Commit b81040f9 authored by Andreas Tille's avatar Andreas Tille
Browse files

New upstream version 2.41+dfsg

parent 2d42ea6e

ChangeLog

+60 −3
Original line number Diff line number Diff line 
Stacks 2.41 - July 8, 2019

--------------------------

    Feature: populations: calculates haplotype-based Dxy (Nei, 1987) and provides for smoothing if a 

             reference genome is available.

    Feature: populations: re-implemented full sequence export for phylip format, including partitioning information.



Stacks 2.4 - May 9, 2019

------------------------

    Feature: populations: re-implemented HZAR export.

    Feature: added reporting code to detect issues with inconsistent versions of libz on a host system

             causing Stacks components to fail to open compressed files.

    Feature: gstacks: improved PCR duplicate reporting to be per-sample.

    Bugfix:  populations: fixed an issues where the basepair position of a small number of loci was reported

                          incorrectly -- they were shifted by a small, fixed offset.



Stacks 2.3 - Jan 11, 2019

--------------------------

    Feature: populations: Backwards-compatibly worked on filtering options; added long names for -r and -p and

             added --min-samples-overall and --filter-haplotype-wise.

    Feature: populations: Implemented --treemix.

    Feature: gstacks: Improved RAD-loci reference sequences around the end of forward (restriction site-bound) reads.

    Feature: gstacks: Improved the way 2-microsatelittes are dealt with.

    Feature: gstacks: Changed the default value for --var-alpha from 0.05 to 0.01 (--gt-alpha is unchanged at 0.05).

    Feature: gstacks: Improved PCR duplicates-related log information (distribution of clone sizes).

    Feature: gstacks: Added an option to save read alignments (--write-alignments).

    Feature: Backwards-compatibly switched to hyphens in command line options (underscores remain accepted

             where they previously were).

    Feature: cstacks/sstacks now report an error when the disk becomes full.



	2.3b - Jan 23, 2019

	----------

	Bugfix: Fixed some limit cases causing an abort at gstacks.cc:1752.

	Bugfix: Fixed some limit cases causing an abort at debruijn.cc:60.

	Bugfix: Fixed some limit cases apparently causing an infinite loop in the de Bruijn code.

	Bugfix: Restored compilation with the oldest C++11 GCC versions (4.9 and 5.0).



	2.3c - Feb 27, 2019

	---------

	Bugfix: Fixed assert failure at gstacks.cc:1171 (corrected with a return on gstacks.cc:1126)

	Bugfix: inadvertantly compiling out BAM support from process_radtags due to the removal of the HAVE_BAM

                config option, which occurred when we moved the BAM library internally to Stacks.

	Bugfix: corrected infinite loop in populations when --write-single-snp and -r were enabled.

        Bugfix: correct missing comment marker in population's FASTA exports and missing ']' character in FASTA comments.



	2.3d - Feb 28, 2019

	---------

	Bugfix: the snps_per_loc_postfilters distribution in the populations.log.distrib file was slightly off due to counting

                the number of SNPs at loci where despite SNP objects present at the locus, all sites were fixed in the

	        focal populations.

	Bugfix: Some haplotypes could pass through the filter, even after particular SNPs were filtered from them.

	Bufgix: Corrected the samples per locus and absent-samples per locus distributions from populations. 



	2.3e - Mar 20, 2019

	---------

	Bugfix: the --write-random-snp flag was causing an infinite loop in populations.



Stacks 2.2 - Aug 22, 2018

--------------------------

    Feature: Added the --bestrad flag to process_radtags. When used it will look for reads that need transposed

             before they are processed.

    Feature: gstacks: New option --max-debrujin-reads to control the construction of the de Bruijn graph; replaces

             --min-kmer-freq which is now deprecated

    Bugfix: Fixed a breaking circumstantial segmentation fault in populations

    Bugfix: Added run number to output FASTQ headers in process_radtags to make sure read IDs are always unique.



