Andreas Tille · Andreas Tille · Andreas Tille · Andreas Tille · Andreas Tille · Andreas Tille
--- a/ChangeLog
+++ b/ChangeLog
+Stacks 2.0 Beta 9 - Mar 12, 2018
+--------------------------------
+    Feature: Cleaned up tags/snps/alleles/matches files. We removed the batch ID from ustacks and cstacks 
+             output, and the deprecated log likelihood fields from ustacks and cstacks. We also removed 
+             the chromosome/bp/strand fields as they are no longer used in these files.
+    Feature: Renamed gstacks output files that represent the new components of the catalog:
+               gstacks.fa.gz => catalog.fa.gz; gstacks.vcf.gz => catalog.calls
+    Feature: Removed read length restrictions from ustacks/cstacks/sstacks core, reads/loci can vary in
+             length throughout the pipeline.
+    Feature: Reimplemented PLINK export format for the populations program.
+    Bugfix: Updated to HTSLib 1.7; changed to a custom build system that will work with the Stacks build
+            system.
+    Bugfix: Made gapped alignments mandatory in ustacks, cstacks, and sstacks. Added check for frameshift 
+            at 3' end of the read -- if found, a match is deferred to the gapped aligner.
+
 Stacks 2.0 Beta 8 - Feb 03, 2018
 --------------------------------
    Feature: populations: Now calculated deviation from Hardy-Weinberg equilibrium at the SNP level

--- a/Makefile.am
+++ b/Makefile.am
+SUBDIRS = htslib
+HTSLIB = htslib/libhts.a
+
+AM_CPPFLAGS = $(OPENMP_CFLAGS) -I$(top_srcdir)/htslib
+AM_LDFLAGS = $(OPENMP_CFLAGS)
+LDADD = $(HTSLIB) libcore.a
+
+noinst_LIBRARIES = libcore.a libclean.a libpop.a
 bin_PROGRAMS = ustacks cstacks sstacks process_radtags process_shortreads \
 	kmer_filter clone_filter populations phasedstacks \
 	tsv2bam gstacks

-noinst_LIBRARIES = libcore.a libclean.a libpop.a
-
 libcore_a_SOURCES = \
 	src/aln_utils.h src/aln_utils.cc \
 	src/BamI.h src/BamI.cc \
@@ -38,7 +44,8 @@ libcore_a_SOURCES = \
 	src/stacks.h src/stacks.cc \
 	src/Tsv.h \
 	src/utils.h src/utils.cc \
-	src/Vcf.h src/Vcf.cc
+	src/Vcf.h src/Vcf.cc \
+	$(HTSLIB)

 libclean_a_SOURCES = \
 	src/clean.h src/clean.cc \
@@ -56,9 +63,6 @@ libpop_a_SOURCES = \
 	src/smoothing_utils.h \
 	src/Hwp.h src/Hwp.cc

-libcore_a_CXXFLAGS = $(OPENMP_CFLAGS) $(BAM_CFLAGS)
-libpop_a_CXXFLAGS  = $(OPENMP_CFLAGS) $(BAM_CFLAGS)
-
 phasedstacks_SOURCES = libcore.a src/phasedstacks.h src/phasedstacks.cc

 process_radtags_SOURCES    = libcore.a libclean.a src/process_radtags.h src/process_radtags.cc
@@ -69,55 +73,17 @@ clone_filter_SOURCES       = libcore.a libclean.a src/clone_filter.h src/clone_f
 ustacks_SOURCES = libcore.a src/ustacks.h src/ustacks.cc
 cstacks_SOURCES = libcore.a src/cstacks.h src/cstacks.cc
 sstacks_SOURCES = libcore.a src/sstacks.h src/sstacks.cc
-
-populations_SOURCES = libcore.a libpop.a src/populations.h src/populations.cc
-
-# tsv2bam & gstacks
 tsv2bam_SOURCES = libcore.a src/tsv2bam.cc
 gstacks_SOURCES = libcore.a src/gstacks.h src/gstacks.cc src/debruijn.h src/debruijn.cc src/Alignment.h src/SuffixTree.h src/SuffixTree.cc
+populations_SOURCES = libcore.a libpop.a src/populations.h src/populations.cc
+
+process_radtags_LDADD    = $(LDADD) libclean.a
+process_shortreads_LDADD = $(LDADD) libclean.a
+clone_filter_LDADD       = $(LDADD) libclean.a
+kmer_filter_LDADD        = $(LDADD) libclean.a
+populations_LDADD        = $(LDADD) libpop.a

