBTOOL = @LIBTOOL@
LIPO = @LIPO@
LN_S = @LN_S@
LTLIBOBJS = @LTLIBOBJS@
+LT_SYS_LIBRARY_PATH = @LT_SYS_LIBRARY_PATH@
MAKEINFO = @MAKEINFO@
MANIFEST_TOOL = @MANIFEST_TOOL@
MKDIR_P = @MKDIR_P@
@@ -384,6 +395,7 @@ pdfdir = @pdfdir@
prefix = @prefix@
program_transform_name = @program_transform_name@
psdir = @psdir@
+runstatedir = @runstatedir@
sbindir = @sbindir@
sharedstatedir = @sharedstatedir@
srcdir = @srcdir@
@@ -415,14 +427,13 @@ $(srcdir)/Makefile.in: $(srcdir)/Makefile.am $(am__configure_deps)
echo ' cd $(top_srcdir) && $(AUTOMAKE) --gnu src/libReadsReader/kseq/Makefile'; \
$(am__cd) $(top_srcdir) && \
$(AUTOMAKE) --gnu src/libReadsReader/kseq/Makefile
-.PRECIOUS: Makefile
Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status
@case '$?' in \
*config.status*) \
cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh;; \
*) \
- echo ' cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__depfiles_maybe)'; \
- cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__depfiles_maybe);; \
+ echo ' cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__maybe_remake_depfiles)'; \
+ cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__maybe_remake_depfiles);; \
esac;
$(top_builddir)/config.status: $(top_srcdir)/configure $(CONFIG_STATUS_DEPENDENCIES)
@@ -513,7 +524,10 @@ cscopelist-am: $(am__tagged_files)
distclean-tags:
-rm -f TAGS ID GTAGS GRTAGS GSYMS GPATH tags
-distdir: $(DISTFILES)
+distdir: $(BUILT_SOURCES)
+ $(MAKE) $(AM_MAKEFLAGS) distdir-am
+
+distdir-am: $(DISTFILES)
@srcdirstrip=`echo "$(srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \
topsrcdirstrip=`echo "$(top_srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \
list='$(DISTFILES)'; \
@@ -665,6 +679,8 @@ uninstall-am: uninstall-kseqHEADERS
mostlyclean-generic mostlyclean-libtool pdf pdf-am ps ps-am \
tags tags-am uninstall uninstall-am uninstall-kseqHEADERS
+.PRECIOUS: Makefile
+
# Tell versions [3.59,3.63) of GNU make to not export all variables.
# Otherwise a system limit (for SysV at least) may be exceeded.
=====================================
src/libSSA/Makefile.in
=====================================
@@ -1,7 +1,7 @@
-# Makefile.in generated by automake 1.14.1 from Makefile.am.
+# Makefile.in generated by automake 1.16.1 from Makefile.am.
# @configure_input@
-# Copyright (C) 1994-2013 Free Software Foundation, Inc.
+# Copyright (C) 1994-2018 Free Software Foundation, Inc.
# This Makefile.in is free software; the Free Software Foundation
# gives unlimited permission to copy and/or distribute it,
@@ -115,7 +115,17 @@
VPATH = @srcdir@
-am__is_gnu_make = test -n '$(MAKEFILE_LIST)' && test -n '$(MAKELEVEL)'
+am__is_gnu_make = { \
+ if test -z '$(MAKELEVEL)'; then \
+ false; \
+ elif test -n '$(MAKE_HOST)'; then \
+ true; \
+ elif test -n '$(MAKE_VERSION)' && test -n '$(CURDIR)'; then \
+ true; \
+ else \
+ false; \
+ fi; \
+}
am__make_running_with_option = \
case $${target_option-} in \
?) ;; \
@@ -180,8 +190,6 @@ build_triplet = @build@
host_triplet = @host@
bin_PROGRAMS = crac-index$(EXEEXT)
subdir = src/libSSA
-DIST_COMMON = $(srcdir)/Makefile.in $(srcdir)/Makefile.am \
- $(top_srcdir)/config/depcomp
ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
am__aclocal_m4_deps = $(top_srcdir)/config/m4/libtool.m4 \
$(top_srcdir)/config/m4/ltoptions.m4 \
@@ -191,10 +199,13 @@ am__aclocal_m4_deps = $(top_srcdir)/config/m4/libtool.m4 \
$(top_srcdir)/configure.ac
am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \
$(ACLOCAL_M4)
+DIST_COMMON = $(srcdir)/Makefile.am $(am__DIST_COMMON)
mkinstalldirs = $(install_sh) -d
CONFIG_HEADER = $(top_builddir)/config/config.h
CONFIG_CLEAN_FILES =
CONFIG_CLEAN_VPATH_FILES =
+am__installdirs = "$(DESTDIR)$(bindir)"
+PROGRAMS = $(bin_PROGRAMS)
LIBRARIES = $(noinst_LIBRARIES)
ARFLAGS = cru
AM_V_AR = $(am__v_AR_ at AM_V@)
@@ -212,8 +223,6 @@ am_libSSA_a_OBJECTS = bitarray.$(OBJEXT) bitrankw32int.$(OBJEXT) \
locateTags.$(OBJEXT) SSA.$(OBJEXT) utils.$(OBJEXT) \
GenomeInfo.$(OBJEXT) $(am__objects_2) $(am__objects_1)
libSSA_a_OBJECTS = $(am_libSSA_a_OBJECTS)
-am__installdirs = "$(DESTDIR)$(bindir)"
-PROGRAMS = $(bin_PROGRAMS)
am_crac_index_OBJECTS = cracIndex.$(OBJEXT)
crac_index_OBJECTS = $(am_crac_index_OBJECTS)
crac_index_LDADD = $(LDADD)
@@ -236,7 +245,13 @@ am__v_at_0 = @
am__v_at_1 =
DEFAULT_INCLUDES = -I. at am__isrc@ -I$(top_builddir)/config
depcomp = $(SHELL) $(top_srcdir)/config/depcomp
-am__depfiles_maybe = depfiles
+am__maybe_remake_depfiles = depfiles
+am__depfiles_remade = ./$(DEPDIR)/GenomeInfo.Po \
+ ./$(DEPDIR)/HuffAlphabetRank.Po ./$(DEPDIR)/Huffman_Codes.Po \
+ ./$(DEPDIR)/SSA.Po ./$(DEPDIR)/bitarray.Po \
+ ./$(DEPDIR)/bitrankw32int.Po ./$(DEPDIR)/chrPosition.Po \
+ ./$(DEPDIR)/cracIndex.Po ./$(DEPDIR)/locateOnGenome.Po \
+ ./$(DEPDIR)/locateTags.Po ./$(DEPDIR)/utils.Po
am__mv = mv -f
CXXCOMPILE = $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) \
$(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS)
@@ -300,6 +315,7 @@ am__define_uniq_tagged_files = \
done | $(am__uniquify_input)`
ETAGS = etags
CTAGS = ctags
+am__DIST_COMMON = $(srcdir)/Makefile.in $(top_srcdir)/config/depcomp
DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
ACLOCAL = @ACLOCAL@
ALLOCA = @ALLOCA@
@@ -348,6 +364,7 @@ LIBTOOL = @LIBTOOL@
LIPO = @LIPO@
LN_S = @LN_S@
LTLIBOBJS = @LTLIBOBJS@
+LT_SYS_LIBRARY_PATH = @LT_SYS_LIBRARY_PATH@
MAKEINFO = @MAKEINFO@
MANIFEST_TOOL = @MANIFEST_TOOL@
MKDIR_P = @MKDIR_P@
@@ -418,6 +435,7 @@ pdfdir = @pdfdir@
prefix = @prefix@
program_transform_name = @program_transform_name@
psdir = @psdir@
+runstatedir = @runstatedir@
sbindir = @sbindir@
sharedstatedir = @sharedstatedir@
srcdir = @srcdir@
@@ -586,14 +604,13 @@ $(srcdir)/Makefile.in: $(srcdir)/Makefile.am $(am__configure_deps)
echo ' cd $(top_srcdir) && $(AUTOMAKE) --gnu src/libSSA/Makefile'; \
$(am__cd) $(top_srcdir) && \
$(AUTOMAKE) --gnu src/libSSA/Makefile
-.PRECIOUS: Makefile
Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status
@case '$?' in \
*config.status*) \
cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh;; \
*) \
- echo ' cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__depfiles_maybe)'; \
- cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__depfiles_maybe);; \
+ echo ' cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__maybe_remake_depfiles)'; \
+ cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__maybe_remake_depfiles);; \
esac;
$(top_builddir)/config.status: $(top_srcdir)/configure $(CONFIG_STATUS_DEPENDENCIES)
@@ -604,14 +621,6 @@ $(top_srcdir)/configure: $(am__configure_deps)
$(ACLOCAL_M4): $(am__aclocal_m4_deps)
cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
$(am__aclocal_m4_deps):
-
-clean-noinstLIBRARIES:
- -test -z "$(noinst_LIBRARIES)" || rm -f $(noinst_LIBRARIES)
-
-libSSA.a: $(libSSA_a_OBJECTS) $(libSSA_a_DEPENDENCIES) $(EXTRA_libSSA_a_DEPENDENCIES)
- $(AM_V_at)-rm -f libSSA.a
- $(AM_V_AR)$(libSSA_a_AR) libSSA.a $(libSSA_a_OBJECTS) $(libSSA_a_LIBADD)
- $(AM_V_at)$(RANLIB) libSSA.a
install-binPROGRAMS: $(bin_PROGRAMS)
@$(NORMAL_INSTALL)
@list='$(bin_PROGRAMS)'; test -n "$(bindir)" || list=; \
@@ -662,6 +671,14 @@ clean-binPROGRAMS:
echo " rm -f" $$list; \
rm -f $$list
+clean-noinstLIBRARIES:
+ -test -z "$(noinst_LIBRARIES)" || rm -f $(noinst_LIBRARIES)
+
+libSSA.a: $(libSSA_a_OBJECTS) $(libSSA_a_DEPENDENCIES) $(EXTRA_libSSA_a_DEPENDENCIES)
+ $(AM_V_at)-rm -f libSSA.a
+ $(AM_V_AR)$(libSSA_a_AR) libSSA.a $(libSSA_a_OBJECTS) $(libSSA_a_LIBADD)
+ $(AM_V_at)$(RANLIB) libSSA.a
+
crac-index$(EXEEXT): $(crac_index_OBJECTS) $(crac_index_DEPENDENCIES) $(EXTRA_crac_index_DEPENDENCIES)
@rm -f crac-index$(EXEEXT)
$(AM_V_CXXLD)$(CXXLINK) $(crac_index_OBJECTS) $(crac_index_LDADD) $(LIBS)
@@ -672,17 +689,23 @@ mostlyclean-compile:
distclean-compile:
-rm -f *.tab.c
- at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/GenomeInfo.Po at am__quote@
- at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/HuffAlphabetRank.Po at am__quote@
- at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/Huffman_Codes.Po at am__quote@
- at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/SSA.Po at am__quote@
- at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/bitarray.Po at am__quote@
- at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/bitrankw32int.Po at am__quote@
- at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/chrPosition.Po at am__quote@
- at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/cracIndex.Po at am__quote@
- at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/locateOnGenome.Po at am__quote@
- at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/locateTags.Po at am__quote@
- at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/utils.Po at am__quote@
+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/GenomeInfo.Po at am__quote@ # am--include-marker
+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/HuffAlphabetRank.Po at am__quote@ # am--include-marker
+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/Huffman_Codes.Po at am__quote@ # am--include-marker