Stacks 2.1 - June 25, 2018

Makefile.am

+1 −17
Original line number Diff line number Diff line
@@ -89,22 +89,11 @@ dist_bin_SCRIPTS = scripts/denovo_map.pl scripts/ref_map.pl \ 


dist_noinst_SCRIPTS = autogen.sh scripts/extract_interpop_chars.pl scripts/convert_stacks.pl



nobase_pkgdata_DATA = sql/mysql.cnf.dist sql/catalog_index.sql sql/stacks.sql sql/tag_index.sql sql/chr_index.sql \

	php/CatalogClass.php php/annotate_marker.php php/constants.php.dist php/index.php php/tags.php php/tag.php \

	php/Locus.php php/catalog.php php/correct_genotypes.php php/correct_genotype.php php/export_batch.php php/last_modified.php  \

	php/version.php php/catalog_genotypes.php php/db_functions.php php/header.php php/samples.php \

	php/stacks_functions.php php/view_sequence.php php/sequence_blast.php \

	php/pop_view.php php/sumstat_view.php php/hapstat_view.php php/fst_view.php php/phist_view.php php/stack_view.php \

	php/population_view.js php/ajax.js php/annotate.js php/stacks.js php/export.js php/stacks.css \

	php/images/caret-d.png php/images/caret-u.png php/images/excel_icon.png php/images/l-arrow-disabled.png \

	php/images/l-arrow.png php/images/r-arrow-disabled.png php/images/r-arrow.png php/images/stacks_bg.png \

	php/images/stacks_logo_rev_small.png



LOG_DRIVER = env AM_TAP_AWK='$(AWK)' $(SHELL) $(abs_top_srcdir)/tests/tap-driver.sh



TESTS = tests/process_radtags.t tests/kmer_filter.t tests/ustacks.t tests/pstacks.t



EXTRA_DIST = $(nobase_pkgdata_DATA) LICENSE INSTALL README ChangeLog $(TESTS)

EXTRA_DIST = LICENSE INSTALL README ChangeLog $(TESTS)



pkglocalstatedir = $(localstatedir)/$(PACKAGE)
@@ -118,11 +107,6 @@ install-data-hook: 
	sed -e 's,_VERSION_,$(VERSION),' -e 's,_BINDIR_,$(bindir)/,g' -e 's,_PKGDATADIR_,$(pkgdatadir)/,g' $(DESTDIR)$(bindir)/ref_map.pl > $(DESTDIR)$(bindir)/ref_map.pl.subst

	mv $(DESTDIR)$(bindir)/ref_map.pl.subst $(DESTDIR)$(bindir)/ref_map.pl

	chmod +x $(DESTDIR)$(bindir)/ref_map.pl

	sed -e 's,_PKGDATADIR_,$(pkgdatadir)/,g' -e 's,_BINDIR_,$(bindir)/,g' \

		$(DESTDIR)$(pkgdatadir)/php/constants.php.dist > $(DESTDIR)$(pkgdatadir)/php/constants.php.dist.subst

	mv $(DESTDIR)$(pkgdatadir)/php/constants.php.dist.subst $(DESTDIR)$(pkgdatadir)/php/constants.php.dist

	echo $(VERSION) > $(DESTDIR)$(pkgdatadir)/php/version.php

	$(install_sh) -d -m 755 $(DESTDIR)$(pkgdatadir)/php/export

	sed -i.bkp -e 's,_VERSION_,$(VERSION),' $(DESTDIR)$(bindir)/stacks-integrate-alignments

	rm -f $(DESTDIR)$(bindir)/stacks-integrate-alignments.bkp

	chmod +x $(DESTDIR)$(bindir)/stacks-integrate-alignments

Makefile.in

+32 −96
Original line number Diff line number Diff line 
# Makefile.in generated by automake 1.15 from Makefile.am.