-phasedstacks_CXXFLAGS = $(OPENMP_CFLAGS)
-phasedstacks_LDFLAGS  = $(OPENMP_CFLAGS)
-phasedstacks_LDADD    = libcore.a $(BAM_LIBS)
-
-ustacks_CXXFLAGS = $(OPENMP_CFLAGS)
-ustacks_LDFLAGS  = $(OPENMP_CFLAGS)
-ustacks_LDADD    = libcore.a $(BAM_LIBS)
-cstacks_CXXFLAGS = $(OPENMP_CFLAGS)
-cstacks_LDFLAGS  = $(OPENMP_CFLAGS)
-cstacks_LDADD    = libcore.a $(BAM_LIBS)
-sstacks_CXXFLAGS = $(OPENMP_CFLAGS) $(BAM_CFLAGS)
-sstacks_LDFLAGS  = $(OPENMP_CFLAGS)
-sstacks_LDADD    = libcore.a $(BAM_LIBS)
-
-process_radtags_CXXFLAGS = $(OPENMP_CFLAGS) $(BAM_CFLAGS)
-process_radtags_LDFLAGS  = $(OPENMP_CFLAGS)
-process_radtags_LDADD    =  libcore.a libclean.a $(BAM_LIBS)
-process_shortreads_CXXFLAGS = $(OPENMP_CFLAGS) $(BAM_CFLAGS)
-process_shortreads_LDFLAGS  = $(OPENMP_CFLAGS)
-process_shortreads_LDADD    =  libcore.a libclean.a $(BAM_LIBS)
-clone_filter_CXXFLAGS = $(OPENMP_CFLAGS) $(BAM_CFLAGS)
-clone_filter_LDFLAGS  = $(OPENMP_CFLAGS)
-clone_filter_LDADD    = libcore.a libclean.a $(BAM_LIBS)
-kmer_filter_CXXFLAGS = $(OPENMP_CFLAGS)
-kmer_filter_LDFLAGS  = $(OPENMP_CFLAGS)
-kmer_filter_LDADD    = libcore.a libclean.a $(BAM_LIBS)
-
-populations_CXXFLAGS = $(OPENMP_CFLAGS) $(BAM_CFLAGS)
-populations_LDFLAGS  = $(OPENMP_CFLAGS)
-populations_LDADD    = libcore.a libpop.a $(BAM_LIBS)
-
-# tsv2bam & gstacks
-tsv2bam_CXXFLAGS = $(OPENMP_CFLAGS) $(BAM_CFLAGS)
-tsv2bam_LDFLAGS  = $(OPENMP_CFLAGS)
-tsv2bam_LDADD    = libcore.a $(BAM_LIBS)
-gstacks_CXXFLAGS = $(OPENMP_CFLAGS) $(BAM_CFLAGS)
-gstacks_LDFLAGS  = $(OPENMP_CFLAGS)
-gstacks_LDADD    = libcore.a $(BAM_LIBS)
-
-dist_bin_SCRIPTS = scripts/denovo_map.pl scripts/ref_map.pl	scripts/export_sql.pl \
-	scripts/sort_read_pairs.pl scripts/exec_velvet.pl scripts/load_sequences.pl \
-	scripts/index_radtags.pl scripts/load_radtags.pl scripts/stacks_export_notify.pl \
+dist_bin_SCRIPTS = scripts/denovo_map.pl scripts/ref_map.pl \
 	scripts/integrate_alignments.py scripts/count_fixed_catalog_snps.py \
 	scripts/stacks-integrate-alignments scripts/stacks-dist-extract scripts/stacks-gdb

@@ -142,8 +108,6 @@ EXTRA_DIST = $(nobase_pkgdata_DATA) LICENSE INSTALL README ChangeLog $(TESTS)

 pkglocalstatedir = $(localstatedir)/$(PACKAGE)

-SUBDIRS = htslib .
-
 debug:
 	$(MAKE) all "CXXFLAGS=-g -Wall -DDEBUG -std=gnu++11"

@@ -154,28 +118,6 @@ 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,_VERSION_,$(VERSION),' -e 's,_PKGDATADIR_,$(pkgdatadir)/,g' $(DESTDIR)$(bindir)/export_sql.pl > $(DESTDIR)$(bindir)/export_sql.pl.subst
-	mv $(DESTDIR)$(bindir)/export_sql.pl.subst $(DESTDIR)$(bindir)/export_sql.pl
-	chmod +x $(DESTDIR)$(bindir)/export_sql.pl
-	sed -e 's,_VERSION_,$(VERSION),' -e 's,_PKGDATADIR_,$(pkgdatadir)/,g' $(DESTDIR)$(bindir)/index_radtags.pl > $(DESTDIR)$(bindir)/index_radtags.pl.subst
-	mv $(DESTDIR)$(bindir)/index_radtags.pl.subst $(DESTDIR)$(bindir)/index_radtags.pl
-	chmod +x $(DESTDIR)$(bindir)/index_radtags.pl
-	sed -e 's,_VERSION_,$(VERSION),' -e 's,_PKGDATADIR_,$(pkgdatadir)/,g' $(DESTDIR)$(bindir)/load_radtags.pl > $(DESTDIR)$(bindir)/load_radtags.pl.subst
-	mv $(DESTDIR)$(bindir)/load_radtags.pl.subst $(DESTDIR)$(bindir)/load_radtags.pl
-	chmod +x $(DESTDIR)$(bindir)/load_radtags.pl
-	sed -e 's,_VERSION_,$(VERSION),' $(DESTDIR)$(bindir)/sort_read_pairs.pl > $(DESTDIR)$(bindir)/sort_read_pairs.pl.subst
-	mv $(DESTDIR)$(bindir)/sort_read_pairs.pl.subst $(DESTDIR)$(bindir)/sort_read_pairs.pl
-	chmod +x $(DESTDIR)$(bindir)/sort_read_pairs.pl
-	sed -e 's,_VERSION_,$(VERSION),' $(DESTDIR)$(bindir)/exec_velvet.pl > $(DESTDIR)$(bindir)/exec_velvet.pl.subst
-	mv $(DESTDIR)$(bindir)/exec_velvet.pl.subst $(DESTDIR)$(bindir)/exec_velvet.pl
-	chmod +x $(DESTDIR)$(bindir)/exec_velvet.pl
-	sed -e 's,_VERSION_,$(VERSION),' -e 's,_PKGDATADIR_,$(pkgdatadir)/,g' $(DESTDIR)$(bindir)/load_sequences.pl > $(DESTDIR)$(bindir)/load_sequences.pl.subst
-	mv $(DESTDIR)$(bindir)/load_sequences.pl.subst $(DESTDIR)$(bindir)/load_sequences.pl
-	chmod +x $(DESTDIR)$(bindir)/load_sequences.pl
-	sed -e 's,_VERSION_,$(VERSION),' -e 's,_PKGDATADIR_,$(pkgdatadir)/,g' -e 's,_BINDIR_,$(bindir)/,g' \
-		$(DESTDIR)$(bindir)/stacks_export_notify.pl > $(DESTDIR)$(bindir)/stacks_export_notify.pl.subst
-	mv $(DESTDIR)$(bindir)/stacks_export_notify.pl.subst $(DESTDIR)$(bindir)/stacks_export_notify.pl
-	chmod +x $(DESTDIR)$(bindir)/stacks_export_notify.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