+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/SSA.Po at am__quote@ # am--include-marker
+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/bitarray.Po at am__quote@ # am--include-marker
+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/bitrankw32int.Po at am__quote@ # am--include-marker
+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/chrPosition.Po at am__quote@ # am--include-marker
+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/cracIndex.Po at am__quote@ # am--include-marker
+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/locateOnGenome.Po at am__quote@ # am--include-marker
+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/locateTags.Po at am__quote@ # am--include-marker
+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/utils.Po at am__quote@ # am--include-marker
+
+$(am__depfiles_remade):
+ @$(MKDIR_P) $(@D)
+ @echo '# dummy' >$@-t && $(am__mv) $@-t $@
+
+am--depfiles: $(am__depfiles_remade)
.cpp.o:
@am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXXCOMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ $<
@@ -763,7 +786,10 @@ cscopelist-am: $(am__tagged_files)
distclean-tags:
-rm -f TAGS ID GTAGS GRTAGS GSYMS GPATH tags
-distdir: $(DISTFILES)
+distdir: $(BUILT_SOURCES)
+ $(MAKE) $(AM_MAKEFLAGS) distdir-am
+
+distdir-am: $(DISTFILES)
@srcdirstrip=`echo "$(srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \
topsrcdirstrip=`echo "$(top_srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \
list='$(DISTFILES)'; \
@@ -795,7 +821,7 @@ distdir: $(DISTFILES)
done
check-am: all-am
check: check-am
-all-am: Makefile $(LIBRARIES) $(PROGRAMS)
+all-am: Makefile $(PROGRAMS) $(LIBRARIES)
installdirs:
for dir in "$(DESTDIR)$(bindir)"; do \
test -z "$$dir" || $(MKDIR_P) "$$dir"; \
@@ -840,7 +866,17 @@ clean-am: clean-binPROGRAMS clean-generic clean-libtool \
clean-noinstLIBRARIES mostlyclean-am
distclean: distclean-am
- -rm -rf ./$(DEPDIR)
+ -rm -f ./$(DEPDIR)/GenomeInfo.Po
+ -rm -f ./$(DEPDIR)/HuffAlphabetRank.Po
+ -rm -f ./$(DEPDIR)/Huffman_Codes.Po
+ -rm -f ./$(DEPDIR)/SSA.Po
+ -rm -f ./$(DEPDIR)/bitarray.Po
+ -rm -f ./$(DEPDIR)/bitrankw32int.Po
+ -rm -f ./$(DEPDIR)/chrPosition.Po
+ -rm -f ./$(DEPDIR)/cracIndex.Po
+ -rm -f ./$(DEPDIR)/locateOnGenome.Po
+ -rm -f ./$(DEPDIR)/locateTags.Po
+ -rm -f ./$(DEPDIR)/utils.Po
-rm -f Makefile
distclean-am: clean-am distclean-compile distclean-generic \
distclean-tags
@@ -886,7 +922,17 @@ install-ps-am:
installcheck-am:
maintainer-clean: maintainer-clean-am
- -rm -rf ./$(DEPDIR)
+ -rm -f ./$(DEPDIR)/GenomeInfo.Po
+ -rm -f ./$(DEPDIR)/HuffAlphabetRank.Po
+ -rm -f ./$(DEPDIR)/Huffman_Codes.Po
+ -rm -f ./$(DEPDIR)/SSA.Po
+ -rm -f ./$(DEPDIR)/bitarray.Po
+ -rm -f ./$(DEPDIR)/bitrankw32int.Po
+ -rm -f ./$(DEPDIR)/chrPosition.Po
+ -rm -f ./$(DEPDIR)/cracIndex.Po
+ -rm -f ./$(DEPDIR)/locateOnGenome.Po
+ -rm -f ./$(DEPDIR)/locateTags.Po
+ -rm -f ./$(DEPDIR)/utils.Po
-rm -f Makefile
maintainer-clean-am: distclean-am maintainer-clean-generic
@@ -907,7 +953,7 @@ uninstall-am: uninstall-binPROGRAMS
.MAKE: install-am install-strip
-.PHONY: CTAGS GTAGS TAGS all all-am check check-am clean \
+.PHONY: CTAGS GTAGS TAGS all all-am am--depfiles check check-am clean \
clean-binPROGRAMS clean-generic clean-libtool \
clean-noinstLIBRARIES cscopelist-am ctags ctags-am distclean \
distclean-compile distclean-generic distclean-libtool \
@@ -922,6 +968,8 @@ uninstall-am: uninstall-binPROGRAMS
mostlyclean-generic mostlyclean-libtool pdf pdf-am ps ps-am \
tags tags-am uninstall uninstall-am uninstall-binPROGRAMS
+.PRECIOUS: Makefile
+
# Tell versions [3.59,3.63) of GNU make to not export all variables.
# Otherwise a system limit (for SysV at least) may be exceeded.
=====================================
test_f/Makefile.in
=====================================
@@ -1,7 +1,7 @@
-# Makefile.in generated by automake 1.14.1 from Makefile.am.
+# Makefile.in generated by automake 1.16.1 from Makefile.am.
# @configure_input@
-# Copyright (C) 1994-2013 Free Software Foundation, Inc.
+# Copyright (C) 1994-2018 Free Software Foundation, Inc.
# This Makefile.in is free software; the Free Software Foundation
# gives unlimited permission to copy and/or distribute it,
@@ -115,7 +115,17 @@
# SUBDIRS=causes cigar
VPATH = @srcdir@
-am__is_gnu_make = test -n '$(MAKEFILE_LIST)' && test -n '$(MAKELEVEL)'
+am__is_gnu_make = { \
+ if test -z '$(MAKELEVEL)'; then \
+ false; \
+ elif test -n '$(MAKE_HOST)'; then \
+ true; \
+ elif test -n '$(MAKE_VERSION)' && test -n '$(CURDIR)'; then \
+ true; \
+ else \
+ false; \
+ fi; \
+}
am__make_running_with_option = \
case $${target_option-} in \
?) ;; \
@@ -179,8 +189,6 @@ POST_UNINSTALL = :
build_triplet = @build@
host_triplet = @host@
subdir = test_f
-DIST_COMMON = $(srcdir)/Makefile.in $(srcdir)/Makefile.am \
- $(top_srcdir)/config/test-driver
ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
am__aclocal_m4_deps = $(top_srcdir)/config/m4/libtool.m4 \
$(top_srcdir)/config/m4/ltoptions.m4 \
@@ -190,6 +198,7 @@ am__aclocal_m4_deps = $(top_srcdir)/config/m4/libtool.m4 \
$(top_srcdir)/configure.ac
am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \
$(ACLOCAL_M4)
+DIST_COMMON = $(srcdir)/Makefile.am $(am__DIST_COMMON)
mkinstalldirs = $(install_sh) -d
CONFIG_HEADER = $(top_builddir)/config/config.h
CONFIG_CLEAN_FILES =
@@ -228,7 +237,7 @@ am__recursive_targets = \
$(RECURSIVE_CLEAN_TARGETS) \
$(am__extra_recursive_targets)
AM_RECURSIVE_TARGETS = $(am__recursive_targets:-recursive=) TAGS CTAGS \
- check recheck distdir
+ check recheck distdir distdir-am
am__tagged_files = $(HEADERS) $(SOURCES) $(TAGS_FILES) $(LISP)
# Read a list of newline-separated strings from the standard input,
# and print each of them once, without duplicates. Input order is
@@ -452,6 +461,8 @@ TEST_LOG_DRIVER = $(SHELL) $(top_srcdir)/config/test-driver
TEST_LOG_COMPILE = $(TEST_LOG_COMPILER) $(AM_TEST_LOG_FLAGS) \
$(TEST_LOG_FLAGS)
DIST_SUBDIRS = $(SUBDIRS)
+am__DIST_COMMON = $(srcdir)/Makefile.in \
+ $(top_srcdir)/config/test-driver
DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
am__relativize = \
dir0=`pwd`; \
@@ -525,6 +536,7 @@ LIBTOOL = @LIBTOOL@
LIPO = @LIPO@
LN_S = @LN_S@
LTLIBOBJS = @LTLIBOBJS@
+LT_SYS_LIBRARY_PATH = @LT_SYS_LIBRARY_PATH@
MAKEINFO = @MAKEINFO@
MANIFEST_TOOL = @MANIFEST_TOOL@
MKDIR_P = @MKDIR_P@
@@ -595,6 +607,7 @@ pdfdir = @pdfdir@
prefix = @prefix@
program_transform_name = @program_transform_name@
psdir = @psdir@
+runstatedir = @runstatedir@
sbindir = @sbindir@
sharedstatedir = @sharedstatedir@
srcdir = @srcdir@
@@ -632,14 +645,13 @@ $(srcdir)/Makefile.in: $(srcdir)/Makefile.am $(am__configure_deps)
echo ' cd $(top_srcdir) && $(AUTOMAKE) --gnu test_f/Makefile'; \
$(am__cd) $(top_srcdir) && \
$(AUTOMAKE) --gnu test_f/Makefile
-.PRECIOUS: Makefile
Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status
@case '$?' in \
*config.status*) \
cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh;; \
*) \
- echo ' cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__depfiles_maybe)'; \
- cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__depfiles_maybe);; \
+ echo ' cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__maybe_remake_depfiles)'; \
+ cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__maybe_remake_depfiles);; \
esac;
$(top_builddir)/config.status: $(top_srcdir)/configure $(CONFIG_STATUS_DEPENDENCIES)
@@ -786,7 +798,7 @@ $(TEST_SUITE_LOG): $(TEST_LOGS)
if test -n "$$am__remaking_logs"; then \
echo "fatal: making $(TEST_SUITE_LOG): possible infinite" \
"recursion detected" >&2; \
- else \
+ elif test -n "$$redo_logs"; then \
am__remaking_logs=yes $(MAKE) $(AM_MAKEFLAGS) $$redo_logs; \
fi; \
if $(am__make_dryrun); then :; else \
@@ -876,7 +888,7 @@ $(TEST_SUITE_LOG): $(TEST_LOGS)
fi; \
$$success || exit 1
-check-TESTS:
+check-TESTS:
@list='$(RECHECK_LOGS)'; test -z "$$list" || rm -f $$list
@list='$(RECHECK_LOGS:.log=.trs)'; test -z "$$list" || rm -f $$list
@test -z "$(TEST_SUITE_LOG)" || rm -f $(TEST_SUITE_LOG)
@@ -933,7 +945,10 @@ test_index.sh.log: test_index.sh
@am__EXEEXT_TRUE@ $(am__common_driver_flags) $(AM_TEST_LOG_DRIVER_FLAGS) $(TEST_LOG_DRIVER_FLAGS) -- $(TEST_LOG_COMPILE) \
@am__EXEEXT_TRUE@ "$$tst" $(AM_TESTS_FD_REDIRECT)
-distdir: $(DISTFILES)
+distdir: $(BUILT_SOURCES)
+ $(MAKE) $(AM_MAKEFLAGS) distdir-am
+
+distdir-am: $(DISTFILES)
@srcdirstrip=`echo "$(srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \
topsrcdirstrip=`echo "$(top_srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \
list='$(DISTFILES)'; \
@@ -1113,6 +1128,8 @@ uninstall-am:
mostlyclean-libtool pdf pdf-am ps ps-am recheck tags tags-am \
uninstall uninstall-am
+.PRECIOUS: Makefile
+
# Tell versions [3.59,3.63) of GNU make to not export all variables.
# Otherwise a system limit (for SysV at least) may be exceeded.
=====================================
test_f/bug/Makefile.in
=====================================
@@ -1,7 +1,7 @@
-# Makefile.in generated by automake 1.14.1 from Makefile.am.