# Makefile.in generated by automake 1.13.4 from Makefile.am.

# @configure_input@



# Copyright (C) 1994-2014 Free Software Foundation, Inc.

# Copyright (C) 1994-2013 Free Software Foundation, Inc.



# This Makefile.in is free software; the Free Software Foundation

# gives unlimited permission to copy and/or distribute it,
@@ -16,19 +16,8 @@ 








VPATH = @srcdir@

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__is_gnu_make = test -n '$(MAKEFILE_LIST)' && test -n '$(MAKELEVEL)'

am__make_running_with_option = \

  case $${target_option-} in \

      ?) ;; \
@@ -95,14 +84,20 @@ bin_PROGRAMS = ustacks$(EXEEXT) cstacks$(EXEEXT) sstacks$(EXEEXT) \ 
	populations$(EXEEXT) phasedstacks$(EXEEXT) tsv2bam$(EXEEXT) \

	gstacks$(EXEEXT)

subdir = .

DIST_COMMON = $(srcdir)/Makefile.in $(srcdir)/Makefile.am \

	$(top_srcdir)/configure $(am__configure_deps) \

	$(srcdir)/config.h.in $(dist_bin_SCRIPTS) \

	$(dist_noinst_SCRIPTS) $(top_srcdir)/config/depcomp \

	$(top_srcdir)/config/test-driver ChangeLog INSTALL README \

	config/ar-lib config/compile config/depcomp config/install-sh \

	config/missing $(top_srcdir)/config/ar-lib \

	$(top_srcdir)/config/compile $(top_srcdir)/config/install-sh \

	$(top_srcdir)/config/missing

ACLOCAL_M4 = $(top_srcdir)/aclocal.m4

am__aclocal_m4_deps = $(top_srcdir)/acinclude.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) $(dist_bin_SCRIPTS) \

	$(dist_noinst_SCRIPTS) $(am__DIST_COMMON)

am__CONFIG_DISTCLEAN_FILES = config.status config.cache config.log \

 configure.lineno config.status.lineno

mkinstalldirs = $(install_sh) -d
@@ -142,8 +137,7 @@ am_libpop_a_OBJECTS = src/export_formats.$(OBJEXT) \ 
	src/genotype_dictionaries.$(OBJEXT) src/PopSum.$(OBJEXT) \

	src/Hwp.$(OBJEXT)

libpop_a_OBJECTS = $(am_libpop_a_OBJECTS)

am__installdirs = "$(DESTDIR)$(bindir)" "$(DESTDIR)$(bindir)" \

	"$(DESTDIR)$(pkgdatadir)"

am__installdirs = "$(DESTDIR)$(bindir)" "$(DESTDIR)$(bindir)"

PROGRAMS = $(bin_PROGRAMS)

am_clone_filter_OBJECTS = src/clone_filter.$(OBJEXT)

clone_filter_OBJECTS = $(am_clone_filter_OBJECTS)
@@ -279,7 +273,6 @@ am__can_run_installinfo = \ 
    n|no|NO) false;; \

    *) (install-info --version) >/dev/null 2>&1;; \

  esac

DATA = $(nobase_pkgdata_DATA)

RECURSIVE_CLEAN_TARGETS = mostlyclean-recursive clean-recursive	\

  distclean-recursive maintainer-clean-recursive

am__recursive_targets = \
@@ -485,12 +478,6 @@ 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 $(srcdir)/config.h.in \