--- a/Makefile.in
+++ b/Makefile.in
--- a/README
+++ b/README
@@ -7,30 +7,10 @@ Stacks should build on any standard UNIX-like environment (Apple OS X, Linux,
 etc.) Stacks is an independent pipeline and can be run without any additional
 external software. 

-     Note: Apple OS X does not use the GNU Compiler Collection, which is 
-     standard on Linux-based systems. Instead, Apple distributes CLANG, 
-     which is a nice compiler but does not yet support the OpenMP library
-     which Stacks relies on for parallel processing. Stacks can still be built
-     and run on an Apple system, however, you will have to disable building
-     with OpenMP (supply the --disable-openmp flag to configure) and use
-     non-parallelized code. If you want to install a parallelized version of
-     Stacks, you can install GCC by hand, or using a package system such as 
-     Homebrew (http://brew.sh/) or MacPorts (http://www.macports.org/).
+If compiling with the standard GCC compiler, Stacks needs a version of the compiler
+newer than GCC 4.9.0.

-1. Install optional components for wrapper programs:
-
-Several Perl scripts are distributed with Stacks to run the pipeline components and
-upload pipeline output to the MySQL database serer. For these to work, you must have
-the Perl DBI module installed with the MySQL driver. Most Linux distributions will
-include the Perl DBI module, but if not Perl modules are easily installed with the
-cpan tool.
-
-% sudo apt-get install libdbd-mysql-perl
-
-A similar set of commands can be executed on Debian using apt-get, or on a RedHat derived Linux
-system using yum, or another package manager on other Linux distributions.
-
-2. Build the software. Stacks uses the standard autotools install:
+1. Build the software. Stacks uses the standard autotools install:

 % tar xfvz stacks-x.xx.tar.gz
 % cd stacks-x.xx
@@ -60,138 +40,4 @@ A default Stacks install will install files in the following way:

 /usr/local/bin - stacks executables and perl scripts

-/usr/local/share/stacks - PHP files for the web interface 
-                          and SQL files for creating the 
-                          MySQL database
-
-The pipeline is now ready to run. The remaining install instructions are to get the
-web interface up and running. The web interface is very useful for visualization and
-more or less required for building genetic maps. However, Stacks does not depend on
-the web interface to run.
-
-
-The Stacks Web Interface
------------------------
-
-To visualize data, Stacks uses a web-based interface (written in PHP) that interacts 
-with a MySQL database server. MySQL provides various functions to store, sort, and 
-export data from a database.  
-
-0. Prerequisites
-
-Most server installations will provide Apache, MySQL, Perl, and PHP by default. If you want
-to export data in Microsoft Excel Spreadsheets, you will need the 
-Spreadsheet::WriteExcel Perl module. While installing these components is beyond these
-instructions, here are some links that might be useful:
-
-  1. MySQL Database: http://dev.mysql.com/downloads/mysql/
-  2. Spreadsheet Perl Module: http://search.cpan.org/~jmcnamara/Spreadsheet-WriteExcel-2.40/
-
-If you are running a version of Linux, the above software can be installed via the 
-package manager. If you are using Ubuntu, you can install the following packages:
-
-% sudo apt-get install mysql-server mysql-client
-% sudo apt-get install php5 php5-mysqlnd
-% sudo apt-get install libspreadsheet-writeexcel-perl
-
-A similar set of commands can be executed on Debian using apt-get, or on a RedHat derived Linux
-system using yum, or another package manager on other Linux distributions.
-
-1. Edit the MySQL configuration file, installed in
-/usr/local/share/stacks/sql/mysql.cnf.dist, to enable access to the
-database from the Stacks scripts.
-
-% cd /usr/local/share/stacks/sql/
-% cp mysql.cnf.dist mysql.cnf
-
-Edit the file to reflect the proper username, password, and host to
-use to access MySQL.
-
-The various scripts that access the database will search for a MySQL
-configuration file in your home directory before using the
-Stacks-distributed copy. If you already have a personal account set up
-and configured (in ~/.my.cnf) you can continue to use these
-credentials instead of setting up new, common ones.
-
-If you just installed MySQL and have not added any users, you can do so with these
-commands:
-
-% mysql
-mysql> GRANT ALL ON *.* TO 'stacks_user'@'localhost' IDENTIFIED BY 'stackspassword';
-
-Edit /usr/local/share/stacks/sql/mysql.cnf to contain the username and password
-you specified to MySQL.
-
-(This information was taken from: http://dev.mysql.com/doc/refman/5.1/en/grant.html)
-
-2. Enable the Stacks web interface in the Apache webserver.
-
-Add the following lines to your Apache configuration to make the Stacks PHP
-files visible to the web server and to provide a easily readable URL to access
-them: 
-
-<Directory "/usr/local/share/stacks/php">
-        Order deny,allow
-        Deny from all
-        Allow from all
-	Require all granted
-</Directory>
-
-Alias /stacks "/usr/local/share/stacks/php"
-
-A sensible way to do this is to create the file stacks.conf with the above lines.
-
-If you are using Apache 2.3 or earlier:
---------------------------------------
-Place the stacks.conf file in either
-
-/etc/apache2/conf.d/ or /etc/httpd/conf.d/
-
-directory (depending on your Linux distro) and 
-restart the apache server:
-
-# vi /etc/apache2/conf.d/stacks.conf
-# apachectl restart
-
-(See the Apache configuration for more information on what these do:
-http://httpd.apache.org/docs/2.0/mod/core.html#directory)
-
-If you are using Apache 2.4 or later:
---------------------------------------
-Place the stacks.conf file in
-
-/etc/apache2/conf-available
-
-directory and then create a symlink to it in the
-
-/etc/apache2/conf-enabled
-
-directory. Then restart Apache. Like so:
-
-# vi /etc/apache2/conf-available/stacks.conf
-# ln -s /etc/apache2/conf-available/stacks.conf /etc/apache2/conf-enabled/stacks.conf
-# apachectl restart
-
-3. Provide access to the MySQL database from the web interface
-
-Edit the PHP configuration file (constants.php.dist) to allow it access to the 
-MySQL database. Change the file to include the proper database
-username ($db_user), password ($db_pass), and hostname ($db_host). Rename the 
-distribution file so it is active.
-
-% cp /usr/local/share/stacks/php/constants.php.dist /usr/local/share/stacks/php/constants.php
-% vi /usr/local/share/stacks/php/constants.php
-
-You may find it advantageous to create a specific MySQL user with limited
-permissions - SELECT, UPDATE, and DELETE to allow users to interact
-with the database through the web interface.
-
-4. Enable web-based exporting from the MySQL database.
-
-Edit the stacks_export_notify.pl script to specify the email and SMTP
-server to use in notification messages.
-
-Ensure that the permissions of the php/export directory allow the
-webserver to write to it. Assuming your web server user is 'www':
-
-% chown www /usr/local/share/stacks/php/export
+The pipeline is now ready to run. 
--- a/config.h.in
+++ b/config.h.in
@@ -3,9 +3,6 @@
 /* Define to 1 if the `closedir' function returns void instead of `int'. */
 #undef CLOSEDIR_VOID