+# Makefile.in generated by automake 1.16.1 from Makefile.am.
# @configure_input@
-# Copyright (C) 1994-2013 Free Software Foundation, Inc.
+# Copyright (C) 1994-2018 Free Software Foundation, Inc.
# This Makefile.in is free software; the Free Software Foundation
# gives unlimited permission to copy and/or distribute it,
@@ -115,7 +115,17 @@
# SUBDIRS=causes cigar
VPATH = @srcdir@
-am__is_gnu_make = test -n '$(MAKEFILE_LIST)' && test -n '$(MAKELEVEL)'
+am__is_gnu_make = { \
+ if test -z '$(MAKELEVEL)'; then \
+ false; \
+ elif test -n '$(MAKE_HOST)'; then \
+ true; \
+ elif test -n '$(MAKE_VERSION)' && test -n '$(CURDIR)'; then \
+ true; \
+ else \
+ false; \
+ fi; \
+}
am__make_running_with_option = \
case $${target_option-} in \
?) ;; \
@@ -179,7 +189,6 @@ POST_UNINSTALL = :
build_triplet = @build@
host_triplet = @host@
subdir = test_f/bug
-DIST_COMMON = $(srcdir)/Makefile.in $(srcdir)/Makefile.am
ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
am__aclocal_m4_deps = $(top_srcdir)/config/m4/libtool.m4 \
$(top_srcdir)/config/m4/ltoptions.m4 \
@@ -189,6 +198,7 @@ am__aclocal_m4_deps = $(top_srcdir)/config/m4/libtool.m4 \
$(top_srcdir)/configure.ac
am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \
$(ACLOCAL_M4)
+DIST_COMMON = $(srcdir)/Makefile.am $(am__DIST_COMMON)
mkinstalldirs = $(install_sh) -d
CONFIG_HEADER = $(top_builddir)/config/config.h
CONFIG_CLEAN_FILES =
@@ -213,6 +223,7 @@ am__can_run_installinfo = \
*) (install-info --version) >/dev/null 2>&1;; \
esac
am__tagged_files = $(HEADERS) $(SOURCES) $(TAGS_FILES) $(LISP)
+am__DIST_COMMON = $(srcdir)/Makefile.in
DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
ACLOCAL = @ACLOCAL@
ALLOCA = @ALLOCA@
@@ -261,6 +272,7 @@ LIBTOOL = @LIBTOOL@
LIPO = @LIPO@
LN_S = @LN_S@
LTLIBOBJS = @LTLIBOBJS@
+LT_SYS_LIBRARY_PATH = @LT_SYS_LIBRARY_PATH@
MAKEINFO = @MAKEINFO@
MANIFEST_TOOL = @MANIFEST_TOOL@
MKDIR_P = @MKDIR_P@
@@ -331,6 +343,7 @@ pdfdir = @pdfdir@
prefix = @prefix@
program_transform_name = @program_transform_name@
psdir = @psdir@
+runstatedir = @runstatedir@
sbindir = @sbindir@
sharedstatedir = @sharedstatedir@
srcdir = @srcdir@
@@ -359,14 +372,13 @@ $(srcdir)/Makefile.in: $(srcdir)/Makefile.am $(am__configure_deps)
echo ' cd $(top_srcdir) && $(AUTOMAKE) --gnu test_f/bug/Makefile'; \
$(am__cd) $(top_srcdir) && \
$(AUTOMAKE) --gnu test_f/bug/Makefile
-.PRECIOUS: Makefile
Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status
@case '$?' in \
*config.status*) \
cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh;; \
*) \
- echo ' cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__depfiles_maybe)'; \
- cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__depfiles_maybe);; \
+ echo ' cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__maybe_remake_depfiles)'; \
+ cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__maybe_remake_depfiles);; \
esac;
$(top_builddir)/config.status: $(top_srcdir)/configure $(CONFIG_STATUS_DEPENDENCIES)
@@ -390,7 +402,10 @@ ctags CTAGS:
cscope cscopelist:
-distdir: $(DISTFILES)
+distdir: $(BUILT_SOURCES)
+ $(MAKE) $(AM_MAKEFLAGS) distdir-am
+
+distdir-am: $(DISTFILES)
@srcdirstrip=`echo "$(srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \
topsrcdirstrip=`echo "$(top_srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \
list='$(DISTFILES)'; \
@@ -538,6 +553,8 @@ uninstall-am:
mostlyclean-generic mostlyclean-libtool pdf pdf-am ps ps-am \
tags-am uninstall uninstall-am
+.PRECIOUS: Makefile
+
# Tell versions [3.59,3.63) of GNU make to not export all variables.
# Otherwise a system limit (for SysV at least) may be exceeded.
=====================================
test_f/bug/bug-17175-2-genome.fa
=====================================
@@ -0,0 +1,600 @@
+>4-393715..393770
+CTTCGGGCCATCTGGATGTATACATGCAGGTCACAGGGGATATGATGGCTTAGCTT
+>4-403014..403069
+CTTCAGGCCATCTGGATGTATACATGCAGGTCACAGGGGATATGATGGCTTAGCTT
+>4-4007431..4007471
+ATGTGTACATGCAGGTCACAGGGGATATGATGGCTTAGTTT
+>4-9096143..9096183
+AAGCTAAGCCATCATATCCCCTGTGACCTGCATGTACATAT
+>4-9109804..9109844
+AAGATAAGCCATCATATCCCCTGTGACCTGCATGTACACAT
+>4-9640614..9640654
+AAGCTAAGCCATCATATCCCCTGTGACCTGCATGTACACAT
+>4-11655532..11655572
+ATGTGTACATGCAGGTCACAGGGGATATGATGGCTTAACTC
+>4-11660819..11660859
+ATGTGTACATGCAGGTCACAGGGGATATGATGGCTTAGCTT
+>4-20631743..20631783
+ATGTGTACATGCAGGTCACAGGGGATATGATGGCTTAGCTT
+>4-30150757..30150798
+GGCCATTTTCACTTCTTTTGTGATTCTTCACTTGCTTTGGGT
+>4-33749398..33749440
+CGCCATTTTCACTTCTTTTGTGATTCTTCACTTGCTTCAGGCC
+>4-35020375..35020430
+AAGCTAAGCCATCATATCCCCTGTGACCTGCATGTATACATCCAGATGGCCTGAAA
+>4-84155682..84155722
+CCCTAGTGACCTGCATGTATACATCCAGATGGCCGGTTCCT
+>4-89270256..89270298
+AGCCATTTTCACTTCTTTTGTGATTCTTCACTTGCTTCAGGCC
+>4-92190023..92190065
+AGCCATTTTCACTTCTTTTGTGATTCTTCACTTGCTTCAGGCC
+>4-98062723..98062765
+GGCCATTTTCACTTCTTTTGTGATTCTTCACTTGCTTCAGGAC
+>4-107331913..107331955
+GGCCATTTTCACTTCTTTTGTGATTCTTCACTTGCTTCTGGCC
+>4-111194705..111194750
+AAGCTAAGCCATCATATCCCCTGTGACCTGCATGTATACATTCAGA
+>4-116897203..116897243
+ATGTGTACATGCAGGTCACAGGGGATATGATGGCTTAGCTT
+>4-118178560..118178600
+AAGCTAAGCCATCATATCCCCTGTGACCTGCATGTACACAT
+>4-128438198..128438238
+ATGTGTACATGCAGGTCACAGGGGATATGATGGCTTAGATT
+>4-131933094..131933149
+AAGCTAAGCCATCATATCCCCTGTGACCTGCATGTATACATCCAGATGGCCTGAAG
+>4-132587212..132587254
+GGCCTGAAGCAAGTGAAGAATCACAAAAGAAGTGAAAATGGCT
+>4-132589638..132589679
+TATCTCCTGTGACCTGCATGTATACATCCAGATGGCCTGAAA
+>4-135599442..135599482
+ATGTGTACATGCAGGTCACAGGGGATATGATGGCTTAGCTT
+>4-135604648..135604688
+ATGTGTACATGCAGGTCACAGGGGATATGATGGCTTAGCTT
+>4-164021415..164021457
+GGCCATTTTCACTTCTTTTGTGATTCTTCACTTGCTTCAGGCC
+>4-164025399..164025444
+CTTCAGGCCATCTGGATGTATACATGCAGGTCACAGGGGATTATGA
+>4-167630137..167630180
+CTCCAGGCCATCTGGATGTATACATGCAGGTCACAGGGGTTATG
+>4-167631210..167631253
+CATAACCCCTGTGACCTGCATGTATACATCCAGATGGCCTGGAG
+>4-169898035..169898081
+ATCTAGATGTATACATGCAGGTCACAGGGGATATGATGGCTTAGCTT
+>4-170840922..170841011
+AACCTAAGCCATCATATCCCCTGTGACCTGCATGTATGCATCCAGATGGCCTGAAGCAAGTGAAGAATCACAAAAGAAGTGAAAATGGCC
+>4-180330122..180330164
+GGCCTGAAGCAAGTGAAGAATCACAAAAGAAGTGAAAATGGTC
+>4-180648882..180648923
+GCCCAAAGCAAGTGAAGAATCACAAAAGAAGTGAAAATGGTC
+>22-35237081..35237126
+CTTCAGGCCATCTGGATGTATACATGCAGGTCACAGGGGATGCTAT
+>22-39452615..39452670
+TTTCAGGCCATCTGGATGTATACATGCAGGTCACAGGGGATATGATGGCTTAGCTT
+>12-13418394..13418434
+GTGTGTACATGCAGGTCACAGGGGATATGATGGCTTAGCTT
+>12-23664432..23664477
+CTTCAGGCCATCTGGATGTATACATGCAGGTCACAGGGGATGTGAT
+>12-30215006..30215046
+AAGCTAAGCCATCATATCCCCTGTGACCTGCATGTACACAT