	$(top_srcdir)/config/ar-lib $(top_srcdir)/config/compile \

	$(top_srcdir)/config/depcomp $(top_srcdir)/config/install-sh \

	$(top_srcdir)/config/missing $(top_srcdir)/config/test-driver \

	ChangeLog INSTALL README config/ar-lib config/compile \

	config/depcomp config/install-sh config/missing

DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)

distdir = $(PACKAGE)-$(VERSION)

top_distdir = $(distdir)
@@ -621,7 +608,6 @@ pdfdir = @pdfdir@ 
prefix = @prefix@

program_transform_name = @program_transform_name@

psdir = @psdir@

runstatedir = @runstatedir@

sbindir = @sbindir@

sharedstatedir = @sharedstatedir@

srcdir = @srcdir@
@@ -710,20 +696,9 @@ dist_bin_SCRIPTS = scripts/denovo_map.pl scripts/ref_map.pl \ 
	scripts/stacks-integrate-alignments scripts/stacks-dist-extract scripts/stacks-gdb # scripts/denovo_map.py



dist_noinst_SCRIPTS = autogen.sh scripts/extract_interpop_chars.pl scripts/convert_stacks.pl

nobase_pkgdata_DATA = sql/mysql.cnf.dist sql/catalog_index.sql sql/stacks.sql sql/tag_index.sql sql/chr_index.sql \

	php/CatalogClass.php php/annotate_marker.php php/constants.php.dist php/index.php php/tags.php php/tag.php \

	php/Locus.php php/catalog.php php/correct_genotypes.php php/correct_genotype.php php/export_batch.php php/last_modified.php  \

	php/version.php php/catalog_genotypes.php php/db_functions.php php/header.php php/samples.php \

	php/stacks_functions.php php/view_sequence.php php/sequence_blast.php \

	php/pop_view.php php/sumstat_view.php php/hapstat_view.php php/fst_view.php php/phist_view.php php/stack_view.php \

	php/population_view.js php/ajax.js php/annotate.js php/stacks.js php/export.js php/stacks.css \

	php/images/caret-d.png php/images/caret-u.png php/images/excel_icon.png php/images/l-arrow-disabled.png \

	php/images/l-arrow.png php/images/r-arrow-disabled.png php/images/r-arrow.png php/images/stacks_bg.png \

	php/images/stacks_logo_rev_small.png



LOG_DRIVER = env AM_TAP_AWK='$(AWK)' $(SHELL) $(abs_top_srcdir)/tests/tap-driver.sh

TESTS = tests/process_radtags.t tests/kmer_filter.t tests/ustacks.t tests/pstacks.t

EXTRA_DIST = $(nobase_pkgdata_DATA) LICENSE INSTALL README ChangeLog $(TESTS)

EXTRA_DIST = LICENSE INSTALL README ChangeLog $(TESTS)

pkglocalstatedir = $(localstatedir)/$(PACKAGE)

all: config.h

	$(MAKE) $(AM_MAKEFLAGS) all-recursive
@@ -745,6 +720,7 @@ $(srcdir)/Makefile.in: $(srcdir)/Makefile.am $(am__configure_deps) 
	echo ' cd $(top_srcdir) && $(AUTOMAKE) --foreign Makefile'; \

	$(am__cd) $(top_srcdir) && \

	  $(AUTOMAKE) --foreign Makefile

.PRECIOUS: Makefile

Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status

	@case '$?' in \

	  *config.status*) \
@@ -765,8 +741,8 @@ $(ACLOCAL_M4): $(am__aclocal_m4_deps) 
$(am__aclocal_m4_deps):



config.h: stamp-h1

	@test -f $@ || rm -f stamp-h1

	@test -f $@ || $(MAKE) $(AM_MAKEFLAGS) stamp-h1

	@if test ! -f $@; then rm -f stamp-h1; else :; fi

	@if test ! -f $@; then $(MAKE) $(AM_MAKEFLAGS) stamp-h1; else :; fi



stamp-h1: $(srcdir)/config.h.in $(top_builddir)/config.status

	@rm -f stamp-h1
@@ -1066,30 +1042,6 @@ distclean-compile: 
@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@	$(AM_V_CXX@am__nodep@)$(CXXCOMPILE) -c -o $@ `$(CYGPATH_W) '$<'`

install-nobase_pkgdataDATA: $(nobase_pkgdata_DATA)

	@$(NORMAL_INSTALL)