-/* Enable compilation with Samtools BAM library */
-#undef HAVE_BAM
-
 /* Define to 1 if you have the `clock_gettime' function. */
 #undef HAVE_CLOCK_GETTIME


--- a/configure
+++ b/configure
 #! /bin/sh
 # Guess values for system-dependent variables and create Makefiles.
-# Generated by GNU Autoconf 2.63 for Stacks 2.0Beta8c.
+# Generated by GNU Autoconf 2.63 for Stacks 2.0Beta9.
 #
 # Copyright (C) 1992, 1993, 1994, 1995, 1996, 1998, 1999, 2000, 2001,
 # 2002, 2003, 2004, 2005, 2006, 2007, 2008 Free Software Foundation, Inc.
@@ -594,11 +594,12 @@ SHELL=${CONFIG_SHELL-/bin/sh}
 # Identity of this package.
 PACKAGE_NAME='Stacks'
 PACKAGE_TARNAME='stacks'
-PACKAGE_VERSION='2.0Beta8c'
-PACKAGE_STRING='Stacks 2.0Beta8c'
+PACKAGE_VERSION='2.0Beta9'
+PACKAGE_STRING='Stacks 2.0Beta9'
 PACKAGE_BUGREPORT=''

 ac_unique_file="src/ustacks.cc"
+ac_unique_file="htslib/hts.c"
 # Factoring default headers for most tests.
 ac_includes_default="\
 #include <stdio.h>
@@ -667,8 +668,6 @@ CPPFLAGS
 LDFLAGS
 CXXFLAGS
 CXX
-BAM_LIBS
-BAM_CFLAGS
 am__untar
 am__tar
 AMTAR
@@ -732,7 +731,6 @@ SHELL'
 ac_subst_files=''
 ac_user_opts='
 enable_option_checking
-enable_bam
 enable_dependency_tracking
 enable_openmp
 '
@@ -1300,7 +1298,7 @@ if test "$ac_init_help" = "long"; then
  # Omit some internal or obsolete options to make the list less imposing.
  # This message is too long to be a string in the A/UX 3.1 sh.
  cat <<_ACEOF
-\`configure' configures Stacks 2.0Beta8c to adapt to many kinds of systems.
+\`configure' configures Stacks 2.0Beta9 to adapt to many kinds of systems.

 Usage: $0 [OPTION]... [VAR=VALUE]...

@@ -1366,7 +1364,7 @@ fi

 if test -n "$ac_init_help"; then
  case $ac_init_help in
-     short | recursive ) echo "Configuration of Stacks 2.0Beta8c:";;
+     short | recursive ) echo "Configuration of Stacks 2.0Beta9:";;
   esac
  cat <<\_ACEOF

@@ -1374,7 +1372,6 @@ Optional Features:
  --disable-option-checking  ignore unrecognized --enable/--with options
  --disable-FEATURE       do not include FEATURE (same as --enable-FEATURE=no)
  --enable-FEATURE[=ARG]  include FEATURE [ARG=yes]
-  --disable-bam           Disable use of BAM files through HTSLib.
  --disable-dependency-tracking  speeds up one-time build
  --enable-dependency-tracking   do not reject slow dependency extractors
  --disable-openmp        do not use OpenMP
@@ -1456,7 +1453,7 @@ fi
 test -n "$ac_init_help" && exit $ac_status
 if $ac_init_version; then
  cat <<\_ACEOF
-Stacks configure 2.0Beta8c
+Stacks configure 2.0Beta9
 generated by GNU Autoconf 2.63

 Copyright (C) 1992, 1993, 1994, 1995, 1996, 1998, 1999, 2000, 2001,
@@ -1470,7 +1467,7 @@ cat >config.log <<_ACEOF
 This file contains any messages produced by compilers while
 running configure, to aid debugging if configure makes a mistake.