+>12-33241108..33241197
+GGCCATTTTCACTTCTTTTGTGATTCTTCACTTGCTTCAGGCCATCTGGATGTATACATGCAGGTCACAGGGGATATGATGGCTTAGTTT
+>12-33243683..33243771
+GGCCATTTTCACTTCTTTTGTGATTCTTCACTTGCTTCAGGCCATCTGGATGTATACATGCAGGTCACAGGGGATATGATGGCTAAGCT
+>12-46715373..46715415
+GGCTATTTTCACTTCTTTTGTGATTCTTCACTTGCTTCAGGCC
+>12-55336603..55336678
+GGCCATTTTCACTTCTTTTGTGATTCTTCACTTGCTTCAGGCCATCTGGATGTATACATGCAGGTCACAGGTGACA
+>12-55342076..55342131
+CTTCAGGCCATCTGGATGTATACATGCAGGTCACAGGGGATATGATGGCTTAGCTT
+>12-57159703..57159748
+ATCACATCCCCTGTGACCTGCATGTATACATCCAGATGGCCTGAAG
+>12-66617003..66617048
+CTTCAGGCCATCTGGATGTATACATGCAGGTCACAGGGGATGCAAT
+>12-76685541..76685583
+GGCCTGAAGCAAGTGAAGAATCACAAAAGAAGTGAAAATGGCT
+>12-76691194..76691236
+GGCCTGAAGCAAGTGAAGAATCACAAAAGAAGTGAAAATGGCT
+>12-88761832..88761872
+AAGCTAAGCCATCATATCCCCTGTGACCTGCATGTACACAT
+>12-108838659..108838714
+CTCCAGGCCATCTGGATGTATACATGCAGGTCACAGGGGATATGATGGCTTAGCTT
+>12-110843157..110843214
+AGGGGTCAGTTAAGGCAGGAACCGGCCCTTTTCACTTCTTTTGTGATTCTTCAGTTAC
+>16-124698..124740
+CAGATGAAGCAAGTGAAGAATCACAAAAGAAGTGAAAATGGCC
+>16-30870800..30870845
+ATCACATCCCCTGTGACCTGCATGTATACATCCAGATGGCCTGAAG
+>16-31263939..31263993
+TTCAAGCCATCTGGATGTATACATGCAGGTCACAGGGGATATGATGGCTTAGCTT
+>16-48370657..48370746
+AACCATTTTCACTTCTTTTGTGATTCTTCACTTGCTTCAGGCCATCTGGATGTATACATGCAGGTCACAGGGGATATGATGGCTTAGCTT
+>16-59647143..59647185
+GGCCTGAAGCAAGTGAAGAATCACAAAAGAAGTGAAAATGGCC
+>16-62251704..62251759
+CTTCAGGCCATCTGGATGTATACATGCAGGTCACAGGGGATATGATGGCTTAGCTT
+>6-16265065..16265105
+ATGTGTACATGCAGGTCACAGGGGATATGATGGCTTAGCTT
+>6-18754706..18754746
+ATGTGTACATGCAGGTCACAGGGGATATGATGGCTTAGCTT
+>6-18760042..18760082
+ATGTGTACATGCAGGTCACAGGGGATATGATGGCTTAGCTT
+>6-38889884..38889924
+ATGTGTACATGCAGGTCACAGGGGATATGATGGCTTAGCTT
+>6-39099615..39099657
+AGCCATTTTCACTTCTTTTGTGATTCTTCACTTGCTTCAGGCC
+>6-40829460..40829502
+GGCCATTTTCACTTCTTTTGTGATTCTTCACTTGCTTCAGGCT
+>6-64671151..64671192
+GGCCTGAAGCAAGTGAAGAATCACAAAAGAAGTGAAAGTGGC
+>6-68577881..68577936
+CTTCAGGCCATCTGGATGTATACATGCAGGTCACAGGGGATATGATGGCTTAGCTT
+>6-78801310..78801352
+GGCCTGAAGCAAGTGAAGAATCACAAAAGAAGTGAAAATGGCC
+>6-81219862..81219902
+ATGTGTACATGCAGGTCACAGGGGATATGATGGCTTAGCTT
+>6-81225461..81225501
+ATGTGTACATGCAGGTCACAGGGGATATGATGGCTTAGCTT
+>6-87313560..87313600
+ATGTGTACATGCAGGTCACAGGGGATATGATGGCTTAGCTT
+>6-123878005..123878045
+AAGCTAAGCCATCATATCCCCTGTGACCTGCATGTACACAT
+>6-123883100..123883140
+AAGCTAAGCCATCATATCCCCTGTGACCTGCATGTACACAT
+>6-140578980..140579020
+ATGTGTACATGCAGGTCACAGGGGATATGATGGCTTAGCTT
+>6-140584158..140584198
+ATGTGTACATGCAGGTCACAGGGGATATGATGGCTTAGCTT
+>6-142151113..142151168
+AAGTTAAGCCATCATATCCCCTGTGACCTGCATGTATACATCCAGATGGCCTGAAG
+>6-160713287..160713327
+ATGTGTACATGCAGGTCACAGGGGATATGATGGCTTAGCTT
+>6-165073525..165073565
+ATGTGTACATGCAGGTCACAGGGGATATGATGGCTTAGCTT
+>6-165078988..165079028
+ATGTGTACATGCAGGTCACAGGGGATATGATGGCTTAGCTT
+>1-10476900..10476984
+AGCCATTTTCACTTCTTTTGTGATTCTTCACTTGCTTCAGGCCATCTGGATGTATACATGCAGGTCACAGGGGATATGATAGTTT
+>1-12773773..12773815
+GGCCTGAAGCAAGTGAAGAATCACAAAAGAAGTGAAAATGGCT
+>1-37680012..37680054
+GGCCTGAAGCAAGTGAAGAATCACAAAAGAAGTGAAAATGGCC
+>1-38373504..38373559
+AAGCTAAGCCATCATATCCCCTGTGACCTGCATGTATACATCCAGATGGCCTGAAG
+>1-38379490..38379531
+CATATCCTGTGACCTGCATGTATACATCCAGATGGCCTGAAG
+>1-45544639..45544681
+GGCCCGAAGCAAGTGAAGAATCACAAAAGAAGTGAAAATGGCT
+>1-48966292..48966334
+GGCCTGAAGCAAGTGAAGAATCACAAAAGAAGTGAAAATGGCT
+>1-57996788..57996830
+GGCCTGAAGCAAGTGAAGAATCACAAAAGAAGTGAAAATGGCC
+>1-70832158..70832224
+CCCCAAGAGAGCATTCTTGGATCTCTTGCAAGAAAGAATTTGAGGCGAATCCATAGAGTAAGGTAAA
+>1-70833290..70833446
+TTTCTTAAGCTTAGTGATGTGTGTCAGACCTCTGAGCCCAAGCAAAGCCATCATATCCCCTGTGACCTGCATGTATACATCCAGATGGCCTGAAGCAAGTGAAGAATCACAAAAGAAGTGAAAAGGGCCGGTTCCTGCCTTAACTGATGACATTCCA
+>1-70839300..70839347
+CCATGATATCCCCTGTGACCTGCATGTATACATCCAGATGGCCTGAAG
+>1-89647080..89647171
+GGCCATTTTCACTTCTTTTGTGATTCTTCACTTGCTTCAGGCCATCTGGACGTATGTACATGCAGGTCACAGGGGATATGATGGCTTAGCTT
+>1-113363093..113363134
+GATGCATACATGCAGGTCACAGGGGATATGATGGCTTAGCTT
+>1-113368621..113368662
+GATGCATACATGCAGGTCACAGGGGATATGATGGCTTGGGCT
+>1-114574723..114574812
+AAGCTAAGCCATCATATCCCCTGTGACCTGCATGTATACATCCAGATGGCCTGAAGCAAGTGAAGAATCACAAAAGAAGTGAAAATGGCC
+>1-169657497..169657539
+GGCCTGAAGCAAGTGAAGAATCACAAAAGAAGTGAAAATGGCT
+>1-178222962..178223004
+GGCCATTTTCACTTCTTTTGTGATTCTTCACTTGCTTCGGGCC
+>1-180890440..180890482
+GGCCATTTTCACTTCTTTTGTGATTCTTCACTTGCTTCAGGCC
+>1-192763312..192763367
+CTTCAGGCCATCTGGATGTATACATGCAGGTCACAGGGGATATGATGGCTTAGCTT
+>1-203460125..203460164
+AAGCTAAGCCATCATATCCCCTGTGACCTGCATGTGCACA
+>1-209645271..209645313
+CTCCAGGCCATCTGGATGTATACATGCAGGTCACAGGGTTTAT
+>1-225027955..225027995
+CTTCAGGCCATCTGGATGTATACATGCAGGTCACAGAGGAT
+>1-225033710..225033750
+CTTCAGGCCATCTGGATGTATACATGCAGGTCACAGAGGAT
+>1-233608880..233608922
+GGCCATTTTCACTTCTTTTGTGATTCTTCACTTGCTTCAGGCT
+>20-1714109..1714151
+GGCCATTTTCACTTCTTTTGTGATTCTTCACTTGCTTCAGGCC
+>20-37221388..37221428
+ATGTGTACATGCAGGTCACAGGGGATATGATGGCTTAGCTT
+>20-42011075..42011117
+GGCCCGAAGCAAGTGAAGAATCACAAAAGAAGTGAAAATGGCC
+>20-43298893..43298942
+AGCCGTCATATCCCCTGTGACCTGCATGTATACATCCAGATGGCCTGAAG
+>Y-4396254..4396293
+TATACACATGCAGGTCACAGGGGATATGATGGCTTAGCTT
+>Y-14489886..14489941
+CTTCAGGCCATCTGGATGTATACATGCAGGTCACAGGGGATATGATGGCTTAGCTT
+>Y-14646162..14646204
+GGCCTGAAGCAAGTGAAGAATCACAAAAGAAGTGAAAATGGCC
+>Y-14677181..14677222
+AGCAATTTTCACTTCTTTTGTGATTCTTCACTTGCTTTAGGC
+>Y-15209074..15209114
+AAGCTAAGCCATCATATCCCCTGTGACCTGCATGTACACAT
+>Y-15317672..15317727
+CTTCAGGCCATCTGGATGTATACATGCAGGTCACAGGGGATATGATGGCTTAGCTT
+>Y-16587507..16587550
+CTTCAGGCCATCTGGATGTATACATGCAGGTCACAGGGGTTATG
+>Y-23058400..23058441
+TATCTCCTGTGACCTGCATGTATACATCCAGATGGCCTGAAG
+>2-3863447..3863502
+CTTCAGGCCATCTGGATGTATACATGCAGGTCACAGGGGATATGATGGCTTAGCTT
+>2-4437680..4437722
+AGACATTTTCACTTCTTTTGTGATTCTTCACTTGCTTCAGGCC
+>2-7836997..7837039
+GGCCATTTTCACTTCTTTTGTGATTCTTCACTTGCTTCAGCCC
+>2-15003739..15003782
+CTGCAGGCCATCTGGATGTATACATGCAGGTCACAGGGGTTACA
+>2-20287517..20287559
+GGCCCGAAGCAAGTGAAGAATCACAAAAGAAGTGAAAATGGCC
+>2-38245232..38245273
+AGCCATTTTCACTTCTTTTGTGATTCTTCACTTGCTTGGGGC
+>2-38308288..38308328
+GTACGTGCAGGTCACAGGGGATATGATGGCTTTGCTTGGGC
+>2-60644587..60644642
+AACCTAAGCCATCATATCCCCTGTGACCTGCATGTATACATCCAGATGGCCTGAAG
+>2-64302241..64302281
+ATGTGTACATGCAGGTCACAGGGGATATGATGGCTTAGCTT
+>2-81624670..81624712
+GGCCATTTTCACTTCTTTTGTGATTCTTCACTTGCTTCAGGCC
+>2-89356037..89356078
+AAGTTAAGCCATCATATCCCCTGTGACCTGCATGTATGCATC
+>2-89502994..89503039
+TTTCAGGCCATCTGGATGTATACATGCAGGTCACAGGGGATGTGAT
+>2-90182838..90182879