	@list='$(nobase_pkgdata_DATA)'; test -n "$(pkgdatadir)" || list=; \

	if test -n "$$list"; then \

	  echo " $(MKDIR_P) '$(DESTDIR)$(pkgdatadir)'"; \

	  $(MKDIR_P) "$(DESTDIR)$(pkgdatadir)" || exit 1; \

	fi; \

	$(am__nobase_list) | while read dir files; do \

	  xfiles=; for file in $$files; do \

	    if test -f "$$file"; then xfiles="$$xfiles $$file"; \

	    else xfiles="$$xfiles $(srcdir)/$$file"; fi; done; \

	  test -z "$$xfiles" || { \

	    test "x$$dir" = x. || { \

	      echo " $(MKDIR_P) '$(DESTDIR)$(pkgdatadir)/$$dir'"; \

	      $(MKDIR_P) "$(DESTDIR)$(pkgdatadir)/$$dir"; }; \

	    echo " $(INSTALL_DATA) $$xfiles '$(DESTDIR)$(pkgdatadir)/$$dir'"; \

	    $(INSTALL_DATA) $$xfiles "$(DESTDIR)$(pkgdatadir)/$$dir" || exit $$?; }; \

	done



uninstall-nobase_pkgdataDATA:

	@$(NORMAL_UNINSTALL)

	@list='$(nobase_pkgdata_DATA)'; test -n "$(pkgdatadir)" || list=; \

	$(am__nobase_strip_setup); files=`$(am__nobase_strip)`; \

	dir='$(DESTDIR)$(pkgdatadir)'; $(am__uninstall_files_from_dir)



# This directory's subdirectories are mostly independent; you can cd

# into them and run 'make' without going through this Makefile.
@@ -1227,7 +1179,7 @@ $(TEST_SUITE_LOG): $(TEST_LOGS) 
	if test -n "$$am__remaking_logs"; then \

	  echo "fatal: making $(TEST_SUITE_LOG): possible infinite" \

	       "recursion detected" >&2; \

	elif test -n "$$redo_logs"; then \

	else \

	  am__remaking_logs=yes $(MAKE) $(AM_MAKEFLAGS) $$redo_logs; \

	fi; \

	if $(am__make_dryrun); then :; else \
@@ -1462,16 +1414,10 @@ dist-xz: distdir 
	$(am__post_remove_distdir)



dist-tarZ: distdir

	@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 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

	$(am__post_remove_distdir)
@@ -1506,17 +1452,16 @@ distcheck: dist 
	esac

	chmod -R a-w $(distdir)

	chmod u+w $(distdir)

	mkdir $(distdir)/_build $(distdir)/_build/sub $(distdir)/_inst

	mkdir $(distdir)/_build $(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/sub \

	  && ../../configure \

	  && $(am__cd) $(distdir)/_build \

	  && ../configure --srcdir=.. --prefix="$$dc_install_base" \

	    $(AM_DISTCHECK_CONFIGURE_FLAGS) \

	    $(DISTCHECK_CONFIGURE_FLAGS) \

	    --srcdir=../.. --prefix="$$dc_install_base" \

	  && $(MAKE) $(AM_MAKEFLAGS) \

	  && $(MAKE) $(AM_MAKEFLAGS) dvi \

	  && $(MAKE) $(AM_MAKEFLAGS) check \
@@ -1572,10 +1517,10 @@ distcleancheck: distclean 
check-am: all-am

	$(MAKE) $(AM_MAKEFLAGS) check-TESTS

check: check-recursive

all-am: Makefile $(LIBRARIES) $(PROGRAMS) $(SCRIPTS) $(DATA) config.h

all-am: Makefile $(LIBRARIES) $(PROGRAMS) $(SCRIPTS) config.h

installdirs: installdirs-recursive

installdirs-am:

	for dir in "$(DESTDIR)$(bindir)" "$(DESTDIR)$(bindir)" "$(DESTDIR)$(pkgdatadir)"; do \

	for dir in "$(DESTDIR)$(bindir)" "$(DESTDIR)$(bindir)"; do \

	  test -z "$$dir" || $(MKDIR_P) "$$dir"; \

	done

install: install-recursive
@@ -1637,7 +1582,7 @@ info: info-recursive 


info-am:



install-data-am: install-nobase_pkgdataDATA

install-data-am:

	@$(NORMAL_INSTALL)

	$(MAKE) $(AM_MAKEFLAGS) install-data-hook

install-dvi: install-dvi-recursive
@@ -1685,8 +1630,7 @@ ps: ps-recursive 


ps-am:



uninstall-am: uninstall-binPROGRAMS uninstall-dist_binSCRIPTS \

	uninstall-nobase_pkgdataDATA

uninstall-am: uninstall-binPROGRAMS uninstall-dist_binSCRIPTS

	@$(NORMAL_INSTALL)

	$(MAKE) $(AM_MAKEFLAGS) uninstall-hook

.MAKE: $(am__recursive_targets) all check-am install-am \
@@ -1704,16 +1648,13 @@ uninstall-am: uninstall-binPROGRAMS uninstall-dist_binSCRIPTS \ 
	install-data-am install-data-hook install-dist_binSCRIPTS \

	install-dvi install-dvi-am install-exec install-exec-am \

	install-html install-html-am install-info install-info-am \

	install-man install-nobase_pkgdataDATA 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 pdf pdf-am ps ps-am \

	recheck tags tags-am uninstall uninstall-am \

	uninstall-binPROGRAMS uninstall-dist_binSCRIPTS uninstall-hook \

	uninstall-nobase_pkgdataDATA



.PRECIOUS: Makefile

	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 pdf pdf-am ps ps-am recheck tags tags-am \

	uninstall uninstall-am uninstall-binPROGRAMS \

	uninstall-dist_binSCRIPTS uninstall-hook





debug:
@@ -1726,11 +1667,6 @@ install-data-hook: 
	sed -e 's,_VERSION_,$(VERSION),' -e 's,_BINDIR_,$(bindir)/,g' -e 's,_PKGDATADIR_,$(pkgdatadir)/,g' $(DESTDIR)$(bindir)/ref_map.pl > $(DESTDIR)$(bindir)/ref_map.pl.subst

	mv $(DESTDIR)$(bindir)/ref_map.pl.subst $(DESTDIR)$(bindir)/ref_map.pl

	chmod +x $(DESTDIR)$(bindir)/ref_map.pl

	sed -e 's,_PKGDATADIR_,$(pkgdatadir)/,g' -e 's,_BINDIR_,$(bindir)/,g' \

		$(DESTDIR)$(pkgdatadir)/php/constants.php.dist > $(DESTDIR)$(pkgdatadir)/php/constants.php.dist.subst

	mv $(DESTDIR)$(pkgdatadir)/php/constants.php.dist.subst $(DESTDIR)$(pkgdatadir)/php/constants.php.dist

	echo $(VERSION) > $(DESTDIR)$(pkgdatadir)/php/version.php

	$(install_sh) -d -m 755 $(DESTDIR)$(pkgdatadir)/php/export

	sed -i.bkp -e 's,_VERSION_,$(VERSION),' $(DESTDIR)$(bindir)/stacks-integrate-alignments

	rm -f $(DESTDIR)$(bindir)/stacks-integrate-alignments.bkp

	chmod +x $(DESTDIR)$(bindir)/stacks-integrate-alignments

aclocal.m4

+64 −146

File changed.

Preview size limit exceeded, changes collapsed.

config.h.in

+3 −0
Original line number Diff line number Diff line
@@ -89,6 +89,9 @@ 
/* Define to 1 if the system has the type `_Bool'. */

#undef HAVE__BOOL



/* Define to 1 if your C compiler doesn't accept -c and -o together. */

#undef NO_MINUS_C_MINUS_O



/* Name of package */

#undef PACKAGE