-It was created by Stacks $as_me 2.0Beta8c, which was
+It was created by Stacks $as_me 2.0Beta9, which was
 generated by GNU Autoconf 2.63.  Invocation command line was

  $ $0 $@
@@ -2319,7 +2316,7 @@ fi

 # Define the identity of the package.
 PACKAGE='stacks'
- VERSION='2.0Beta8c'
+ VERSION='2.0Beta9'


 cat >>confdefs.h <<_ACEOF
@@ -2360,6 +2357,7 @@ am__tar='${AMTAR} chof - "$$tardir"'; am__untar='${AMTAR} xf -'



+
 ac_config_headers="$ac_config_headers config.h"


@@ -2367,28 +2365,15 @@ ac_config_headers="$ac_config_headers config.h"
 #
 # Get BAM, aka HTSLib library and include locations if requested
 #
-# Check whether --enable-bam was given.
-if test "${enable_bam+set}" = set; then
-  enableval=$enable_bam;
-fi
-
-
-if test "x$enable_bam" != "xno"; then
-
-
-cat >>confdefs.h <<\_ACEOF
-#define HAVE_BAM 1
-_ACEOF
-
-
-BAM_CFLAGS='-I./htslib/htslib'
-
-BAM_LIBS='./htslib/libhts.a'
-
-
-
-fi
-
+#AC_ARG_ENABLE([bam],
+#    AS_HELP_STRING([--disable-bam], [Disable use of BAM files through HTSLib.]))
+#AS_IF([test "x$enable_bam" != "xno"], [
+#AC_DEFINE([HAVE_BAM], [1], [Enable compilation with Samtools BAM library])
+#BAM_CFLAGS='-I./htslib/htslib'
+#AC_SUBST([BAM_CFLAGS])
+#BAM_LIBS='./htslib/libhts.a'
+#AC_SUBST([BAM_LIBS])
+#])

 # Checks for programs.
 ac_ext=cpp
@@ -8166,7 +8151,7 @@ fi
 done


-ac_config_files="$ac_config_files Makefile"
+ac_config_files="$ac_config_files Makefile htslib/Makefile"

 cat >confcache <<\_ACEOF
 # This file is a shell script that caches the results of configure
@@ -8616,7 +8601,7 @@ exec 6>&1
 # report actual input values of CONFIG_FILES etc. instead of their
 # values after options handling.
 ac_log="
-This file was extended by Stacks $as_me 2.0Beta8c, which was
+This file was extended by Stacks $as_me 2.0Beta9, which was
 generated by GNU Autoconf 2.63.  Invocation command line was

  CONFIG_FILES    = $CONFIG_FILES
@@ -8679,7 +8664,7 @@ Report bugs to <bug-autoconf@gnu.org>."
 _ACEOF
 cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
 ac_cs_version="\\
-Stacks config.status 2.0Beta8c
+Stacks config.status 2.0Beta9
 configured by $0, generated by GNU Autoconf 2.63,
  with options \\"`$as_echo "$ac_configure_args" | sed 's/^ //; s/[\\""\`\$]/\\\\&/g'`\\"

@@ -8805,6 +8790,7 @@ do
    "config.h") CONFIG_HEADERS="$CONFIG_HEADERS config.h" ;;
    "depfiles") CONFIG_COMMANDS="$CONFIG_COMMANDS depfiles" ;;
    "Makefile") CONFIG_FILES="$CONFIG_FILES Makefile" ;;
+    "htslib/Makefile") CONFIG_FILES="$CONFIG_FILES htslib/Makefile" ;;

  *) { { $as_echo "$as_me:$LINENO: error: invalid argument: $ac_config_target" >&5
 $as_echo "$as_me: error: invalid argument: $ac_config_target" >&2;}

--- a/configure.ac
+++ b/configure.ac
@@ -2,28 +2,26 @@
 # Process this file with autoconf to produce a configure script.

 AC_PREREQ(2.59)
-AC_INIT([Stacks], [2.0Beta8c])
+AC_INIT([Stacks], [2.0Beta9])
 AC_CONFIG_AUX_DIR([config])
 AM_INIT_AUTOMAKE([-Wall -Werror foreign parallel-tests subdir-objects])
 AC_CONFIG_SRCDIR([src/ustacks.cc])
+AC_CONFIG_SRCDIR([htslib/hts.c])
 AC_CONFIG_HEADERS([config.h])
 m4_pattern_allow([AC_OPENMP])

 #
 # Get BAM, aka HTSLib library and include locations if requested
 #
-AC_ARG_ENABLE([bam],
-    AS_HELP_STRING([--disable-bam], [Disable use of BAM files through HTSLib.]))
-
-AS_IF([test "x$enable_bam" != "xno"], [
-AC_DEFINE([HAVE_BAM], [1], [Enable compilation with Samtools BAM library])
-
-BAM_CFLAGS='-I./htslib/htslib'
-AC_SUBST([BAM_CFLAGS])
-BAM_LIBS='./htslib/libhts.a'
-AC_SUBST([BAM_LIBS])
-
-])
+#AC_ARG_ENABLE([bam],
+#    AS_HELP_STRING([--disable-bam], [Disable use of BAM files through HTSLib.]))
+#AS_IF([test "x$enable_bam" != "xno"], [
+#AC_DEFINE([HAVE_BAM], [1], [Enable compilation with Samtools BAM library])
+#BAM_CFLAGS='-I./htslib/htslib'
+#AC_SUBST([BAM_CFLAGS])
+#BAM_LIBS='./htslib/libhts.a'
+#AC_SUBST([BAM_LIBS])
+#])