+GATGCATACATGCAGGTCACAGGGGATATGATGGCTTAACTT
+>2-113860428..113860470
+GGCCATTTTCACTTCTTTTGTGATTCTTCACTTGCTTCAGGCC
+>2-116899589..116899630
+AGTCATTTTCACTTCTTTTGTGATTCTTCACTTGCTTTGGGC
+>2-121935385..121935440
+CTTCAGGCCATCTGGATGTATACATGCAGGTCACAGGGGATATGATGGCTTAGCTT
+>2-157576948..157576987
+ATGTGTACATGCAGGTCACAGGGGATATGATGGCTCAGCT
+>2-157582297..157582337
+ATGTGTACATGCAGGTCACAGGGGATATGATGGCTTAGCTT
+>2-172354884..172354939
+CTTCAGGCCATCTGGATGTATACATGCAGGTCACAGGGGATATGATGGCTTAGCTT
+>2-183908556..183908598
+GGCCTGAAGCAAGTGAAGAATCACAAAAGAAGTGAAAATGGCA
+>2-183914046..183914088
+GGCCTGAAGCAAGTGAAGAATCACAAAAGAAGTGAAAATGGCT
+>2-193783046..193783086
+AAGCTAAGCCATCATATCCCCTGTGACCTGCATGTACATAT
+>2-207887614..207887654
+AAGCTAAGCCATCATATCCCCTGTGACCTGCATGTACACAT
+>2-209086605..209086645
+ATGTGTACATGCAGGTCACAGGGGATATGATGGCTTAGCTT
+>7-6988171..6988211
+ATGTGTACATGCAGGTCACAGGGGATATGATGGCTTAGCTT
+>7-9510362..9510404
+GGCCAGAAGCAAGTGAAGAATCACAAAAGAAGTGAAAATGGCC
+>7-17453751..17453793
+GACCTGAAGCAAGTGAAGAATCACAAAAGAAGTGAAAATGGCC
+>7-31506815..31506855
+ATGTGTACATGCAGGTCACAGGGGATATGATGGCTTAGATT
+>7-43242325..43242380
+AAGCTAAGCCATCATATCCCCTGTGACCTGCATGTATACATCCAGATGGCCTGAAG
+>7-51936032..51936074
+GGCCTGAAGCAAGTGAAGAATCACAAAAGAAGTGAAAATGGCC
+>7-66057717..66057756
+TCCCTTGTGACCTGCATGTATACATCCAGATGGCCTGAAG
+>7-109282090..109282132
+AGCCATTTTCACTTCTTTTGTGATTCTTCACTTGCTTCAGGCC
+>7-120417019..120417059
+ATGTGTACATGCAGGTCACAGGGGATATGATGGCTTAGCTT
+>7-120422881..120422921
+ATGTGTACATGCAGGTCACAGGGGATATGATGGCTTAGCTT
+>7-121204042..121204082
+ATGTGTACATGCAGGTCACAGGGGATATGATGGCTTAGCTT
+>7-123648336..123648391
+AAGCTAAGCCATCATATCCCCTGTGACCTGCATGTATACATCCAGATGGCCTGAAG
+>7-131272947..131272989
+GGTCATTTTCACTTCTTTTGTGATTCTTCACTTGCTTCAGGCC
+>7-141278167..141278209
+GGCCATTTTCACTTCTTTTGTGATTCTTCACTTGCTTCGGGCC
+>7-142802227..142802271
+AAGCTAAGCCATCATATCCCCTGTGACCTGCATGTATACAGCCAG
+>7-146863947..146863987
+ATGTGTACATGCAGGTCACAGGGGATATGATGGCTTAGCTT
+>14-39169407..39169450
+CTTCAGGCCATCTGGATGTATACATGCAGGTCACAGGGGTTATG
+>14-71596333..71596373
+AAGCTAAGCCATCATATCCCCTGTGACCTGCATGTACACAT
+>14-87203012..87203052
+AAGCTAAGCCATCATATCCCCTGTGACCTGCATGTACACAT
+>14-87720270..87720312
+GGCCTGAAGCAAGTGAAGAATCACAAAAGAAGTGAAAATGGCC
+>14-96434611..96434653
+GGCCTGAAGCAAGTGAAGAATCACAAAAGAAGTGAAAATGGCC
+>14-102706334..102706376
+GGCCCGAAGCAAGTGAAGAATCACAAAAGAAGTGAAAATGGCC
+>14-102711781..102711823
+GGCCTGAAGCAAGTGAAGAATCACAAAAGAAGTGAAAATGGCC
+>5-7055443..7055485
+GGCTATTTTCACTTCTTTTGTGATTCTTCACTTGCTTCAGGCC
+>5-10102400..10102442
+GGCCTGAAGCAAGTGAAGAATCACAAAAGAAGTGAAAATGGCC
+>5-23468361..23468400
+CTTCAGGCCATCTGGATGTATACATGCAGGTCACAAGGGA
+>5-28051962..28052017
+AAGCTAAGCCATCATATCCCCTGTGACCTGCATGTATACATCCAGATGGCCTGAAG
+>5-66232487..66232527
+ATGTGTACATGCAGGTCACAGGGGATATGATGGCTTAGCTT
+>5-97420636..97420676
+AAGCTAAGCCATCATATCCCCTGTGACCTGCATGTACACAT
+>5-100492110..100492152
+GGATTTATACATGCAGGTCACAGGGGATATGATGGCTTAGCTT
+>5-100655909..100655949
+AAGCTAAGCCATCATATCCCCTGTGACCTGCATGTACACAT
+>5-114990359..114990399
+GCCCAAGCAAAGCCATCATATCCCCTGTGACCTGCAGGTAT
+>5-118288256..118288298
+GGCCATTTTCACTTCTTTTGTGATTCTTCACTTGCTTCATGCC
+>5-124302707..124302753
+CTTCAGGCCATCTGGATGTATACATGCAGGTCACAGGGGATACGATG
+>5-126003433..126003488
+CTTCAGGCCATCTGGATGTATACATGCAGGTCACAGGGGATATGATGGCTTAGCTT
+>5-128071325..128071367
+GGCCTGAAGCAAGTGAAGAATCACAAAAGAAGTGAAAATGGCT
+>9-11102595..11102636
+CTTCAGGCCATCTGGATGTATACATGCAGGTCACAGGAGATA
+>9-25293759..25293799
+AAGCTAAGCCATCATATCCCCTGTGACCTGCATGTACACAT
+>9-33377887..33377942
+CTTCAGGCCATCTGGATGTATACATGCAGGTCACAGGGGATATGATGGCTTAGCTT
+>9-35003307..35003347
+AAGCTAAGCCATCATATCCCCTGTGACCTGCATGTACACAT
+>9-35008987..35009027
+AAGCTAAGCCATCATATCCCCTGTGACCTGCATGTACACAT
+>9-46103265..46103307
+AGCCATTTTCACTTCTTTTGTGATTCTTCACTTGCTTCAGGCC
+>9-46401007..46401049
+GGCCTGAAGCAAGTGAAGAATCACAAAAGAAGTGAAAATGGCT
+>9-77966413..77966453
+ATGTGTACATGCAGGTCACAGGGGATATGATGGCTTAGCTT
+>9-88494458..88494513
+TTTCAGGCCATCTGGATGTATACATGCAGGTCACAGGGGATATGATGGCTTAGCTT
+>9-97412787..97412841
+ATGCTAAGCCATCATATCCCCTGTGACCTGCATGTATACATCCAGATGGCGTGAA
+>9-134426933..134426973
+AAGCTAAGCCATCATATCCCCTGTGACCTGCATGTACACAT
+>21-17764801..17764856
+CTTCAGGCCATCTGGATGTATACATGCAGGTCACAGGGGATATGATGGCTTAGCTT
+>21-18264547..18264587
+AAGCTAAGCCATCATATCCCCTGTGACCTGCATGTACACAT
+>21-27453869..27453911
+GGCCATTTTCACTTCTTTTGTGATTCTTCACTTGCTTCGGGCC
+>21-42616530..42616572
+GGCCATTTTCACTTCTTTTGTGATTCTTCACTTGCTTCAGGCC
+>8-3095868..3095908
+ATGTGTACATGCAGGTCACAGGGGATATGATGGCTTAGTTT
+>8-3101174..3101214
+ATGTGTACATGCAGGTCACAGGGGATATGATGGCTTAGCTT
+>8-8041001..8041041
+AAGCTAAGCCATCATATCCCCTGTGACCTGCATGTACACAT
+>8-8916764..8916804
+ATGTGTACATGCAGGTCACAGGGGATATGATGGCTTAGCTT
+>8-10434465..10434505
+AAGCTAAGCCATCATATCCCCTGTGACCTGCATGTACACAT
+>8-12339651..12339691
+ATGTGTACATGCAGGTCACAGGGGATATGATGGCTTAGCTT
+>8-49174631..49174671
+ATGTGTACATGCAGGTCACAGGGGATATGATGGCTTAGCTT
+>8-58787394..58787434
+ATGTGTACATGCAGGTCACAGGGGATATGATGGCTTAGCTT
+>8-72582363..72582405
+GGCCTGAAGCAAGTGAAGAATCACAAAAGAAGTGAAAATGGCT
+>8-82831800..82831842
+GGCCTGAAGCAAGTGAAGAATCACAAAAGAAGTGAAAATGGCC
+>8-102174789..102174834
+AGCCGTCATATCCCCTGTGACCTGCATGTATACATCCAGATCACCT
+>8-104016445..104016500
+AAGCCAAGCCATCATATCCCCTGTGACCTGCATGTATACATCCAGATGGCCTGAAG
+>8-110319280..110319335
+AAGTTAAGCCATCATATCCCCTGTGACCTGCATGTATACATCCAGATGGCCTGAAA
+>8-132758489..132758529
+AAGCTAAGCCATCATATCCCCTGTGACCTGCATGTACACAT
+>8-132836960..132837000
+AAGCTAAGCCATCATATCCCCTGTGACCTGCATGTACACAT
+>13-25202670..25202724
+AAGTTAAGCCATCATATCCCCTGTGACCTGCATGTATACATCCAGATGGCTTGAG
+>13-27086964..27087006
+AGCCTGAAGCAAGTGAAGAATCACAAAAGAAGTGAAAATGGCC
+>13-32181758..32181800
+AGCCATTTTCACTTCTTTTGTGATTCTTCACTTGCTTCAGGCC
+>13-86317649..86317690
+GGCTATTTTCACTTCTTTTGTGATTCTTCACTTGCTTTGGGC
+>13-95961318..95961358
+ACGTGTACATGCAGGTCACAGGGGATATGATGGCTTAGCTT
+>13-98300078..98300118
+AAGCTAAGCCATCATATCCCCTGTGACCTGCATGTACACAT
+>13-104866100..104866146
+GAACTGGCCATCTGGATGTATACATGCAGGTCACAGGGGATAGGATG
+>17-38073697..38073739
+ATATTCCCTGTGACCTGCATGTATACATCCAGATGGCCTGAAG
+>17-53553457..53553546
+AAGCTAAGCCATCATATCCCCTGTGACCTGCATGTATACATCCAGATGGCCTGAAGCAAGTGAAGAATCACAAAAGAAGTGAAAATGGCC
+>17-60224681..60224732
+AAGCTAAGCCATCATATCCCCTGTGACCTGCATGTATACATCCAGATAGCCT
+>19-12682589..12682631
+GGCCTGAAGCAAGTGAAGAATCACAAAAGAAGTGAAAATAGCT
+>19-17704392..17704432
+AAGCTAAGCCATCATATCCCCTGTGACCTGCATGTACACAT
+>19-20487173..20487215
+GGCCTGAAGCAAGTGAAGAATCACAAAAGAAGTGAAAACAGCC
+>19-23208695..23209563