 # Checks for programs.
 AC_PROG_CXX
@@ -99,5 +97,5 @@ AC_REGEX_FUNC
 # For test harness
 AC_PROG_AWK

-AC_CONFIG_FILES([Makefile])
+AC_CONFIG_FILES([Makefile htslib/Makefile])
 AC_OUTPUT
--- a/debian/changelog
+++ b/debian/changelog
+stacks (2.0Beta9+dfsg-1) unstable; urgency=medium
+
+  * New upstream Beta release
+
+ -- Andreas Tille <tille@debian.org>  Mon, 19 Mar 2018 12:10:23 +0100
+
 stacks (2.0Beta8c+dfsg-1) unstable; urgency=medium

  * New upstream version

--- a/debian/copyright
+++ b/debian/copyright
@@ -3,6 +3,7 @@ Upstream-Name: Stacks
 Upstream-Contact: Julian Catchen <jcatchen@uoregon.edu>
 Source: http://creskolab.uoregon.edu/stacks/
 Files-Excluded: */htslib
+                */*.a

 Files: *
 Copyright: © Julian Catchen <jcatchen@uoregon.edu>

--- a/debian/patches/email-settings.patch
+++ b/debian/patches/email-settings.patch
-Author: Tim Booth <tbooth@ceh.ac.uk>
-Last-Update: Wed, 18 Feb 2015 11:34:22 +0000
-Description: Enable adapting to local settings
-
-
--- a/scripts/stacks_export_notify.pl
-+++ b/scripts/stacks_export_notify.pl
-@@ -41,11 +41,11 @@ use constant stacks_version => "_VERSION
- #  from:        email address to use in the 'From' field of the message
- #
- my $exe_path      = "_BINDIR_" . "export_sql.pl";
-my $output_path   = "_PKGDATADIR_" . "php/export/"; 
-my $url           = "http://stackshost.edu/stacks/export/";
-+my $output_path   = "_PKGDATADIR_" . "php/export/";
-+my $url           = "http://localhost/stacks/export/";
- my $local_host    = "localhost";
- my $smtp_host     = "localhost";
-my $from          = "stacks\@stackshost.edu";
-+my $from          = "stacks\@" + `hostname --fqdn`;  chomp $from;
- 
- 
- my $debug         = 0;
--- a/debian/patches/script-exe-paths
+++ b/debian/patches/script-exe-paths
@@ -9,7 +9,7 @@ Last-Update: 2016-10-21
 This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
 --- a/Makefile.am
 +++ b/Makefile.am
-@@ -148,10 +148,10 @@ debug:
+@@ -112,13 +112,13 @@ debug:
 	$(MAKE) all "CXXFLAGS=-g -Wall -DDEBUG -std=gnu++11"
 
 install-data-hook:
@@ -21,16 +21,6 @@ This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
 +	sed -e 's,_VERSION_,$(VERSION),' -e 's,_BINDIR_,/usr/lib/stacks/bin/,g' -e 's,_PKGDATADIR_,$(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,_VERSION_,$(VERSION),' -e 's,_PKGDATADIR_,$(pkgdatadir)/,g' $(DESTDIR)$(bindir)/export_sql.pl > $(DESTDIR)$(bindir)/export_sql.pl.subst
-@@ -172,11 +172,11 @@ install-data-hook:
- 	sed -e 's,_VERSION_,$(VERSION),' -e 's,_PKGDATADIR_,$(pkgdatadir)/,g' $(DESTDIR)$(bindir)/load_sequences.pl > $(DESTDIR)$(bindir)/load_sequences.pl.subst
- 	mv $(DESTDIR)$(bindir)/load_sequences.pl.subst $(DESTDIR)$(bindir)/load_sequences.pl
- 	chmod +x $(DESTDIR)$(bindir)/load_sequences.pl
-	sed -e 's,_VERSION_,$(VERSION),' -e 's,_PKGDATADIR_,$(pkgdatadir)/,g' -e 's,_BINDIR_,$(bindir)/,g' \
-+	sed -e 's,_VERSION_,$(VERSION),' -e 's,_PKGDATADIR_,$(pkgdatadir)/,g' -e 's,_BINDIR_,/usr/lib/stacks/bin/,g' \
- 		$(DESTDIR)$(bindir)/stacks_export_notify.pl > $(DESTDIR)$(bindir)/stacks_export_notify.pl.subst
- 	mv $(DESTDIR)$(bindir)/stacks_export_notify.pl.subst $(DESTDIR)$(bindir)/stacks_export_notify.pl
- 	chmod +x $(DESTDIR)$(bindir)/stacks_export_notify.pl
 -	sed -e 's,_PKGDATADIR_,$(pkgdatadir)/,g' -e 's,_BINDIR_,$(bindir)/,g' \
 +	sed -e 's,_PKGDATADIR_,$(pkgdatadir)/,g' -e 's,_BINDIR_,/usr/lib/stacks/bin/,g' \
 		$(DESTDIR)$(pkgdatadir)/php/constants.php.dist > $(DESTDIR)$(pkgdatadir)/php/constants.php.dist.subst

--- a/debian/patches/series
+++ b/debian/patches/series
 constants.php.patch
-email-settings.patch
 script-exe-paths
 use_debian_packaged_htslib.patch
--- a/debian/patches/use_debian_packaged_htslib.patch
+++ b/debian/patches/use_debian_packaged_htslib.patch
@@ -4,26 +4,29 @@ Last-Update: Sun, 18 Feb 2018 17:00:11 +0100

 --- a/Makefile.am
 +++ b/Makefile.am
-@@ -142,7 +142,7 @@ EXTRA_DIST = $(nobase_pkgdata_DATA) LICE
+@@ -1,5 +1,5 @@
+-SUBDIRS = htslib
+-HTSLIB = htslib/libhts.a
+SUBDIRS = 
+HTSLIB = -lhts
 
- pkglocalstatedir = $(localstatedir)/$(PACKAGE)
- 
-SUBDIRS = htslib .
-+SUBDIRS = .
- 
- debug:
- 	$(MAKE) all "CXXFLAGS=-g -Wall -DDEBUG -std=gnu++11"
+ AM_CPPFLAGS = $(OPENMP_CFLAGS) -I$(top_srcdir)/htslib
+ AM_LDFLAGS = $(OPENMP_CFLAGS)
 --- a/configure.ac
 +++ b/configure.ac
-@@ -18,9 +18,9 @@ AC_ARG_ENABLE([bam],
- AS_IF([test "x$enable_bam" != "xno"], [
- AC_DEFINE([HAVE_BAM], [1], [Enable compilation with Samtools BAM library])
+@@ -6,7 +6,7 @@ AC_INIT([Stacks], [2.0Beta9])
+ AC_CONFIG_AUX_DIR([config])
+ AM_INIT_AUTOMAKE([-Wall -Werror foreign parallel-tests subdir-objects])
+ AC_CONFIG_SRCDIR([src/ustacks.cc])
+-AC_CONFIG_SRCDIR([htslib/hts.c])
+#AC_CONFIG_SRCDIR([htslib/hts.c])
+ AC_CONFIG_HEADERS([config.h])
+ m4_pattern_allow([AC_OPENMP])
 
-BAM_CFLAGS='-I./htslib/htslib'
-+BAM_CFLAGS='-I/usr/include/htslib'
- AC_SUBST([BAM_CFLAGS])
-BAM_LIBS='./htslib/libhts.a'
-+BAM_LIBS='-lhts'
- AC_SUBST([BAM_LIBS])
+@@ -97,5 +97,5 @@ AC_REGEX_FUNC
+ # For test harness
+ AC_PROG_AWK
 