+AGCAATTTTCACTTCTTTTGTGATTCTTCACTTGCTTCAGGCCATCCGCATGTATTCCTGCAGGTCACAGGGGATATCATGGCTTAGCTTGGGCTCAGAGGCCTGACAGTTAGGTCACCTGTGTGTGAGGCCCAGTGATAAGCCACTCTTCCTTTTGTGCACAGGGTCTAAGCAAAAGATGAAAAGTCACATCACCTAGGTGCTGGGCTTACAGAATTGTCTCAATCTCTCCTATGGTCAAAGCCAATTTAAGAGACATAAATCATATTAGCTGCTCTGCCTATGGAGCAGCCATCTTTTTGTTTCTTTACTTCTCTAATAAACTTGGTTTCACTTTACTGCATGGACTCACCTTGGCTTCTTTCTTTCTTGCATGAGATCCAAGAACCCTTTCTTGGGGTGTGAATCAAAAGCCCTTTCCAGAACAGCTTTTTGGCAAACTATAAAGGGACTATACTGATGAGAAACCTGACCCAAAGGAAATAACTACAGCACCAATTAGCCTGCTTTGGGTAACTAGTGGGGTACATTTTTTTCACACACGTCCATGTGAAGAGACCACCAAACAGGCTTTGTGTGAGCAATAAAGCTTTTTAATCACCTGGATGCAGGTGGGCTGAGTCTGAAAAGAAAGTCAGTGAAGGGAGATAGGGGTAGGGCCATTTTATAGGATTCGGGTAGGTAATGGAAAATTACAGTCAAAGGGGGTTGTTCTCTGGTTGGCAGGGGTTGGGGGTCACAAGGTGCTCAGTGGGGGAGCTTTTGAGCCAGGATGAGCCAGGAGAAGGAATTTCACAAAGTAATGTCATCAGTTAAGGCAGGAACTGGCCATTTTCACTTCTTTTGTGATTCTTCACTTGCTTCAGGTC
+>19-23214925..23215014
+GGCCATTTTCACTTCTTTTGTGATTCTTCACTTGCTTCAGGCCATCTGGATATATACATGCAGGTCACAGGGGATATGATGGCTTAGCTT
+>19-35005018..35005073
+AAGCTAAGCCATCATATCCCCTGTGACCTGCATGTATACATCCAGATGGCCTGAAG
+>3-938037..938077
+ATGTGTACATGCAGGTCACAGGGGATATGATGGCTTAGCTT
+>3-27644208..27644263
+AAGCTAAGCCATCATATCCCCTGTGACCTGCATGTATACATCCAGATGGCCTGAAG
+>3-31548439..31548479
+ATGTGTACATGCAGGTCACAGGGGATATGATGGCTTAGCTT
+>3-32838277..32838319
+GGCCATTTTCACTTCTTTTGTGATTCTTCACTTGCTTCAGGCC
+>3-39619656..39619713
+AGGAACCGGCCATCTGGATGTATACATGCAGGTCACAGGGGATATGATGGCTTAGCTT
+>3-58436116..58436156
+ATCCTCTGTGACCTGCATGTATACATCCAGATGGCCTGAAG
+>3-67094500..67094542
+GGCCATTTTCACTTCTTTTGTGATTCTTCACTTGCTTCAGGCC
+>3-86586542..86586584
+AGCCGTTTTCACTTCTTTTGTGATTCTTCACTTGCTTCAGGCC
+>3-86593006..86593052
+TTTCAGGCCATCTGGATGTATACATGCAGGTCACAGGGGATACAATG
+>3-124546567..124546607
+CCCGCAGCAAGTGAAGAATCACAAAAGAAGTGAAAATGGCC
+>3-128555291..128555338
+CAGAGGGATGTATACATGCAGGTCACAGGGGATATGATGGCTTAGCTT
+>3-129871474..129871514
+ATGTGTACATGCAGGTCACAGGGGATATGATGGCTTAGCTT
+>3-142791486..142791528
+GGCCATTTTCACTTCTTTTGTGATTCTTCACTTGCTTCAGGCC
+>3-142836195..142836235
+ATGTGTACATGCAGGTCACAGGGGATATGATGGCTTAGCTT
+>3-143524383..143524425
+GGCCCGAAGCAAGTGAAGAATCACAAAAGAAGTGAAAATGGCT
+>3-153547172..153547211
+TGTACACATGCAGGTCACAGGGGATATGATGGCTTAGCTT
+>3-154992556..154992596
+CTTCAGGCCATCTGGATGTATACATGCAGGTCACAGAGGAT
+>3-154998529..154998568
+TGTACACATGCAGGTCACAGGGGATATGATGGCTTAGCTT
+>3-161871564..161871619
+CTTCAGGCCATCTGGATGTATACATGCAGGTCACAGGGGATATGATGGCTTAGCTT
+>3-162435664..162435719
+AAGCTAAGCCATCATATCCCCTGTGACCTGCATGTATACATCCAGATGGCCTGAAG
+>3-166224147..166224187
+ATGTGTACATGCAGGTCACAGGGGATATGATGGCTTAGCTT
+>3-167148636..167148677
+CCCCAAAGCAAGTGAAGAATCACAAAAGAAGTGAAAATGGCC
+>3-175543357..175543446
+AGCCATTTTCACTTCTTTTGTGATTCTTCACTTGCTGCAGGCCATCTGGATGTATACATGCAGGTCACAGGGGATATGATGGCTTAGCTT
+>3-179233406..179233458
+CTTCAGGCCATCTGGATGTATACATGCAGGTCACAGGGGATATGATGGATTAG
+>3-179239886..179239926
+AAGCTAAGCCATCATATCCCCTGTGACCTGCATGTACACAT
+>3-191645172..191645214
+GGCCCGAAGCAAGTGAAGAATCACAAAAGAAGTGAAAATGGCC
+>3-192713451..192713491
+AAGCTAAGCCATCATATCCCCTGTGACCTGCATGTACACAT
+>X-6226061..6226101
+AAGCTAAGCCATCATATCCCCTGTGACCTGCATGTACACAT
+>X-8324430..8324472
+GGCCATTTTCACTTCTTTTGTGATTCTTCACTTGCTTCAGGCC
+>X-16235303..16235357
+CTTCAGGCCATCTGGATGTATACATGCAGGTCACAGGGGATATGATGGCTGAGCT
+>X-16240306..16240361
+CTTCAGGCCATCTGGATGTATACATGCAGGTCACAGGGGATATGATGGCTTAGCTT
+>X-16474975..16475017
+CTTCAGGCCATCTGGATGTATACATGCAGGTCACAGGGAATAT
+>X-25595530..25595572
+GGCCTGAAGCAAGTGAAGAATCACAAAAGAAGTGAAAATGGCC
+>X-28521030..28521072
+GGCCATTTTCACTTCTTTTGTGATTCTTCACTTGCTTCAGGCC
+>X-33121409..33121452
+AAGCTAAGCCATCATATCCCCTGTGACCTGCATGTATACGCCCA
+>X-34248391..34248433
+GGCCATTTTCACTTCTTTTGTGATTCTTCACTTGCTTCAGGCC
+>X-37320393..37320435
+AGCCATTTTCACTTCTTTTGTGATTCTTCACTTGCTTCAGGCC
+>X-81982232..81982287
+AAGCTAAGCCATCATATCCCCTGTGACCTGCATGTATACATCCAGATGGCCTGAAA
+>X-81987984..81988035
+AAGCTAAGCCATCATATCCCCTGTGACCTGCATGTATACATCCAGATAGTCT
+>X-84213601..84213642
+GGCCATTTTCACTTCTTTTGTGATTCTTCACTTGCTTGAGGC
+>X-86943493..86943534
+GCCCTAAGCAAGTGAAGAATCACAAAAGAAGTGAAAATGGCC
+>X-90207753..90207792
+TATACACATGCAGGTCACAGGGGATATGATGGCTTAGCTT
+>X-93476782..93476824
+GGCCTGAAGCAAGTGAAGAATCACAAAAGAAGTGAAAATGGCC
+>X-103022149..103022191
+AGCCATTTTCACTTCTTTTGTGATTCTTCACTTGCTTCAGGCC
+>X-116059282..116059324
+AGCCATTTTCACTTCTTTTGTGATTCTTCACTTGCTTCAGGCC
+>X-119175784..119175826
+GGCCTGAAGCAAGTGAAGAATCACAAAAGAAGTGAAAATGGCC
+>X-119328356..119328398
+GGCCATTTTCACTTCTTTTGTGATTCTTCACTTGCTTCAGGCC
+>X-137352435..137352475
+ATGTGTACATGCAGGTCACAGGGGATATGATGGCTTAGCTT
+>X-142590292..142590334
+GGCCATTTTCACTTCTTTTGTGATTCTTCACTTGCTTCAGGCC
+>X-148764699..148764740
+GCCTAAAGCAAGTGAAGAATCACAAAAGAAGTGAAAATGGCT
+>18-28192769..28192811
+GGCCTGAAGCAAGTGAAGAATCACAAAAGAAGTGAAAATGGCC
+>18-40571479..40571519
+AAGCTAAGCCATCATATCCCCTGTGACCTGCATGTACAGGG
+>11-334057..334099
+GGCCATTTTCACTTCTTTTGTGATTCTTCACTTGCTTCAGGCC
+>11-4240899..4240954
+CTTCAGGCCATCTGGATGTATACATGCAGGTCACAGGGGATATGATGGCTTAGCCT
+>11-4246478..4246528
+GGCCCTCTGGATGTATACATGCAGGTCACAGGGGATATGATGGCTTAGCTT
+>11-4343062..4343112
+GGCCCTCTGGATGTATACATGCAGGTCACAGGGGATATGATGGCTTAGCTT
+>11-6823095..6823135
+AGGCTAAGCCATCATATCCCCTGTGACCTGCATGTACACAT
+>11-39762215..39762254
+TCCCTTGTGACCTGCATGTATACATCCAGATGGCCTGAAG
+>11-55330948..55330990
+AAGCTAAGCCATCATATCCCCTGTGACCTGCATGTATATATCC
+>11-60591260..60591302
+ATTTTCCCTGTGACCTGCATGTATACATCCAGATGGCCTGAAG
+>11-67609714..67609754
+ATGTGTACATGCAGGTCACAGGGGATATGATGGCTTAGCTT
+>11-70066203..70066243
+ATGTGTACATGCAGGTCACAGGGGATATGATGGCTTAGCTA
+>11-71448638..71448678
+AACCTAAGCCATCATATCCCCTGTGACCTGCATGTACACAT
+>11-71463364..71463404
+AAGCTAAGCCATCATATCCCCTGTGACCTGCATGTACACAT
+>11-74249326..74249415
+AGCCATTTTCACTTCTTTTGTGATTCTTCACTTGCTTCAGGCCATCTGGATGTATACATGCAGGTCACAGGGGATATGATGGCTTAGCTT
+>11-81513291..81513331
+AAGCTAAGCCATCATATCCCCTGTGACCTGCATGTACACAT
+>11-94078908..94078948
+AAGCTAAGCCATCATATCCCCTGTGACCTGCATGTACACAT
+>11-94084195..94084235
+AAGTTAAGCCATCATATCCCCTGTGACCTGCATGTAGACCA
+>11-131130115..131130155
+ATGTGTACATGCAGGTCACAGGGGATATGATGGCTTAGCTT
+>10-57731336..57731378
+GGCCTGAAGCAAGTGAAGAATCACAAAAGAAGTGAAAATAGCT
+>10-66266641..66266683
+GGCCTGAAGCAAGTGAAGAATCACAAAAGAAGTGAAAATGGCC
+>10-92144326..92144366
+AAGCTAAGCCATCATATCCCCTGTGACCTGCATGTACACAT
+>10-93067027..93067067
+ATGTGTACATGCAGGTCACAGGGGATATGATGGCTTAGCTT
+>10-102140694..102140739
+AAACTAAGCCATCATATCCCCTGTGACCTGCATGTATACATACAGA
+>10-107487436..107487478
+GGCCTGAAGCAAGTGAAGAATCACAAAAGAAGTGAAAATTGCT
+>15-24930838..24930878
+ATGTGTACATGCAGGTCACAGGGGATATGATGGCTTAGCTT
+>15-33882423..33882465
+GGCCATTTTCACTTCTTTTGTGATTCTTCACTTGCTTCAGGCC
+>15-45843716..45843758
+AGCCATTTTCACTTCTTTTGTGATTCTTCACTTGCTTCAGGCC
+>15-55710196..55710238
+GGCCATTTTCACTTCTTTTGTGATTCTTCACTTGCTTCAGGCC
+>15-93323315..93323355
+CAGGTCATCTGGATGTATACATGCAGGTCACAGGGGTTATG
+>15-95586603..95586643
+CCCGCAGCAAGTGAAGAATCACAAAAGAAGTGAAAATGGCT
=====================================
test_f/bug/bug-17175-2-reads.fa
=====================================
@@ -0,0 +1,6 @@
+>seq1
+AGAGAGCATTCTTGGATCTCTTGCAAGAAAGAATTTGAGGCGAATCCATAGAGTAAGCTTAGTGATGTGTGTCAGACCTCTGAGCCCTAGCAAAGCCATCATATCCCCTGTGACCTGCATGTATACATCCAGATGGCCGGAAGCAAGTGAAGAATCACAAAAGAAGTGAAAAGGGCCGGTTCCTGCCTTAACTGATGACA
+>seq2
+AGAGAGCATTCTTGGATCTCTTGCAAGAAAGAATTTGAGGCGAATCCATAGAGTAAGCTTAGTGATGTGTGTCAGACCTCTGAGCCCTAGCAAAGCCATCATATCCCCTGTGACCTGCATGTATACATCCAGATGGCCGGAAGCAAGTGAAGAATCACAAAAGAAGTGAAAAGGGCCGGTTCCTGCCTTAACTGATGACA
+>seq3
+AGAGAGCATTCTTGGATCTCTTGCAAGAAAGAATTTGAGGCGAATCCATAGAGTAAGCTTAGTGATGTGTGTCAGACCTCTGAGCCCTAGCAAAGCCATCATATCCCCTGTGACCTGCATGTATACATCCAGATGGCCGGAAGCAAGTGAAGAATCACAAAAGAAGTGAAAAGGGCCGGTTCCTGCCTTAACTGATGACA
\ No newline at end of file
=====================================
test_f/bug/test.fa
=====================================
@@ -0,0 +1,2 @@
+>HWI-M04117:13:000000000-AGD5G:1:1108:20346:1958
+TTTTCAATCCACCAACCGTGTC
\ No newline at end of file
=====================================
test_f/bug/test0.fa
=====================================
@@ -0,0 +1,2 @@
+>HWI-M04117:13:000000000-AGD5G:1:1108:20346:1958
+AGGCAACACAATCTGCATCTGGAAGTGATAAACTTCCATGATTCTGTGAAGCTGTAAACACCCCACAGAAGGGCGACAACAGCCCCCAGGGTAAGTGCGACACGGTTGGCGGATTGAAAATGCACATATG
=====================================
test_f/bug/tmp-genome.fa
=====================================
The diff for this file was not included because it is too large.
=====================================
test_f/bug/tmp-reads.fa
=====================================
@@ -0,0 +1,6 @@
+>seq1
+AGAGAGCATTCTTGGATCTCTTGCAAGAAAGAATTTGAGGCGAATCCATAGAGTAAGCTTAGTGATGTGTGTCAGACCTCTGAGCCCTAGCAAAGCCATCATATCCCCTGTGACCTGCATGTATACATCCAGATGGCCGGAAGCAAGTGAAGAATCACAAAAGAAGTGAAAAGGGCCGGTTCCTGCCTTAACTGATGACA
+>seq2
+AGAGAGCATTCTTGGATCTCTTGCAAGAAAGAATTTGAGGCGAATCCATAGAGTAAGCTTAGTGATGTGTGTCAGACCTCTGAGCCCTAGCAAAGCCATCATATCCCCTGTGACCTGCATGTATACATCCAGATGGCCGGAAGCAAGTGAAGAATCACAAAAGAAGTGAAAAGGGCCGGTTCCTGCCTTAACTGATGACA
+>seq3
+AGAGAGCATTCTTGGATCTCTTGCAAGAAAGAATTTGAGGCGAATCCATAGAGTAAGCTTAGTGATGTGTGTCAGACCTCTGAGCCCTAGCAAAGCCATCATATCCCCTGTGACCTGCATGTATACATCCAGATGGCCGGAAGCAAGTGAAGAATCACAAAAGAAGTGAAAAGGGCCGGTTCCTGCCTTAACTGATGACA
\ No newline at end of file
=====================================
test_f/causes/Makefile.in
=====================================
@@ -1,7 +1,7 @@
-# Makefile.in generated by automake 1.14.1 from Makefile.am.
+# Makefile.in generated by automake 1.16.1 from Makefile.am.
# @configure_input@
-# Copyright (C) 1994-2013 Free Software Foundation, Inc.
+# Copyright (C) 1994-2018 Free Software Foundation, Inc.
# This Makefile.in is free software; the Free Software Foundation
# gives unlimited permission to copy and/or distribute it,
@@ -113,7 +113,17 @@
# #
###############################################################################
VPATH = @srcdir@
-am__is_gnu_make = test -n '$(MAKEFILE_LIST)' && test -n '$(MAKELEVEL)'
+am__is_gnu_make = { \
+ if test -z '$(MAKELEVEL)'; then \
+ false; \
+ elif test -n '$(MAKE_HOST)'; then \
+ true; \
+ elif test -n '$(MAKE_VERSION)' && test -n '$(CURDIR)'; then \
+ true; \
+ else \
+ false; \
+ fi; \
+}
am__make_running_with_option = \
case $${target_option-} in \
?) ;; \
@@ -177,7 +187,6 @@ POST_UNINSTALL = :
build_triplet = @build@
host_triplet = @host@
subdir = test_f/causes
-DIST_COMMON = $(srcdir)/Makefile.in $(srcdir)/Makefile.am
ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
am__aclocal_m4_deps = $(top_srcdir)/config/m4/libtool.m4 \
$(top_srcdir)/config/m4/ltoptions.m4 \
@@ -187,6 +196,7 @@ am__aclocal_m4_deps = $(top_srcdir)/config/m4/libtool.m4 \
$(top_srcdir)/configure.ac
am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \
$(ACLOCAL_M4)
+DIST_COMMON = $(srcdir)/Makefile.am $(am__DIST_COMMON)
mkinstalldirs = $(install_sh) -d
CONFIG_HEADER = $(top_builddir)/config/config.h
CONFIG_CLEAN_FILES =
@@ -211,6 +221,7 @@ am__can_run_installinfo = \
*) (install-info --version) >/dev/null 2>&1;; \
esac
am__tagged_files = $(HEADERS) $(SOURCES) $(TAGS_FILES) $(LISP)
+am__DIST_COMMON = $(srcdir)/Makefile.in
DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
ACLOCAL = @ACLOCAL@
ALLOCA = @ALLOCA@
@@ -259,6 +270,7 @@ LIBTOOL = @LIBTOOL@
LIPO = @LIPO@
LN_S = @LN_S@
LTLIBOBJS = @LTLIBOBJS@
+LT_SYS_LIBRARY_PATH = @LT_SYS_LIBRARY_PATH@
MAKEINFO = @MAKEINFO@
MANIFEST_TOOL = @MANIFEST_TOOL@
MKDIR_P = @MKDIR_P@
@@ -329,6 +341,7 @@ pdfdir = @pdfdir@
prefix = @prefix@
program_transform_name = @program_transform_name@
psdir = @psdir@
+runstatedir = @runstatedir@
sbindir = @sbindir@
sharedstatedir = @sharedstatedir@
srcdir = @srcdir@
@@ -357,14 +370,13 @@ $(srcdir)/Makefile.in: $(srcdir)/Makefile.am $(am__configure_deps)
echo ' cd $(top_srcdir) && $(AUTOMAKE) --gnu test_f/causes/Makefile'; \
$(am__cd) $(top_srcdir) && \
$(AUTOMAKE) --gnu test_f/causes/Makefile
-.PRECIOUS: Makefile
Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status
@case '$?' in \
*config.status*) \
cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh;; \
*) \
- echo ' cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__depfiles_maybe)'; \
- cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__depfiles_maybe);; \
+ echo ' cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__maybe_remake_depfiles)'; \
+ cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__maybe_remake_depfiles);; \
esac;
$(top_builddir)/config.status: $(top_srcdir)/configure $(CONFIG_STATUS_DEPENDENCIES)
@@ -388,7 +400,10 @@ ctags CTAGS:
cscope cscopelist:
-distdir: $(DISTFILES)
+distdir: $(BUILT_SOURCES)
+ $(MAKE) $(AM_MAKEFLAGS) distdir-am
+
+distdir-am: $(DISTFILES)
@srcdirstrip=`echo "$(srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \
topsrcdirstrip=`echo "$(top_srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \
list='$(DISTFILES)'; \
@@ -536,6 +551,8 @@ uninstall-am:
mostlyclean-generic mostlyclean-libtool pdf pdf-am ps ps-am \
tags-am uninstall uninstall-am
+.PRECIOUS: Makefile
+
# Tell versions [3.59,3.63) of GNU make to not export all variables.
# Otherwise a system limit (for SysV at least) may be exceeded.
=====================================
test_f/cigar/Makefile.in
=====================================
@@ -1,7 +1,7 @@
-# Makefile.in generated by automake 1.14.1 from Makefile.am.
+# Makefile.in generated by automake 1.16.1 from Makefile.am.
# @configure_input@
-# Copyright (C) 1994-2013 Free Software Foundation, Inc.
+# Copyright (C) 1994-2018 Free Software Foundation, Inc.
# This Makefile.in is free software; the Free Software Foundation
# gives unlimited permission to copy and/or distribute it,
@@ -115,7 +115,17 @@
# SUBDIRS=causes cigar
VPATH = @srcdir@
-am__is_gnu_make = test -n '$(MAKEFILE_LIST)' && test -n '$(MAKELEVEL)'
+am__is_gnu_make = { \
+ if test -z '$(MAKELEVEL)'; then \
+ false; \
+ elif test -n '$(MAKE_HOST)'; then \
+ true; \
+ elif test -n '$(MAKE_VERSION)' && test -n '$(CURDIR)'; then \
+ true; \
+ else \
+ false; \
+ fi; \
+}
am__make_running_with_option = \
case $${target_option-} in \
?) ;; \
@@ -179,7 +189,6 @@ POST_UNINSTALL = :
build_triplet = @build@
host_triplet = @host@
subdir = test_f/cigar
-DIST_COMMON = $(srcdir)/Makefile.in $(srcdir)/Makefile.am
ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
am__aclocal_m4_deps = $(top_srcdir)/config/m4/libtool.m4 \
$(top_srcdir)/config/m4/ltoptions.m4 \
@@ -189,6 +198,7 @@ am__aclocal_m4_deps = $(top_srcdir)/config/m4/libtool.m4 \
$(top_srcdir)/configure.ac
am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \
$(ACLOCAL_M4)
+DIST_COMMON = $(srcdir)/Makefile.am $(am__DIST_COMMON)
mkinstalldirs = $(install_sh) -d
CONFIG_HEADER = $(top_builddir)/config/config.h
CONFIG_CLEAN_FILES =
@@ -213,6 +223,7 @@ am__can_run_installinfo = \
*) (install-info --version) >/dev/null 2>&1;; \
esac
am__tagged_files = $(HEADERS) $(SOURCES) $(TAGS_FILES) $(LISP)
+am__DIST_COMMON = $(srcdir)/Makefile.in
DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
ACLOCAL = @ACLOCAL@
ALLOCA = @ALLOCA@
@@ -261,6 +272,7 @@ LIBTOOL = @LIBTOOL@
LIPO = @LIPO@
LN_S = @LN_S@
LTLIBOBJS = @LTLIBOBJS@
+LT_SYS_LIBRARY_PATH = @LT_SYS_LIBRARY_PATH@
MAKEINFO = @MAKEINFO@
MANIFEST_TOOL = @MANIFEST_TOOL@
MKDIR_P = @MKDIR_P@
@@ -331,6 +343,7 @@ pdfdir = @pdfdir@
prefix = @prefix@
program_transform_name = @program_transform_name@
psdir = @psdir@
+runstatedir = @runstatedir@
sbindir = @sbindir@
sharedstatedir = @sharedstatedir@
srcdir = @srcdir@
@@ -359,14 +372,13 @@ $(srcdir)/Makefile.in: $(srcdir)/Makefile.am $(am__configure_deps)
echo ' cd $(top_srcdir) && $(AUTOMAKE) --gnu test_f/cigar/Makefile'; \
$(am__cd) $(top_srcdir) && \
$(AUTOMAKE) --gnu test_f/cigar/Makefile
-.PRECIOUS: Makefile
Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status
@case '$?' in \
*config.status*) \
cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh;; \
*) \
- echo ' cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__depfiles_maybe)'; \
- cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__depfiles_maybe);; \
+ echo ' cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__maybe_remake_depfiles)'; \
+ cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__maybe_remake_depfiles);; \
esac;
$(top_builddir)/config.status: $(top_srcdir)/configure $(CONFIG_STATUS_DEPENDENCIES)
@@ -390,7 +402,10 @@ ctags CTAGS:
cscope cscopelist:
-distdir: $(DISTFILES)
+distdir: $(BUILT_SOURCES)
+ $(MAKE) $(AM_MAKEFLAGS) distdir-am
+
+distdir-am: $(DISTFILES)
@srcdirstrip=`echo "$(srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \
topsrcdirstrip=`echo "$(top_srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \
list='$(DISTFILES)'; \
@@ -538,6 +553,8 @@ uninstall-am:
mostlyclean-generic mostlyclean-libtool pdf pdf-am ps ps-am \
tags-am uninstall uninstall-am
+.PRECIOUS: Makefile
+
# Tell versions [3.59,3.63) of GNU make to not export all variables.
# Otherwise a system limit (for SysV at least) may be exceeded.
=====================================
test_f/cigar/genome2.fasta
=====================================
The diff for this file was not included because it is too large.
=====================================
test_f/cigar/read_c4.fasta
=====================================
@@ -0,0 +1,6 @@
+>seq1
+CCTGAGGCCTCCCAAGCTGTGCTGAACTACGGCACCGAAAGCGAAGGAAGCTCCTGCTCCTCCTAAAGCCGAAGCGAAAGTGAAGGTTTTAAAGGCCAAG
+>seq2
+CCTGAGGCCTCCCAAGCTGTGCTGAACTACGGCACCGAAAGCGAAGGAAGCTCCTGCTCCTCCTAAAGCCGAAGCGAAAGTGAAGGTTTTAAAGGCCAAG
+>seq3
+CCTGAGGCCTCCCAAGCTGTGCTGAACTACGGCACCGAAAGCGAAGGAAGCTCCTGCTCCTCCTAAAGCCGAAGCGAAAGTGAAGGTTTTAAAGGCCAAG
\ No newline at end of file
=====================================
test_f/splices_adjust/Makefile.in
=====================================
@@ -1,7 +1,7 @@
-# Makefile.in generated by automake 1.14.1 from Makefile.am.
+# Makefile.in generated by automake 1.16.1 from Makefile.am.
# @configure_input@
-# Copyright (C) 1994-2013 Free Software Foundation, Inc.
+# Copyright (C) 1994-2018 Free Software Foundation, Inc.
# This Makefile.in is free software; the Free Software Foundation
# gives unlimited permission to copy and/or distribute it,
@@ -113,7 +113,17 @@
# #
###############################################################################
VPATH = @srcdir@
-am__is_gnu_make = test -n '$(MAKEFILE_LIST)' && test -n '$(MAKELEVEL)'
+am__is_gnu_make = { \
+ if test -z '$(MAKELEVEL)'; then \
+ false; \
+ elif test -n '$(MAKE_HOST)'; then \
+ true; \
+ elif test -n '$(MAKE_VERSION)' && test -n '$(CURDIR)'; then \
+ true; \
+ else \
+ false; \
+ fi; \
+}
am__make_running_with_option = \
case $${target_option-} in \
?) ;; \
@@ -177,7 +187,6 @@ POST_UNINSTALL = :
build_triplet = @build@
host_triplet = @host@
subdir = test_f/splices_adjust
-DIST_COMMON = $(srcdir)/Makefile.in $(srcdir)/Makefile.am
ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
am__aclocal_m4_deps = $(top_srcdir)/config/m4/libtool.m4 \
$(top_srcdir)/config/m4/ltoptions.m4 \
@@ -187,6 +196,7 @@ am__aclocal_m4_deps = $(top_srcdir)/config/m4/libtool.m4 \
$(top_srcdir)/configure.ac
am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \
$(ACLOCAL_M4)
+DIST_COMMON = $(srcdir)/Makefile.am $(am__DIST_COMMON)
mkinstalldirs = $(install_sh) -d
CONFIG_HEADER = $(top_builddir)/config/config.h
CONFIG_CLEAN_FILES =
@@ -211,6 +221,7 @@ am__can_run_installinfo = \
*) (install-info --version) >/dev/null 2>&1;; \
esac
am__tagged_files = $(HEADERS) $(SOURCES) $(TAGS_FILES) $(LISP)
+am__DIST_COMMON = $(srcdir)/Makefile.in
DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
ACLOCAL = @ACLOCAL@
ALLOCA = @ALLOCA@
@@ -259,6 +270,7 @@ LIBTOOL = @LIBTOOL@
LIPO = @LIPO@
LN_S = @LN_S@
LTLIBOBJS = @LTLIBOBJS@
+LT_SYS_LIBRARY_PATH = @LT_SYS_LIBRARY_PATH@
MAKEINFO = @MAKEINFO@
MANIFEST_TOOL = @MANIFEST_TOOL@
MKDIR_P = @MKDIR_P@
@@ -329,6 +341,7 @@ pdfdir = @pdfdir@
prefix = @prefix@
program_transform_name = @program_transform_name@
psdir = @psdir@
+runstatedir = @runstatedir@
sbindir = @sbindir@
sharedstatedir = @sharedstatedir@
srcdir = @srcdir@
@@ -357,14 +370,13 @@ $(srcdir)/Makefile.in: $(srcdir)/Makefile.am $(am__configure_deps)
echo ' cd $(top_srcdir) && $(AUTOMAKE) --gnu test_f/splices_adjust/Makefile'; \
$(am__cd) $(top_srcdir) && \
$(AUTOMAKE) --gnu test_f/splices_adjust/Makefile
-.PRECIOUS: Makefile
Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status
@case '$?' in \
*config.status*) \
cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh;; \
*) \
- echo ' cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__depfiles_maybe)'; \
- cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__depfiles_maybe);; \
+ echo ' cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__maybe_remake_depfiles)'; \
+ cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__maybe_remake_depfiles);; \
esac;
$(top_builddir)/config.status: $(top_srcdir)/configure $(CONFIG_STATUS_DEPENDENCIES)
@@ -388,7 +400,10 @@ ctags CTAGS:
cscope cscopelist:
-distdir: $(DISTFILES)
+distdir: $(BUILT_SOURCES)
+ $(MAKE) $(AM_MAKEFLAGS) distdir-am
+
+distdir-am: $(DISTFILES)
@srcdirstrip=`echo "$(srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \
topsrcdirstrip=`echo "$(top_srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \
list='$(DISTFILES)'; \
@@ -536,6 +551,8 @@ uninstall-am:
mostlyclean-generic mostlyclean-libtool pdf pdf-am ps ps-am \
tags-am uninstall uninstall-am
+.PRECIOUS: Makefile
+
# Tell versions [3.59,3.63) of GNU make to not export all variables.
# Otherwise a system limit (for SysV at least) may be exceeded.
=====================================
test_f/tmp-genome.fa
=====================================
The diff for this file was not included because it is too large.
View it on GitLab: https://salsa.debian.org/med-team/crac/commit/1e9463969d02b1e3d79ddede609ac9aef792dee1
--
View it on GitLab: https://salsa.debian.org/med-team/crac/commit/1e9463969d02b1e3d79ddede609ac9aef792dee1
You're receiving this email because of your account on salsa.debian.org.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://alioth-lists.debian.net/pipermail/debian-med-commit/attachments/20190719/69d79fed/attachment-0001.html>
More information about the debian-med-commit
mailing list