- ])
+-AC_CONFIG_FILES([Makefile htslib/Makefile])
+AC_CONFIG_FILES([Makefile])
+ AC_OUTPUT
--- a/libclean.a
+++ b/libclean.a
--- a/libcore.a
+++ b/libcore.a
--- a/libpop.a
+++ b/libpop.a
--- a/scripts/denovo_map.pl
+++ b/scripts/denovo_map.pl
--- a/scripts/exec_velvet.pl
+++ b/scripts/exec_velvet.pl
-#!/usr/bin/env perl
-#
-# Copyright 2011, Julian Catchen <jcatchen@uoregon.edu>
-#
-# This file is part of Stacks.
-#
-# Stacks is free software: you can redistribute it and/or modify
-# it under the terms of the GNU General Public License as published by
-# the Free Software Foundation, either version 3 of the License, or
-# (at your option) any later version.
-#
-# Stacks is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-# GNU General Public License for more details.
-#
-# You should have received a copy of the GNU General Public License
-# along with Stacks.  If not, see <http://www.gnu.org/licenses/>.
-#
-
-use strict;
-use constant stacks_version => "_VERSION_";
-
-my $debug        = 0;
-my $paired       = 0;
-my $amos         = 0;
-my $ins_len_dist = 0;
-my $single_path  = "";
-my $paired_path  = "";
-my $sanger_path  = "";
-my $out_path     = ".";
-my $white_list   = "";
-my $hash_len     = 27;
-my $insert_len   = 0;
-my $exp_cov      = 0;
-my $cov_cut      = 0.0;
-my $min_len      = 0;
-my $read_trk     = 0;
-my $clean        = 1;
-my $collate      = 0;
-my $exe_path     = "";
-my $velveth      = "velveth";
-my $velvetg      = "velvetg";
-
-parse_command_line();
-
-if (length($exe_path) > 0) {
-    $velveth = $exe_path . "/" . $velveth;
-    $velvetg = $exe_path . "/" . $velvetg;
-}
-
-#
-# Test that we can execute the velvet programs
-#
-die ("Unable to find '" . $velveth . "'.\n") if (!-e $velveth || !-x $velveth);
-die ("Unable to find '" . $velvetg . "'.\n") if (!-e $velvetg || !-x $velvetg);
-
-my (@locus_files, $num_files, $file, $input_file, $output_file, $hres_file, $gres_file, $collate_fh);
-
-build_file_list(\@locus_files);
-$num_files = scalar(@locus_files);
-
-if ($collate) {
-    open($collate_fh, ">$out_path/collated.fa") or die("Unable to open collate file, $!\n");
-}
-
-my ($sing_data, $pair_data, $sang_data, $ins, $cov, $afg, $cut, $min, $read, $cln);
-
-$ins   = $paired   > 0 ? "-ins_length $insert_len"   : "-ins_length auto";
-$cov   = $paired   > 0 ? "-exp_cov $exp_cov"         : "-exp_cov auto";
-$cut   = $cov_cut  > 0 ? "-cov_cutoff $cov_cut"      : "-cov_cutoff auto";
-$read  = $read_trk > 0 ? "-read_trkg yes"            : "";
-$cln   = $clean    > 0 ? "-very_clean yes"           : "";
-#$min   = $min_len  > 0 ? "-min_contig_lgth $min_len" : ""
-
-#
-# Write out the parameters for this assembly
-#
-open(PARAM, "> $out_path/velvet_parameters.txt") or die("Unable to open parameter file: $!\n");
-print PARAM
-    "Single-end Path: ", $single_path, "\n",
-    "Paired-end Path: ", $paired_path, "\n",
-    "Sanger Path:     ", $sanger_path, "\n",
-    "Hash Length:     ", $hash_len, "\n",
-    "Insert Length:   ", $ins, "\n",
-    "Coverage:        ", $cov, "\n",
-    "Coverage Cutoff: ", $cut, "\n",
-    "Miniumum contig length: ", $min, "\n",
-    "Read tracking:   ", $read, "\n",
-    "Very Clean:      ", $cln, "\n"; 
-close(PARAM);
-
-my $i = 1;
-
-foreach $file (@locus_files) {
-
-    ($file) = ($file =~ /(.+)\.fa/); 
-    $output_file = $out_path . "/" . $file;
-    $hres_file   = $out_path . "/" . $file . "-h.output";
-    $gres_file   = $out_path . "/" . $file . "-g.output";
-
-    $sing_data = length($single_path) > 0 ? '-short '       . $single_path . "/" . $file . ".fa" : "";
-    $pair_data = length($paired_path) > 0 ? '-shortPaired ' . $paired_path . "/" . $file . ".fa" : "";
-    $sang_data = length($sanger_path) > 0 ? '-long '        . $sanger_path . "/" . $file . ".fa" : "";
-
-    print STDERR "Assembling locus '$file'; run $i of $num_files        \r";
-
-    # Execute velveth to build hash table, then velvetg to assemble
-    print STDERR "$velveth $output_file $hash_len -fasta $sing_data $pair_data $sang_data &> $hres_file\n" if ($debug);
-    `$velveth $output_file $hash_len -fasta $sing_data $pair_data $sang_data &> $hres_file`;
-
-    print STDERR "$velvetg $output_file $ins $cov $cut $min $read $cln &> $gres_file\n" if ($debug);
-    `$velvetg $output_file $ins $cov $cut $min $read $cln &> $gres_file`;
-
-    collate_and_clean($out_path, $file, $collate_fh) if ($collate);
-
-    $i++;
-}
-
-close($collate_fh) if ($collate);
-
-sub collate_and_clean {
-    my ($out_path, $file, $collate_fh) = @_;
-
-    my (@seqs, $seq);
-
-    parse_fasta("$out_path/$file/contigs.fa", \@seqs);
-
-    foreach $seq (@seqs) {
-	next if (length($seq->{'seq'}) < $min_len);
-
-	$seq->{'id'} = $file . "|" . $seq->{'id'};
-
-	print_fasta($collate_fh, $seq);
-    }
-
-    `rm $out_path/$file-g.output`;
-    `rm $out_path/$file-h.output`;
-    `rm -r $out_path/$file`;
-}
-
-sub parse_fasta {
-    my ($file, $seqs) = @_;
-
-    my ($fh, $line, $buf, $id, $seq);
-
-    open($fh, "<$file") 
-	or die("Unable to open Velvet output file: $file, $!\n");
-
-    while ($line = <$fh>) {
-	chomp $line;
-
-	if (substr($line, 0, 1) eq ">") {
-	    if (length($buf) > 0) {
-		$seq = {};
-		$seq->{'id'}  = $id;
-		$seq->{'seq'} = $buf;
-
-		push(@{$seqs}, $seq);
-		$buf = "";
-	    }
-	    $id = substr($line, 1);
-
-	} else {
-	    $buf .= $line;
-	}
-    }
-
-    if (length($buf) > 0 && length($id) > 0) {
-	$seq = {};
-	$seq->{'id'}  = $id;
-	$seq->{'seq'} = $buf;
-	push(@{$seqs}, $seq);
-    }
-
-    close($fh);
-}
-
-sub print_fasta {
-    my ($fh, $seq) = @_;
-
-    my ($s);
-
-    print $fh ">", $seq->{'id'}, "\n";
-
-    $s = $seq->{'seq'};
-
-    while (length($s) > 60) {
-	print $fh substr($s, 0, 60), "\n";
-	$s = substr($s, 60);
-    }
-
-    print $fh $s, "\n" if (length($s) > 0);
-}
-
-sub build_file_list {
-    my ($files) = @_;
-
-    my (@ls, $line, $file, $path);
-
-    # Load a white list of files to process if it is supplied.
-    my @wl;
-    if (length($white_list) > 0) {
-	load_white_list(\@wl);
-    }
-
-    $path = length($paired_path) > 0 ? $paired_path : $single_path;
-
-    @ls = `ls -1 $path/`;
-
-    foreach $line (@ls) {
-	chomp $line;
-
-	next if (length($line) == 0);
-        next if ($line !~ /.+\.fa$/ && $line !~ /.+\.fasta$/);	
-
-	($file) = ($line =~ /^(.+\.fas?t?a?)/); 
-
-        if (scalar(@wl) > 0) {
-	    next if (!grep(/^$file$/, @wl));
-	}
-
-	push(@{$files}, $file);
-    }
-}
-
-sub load_white_list {
-    my ($wl) = @_;
-
-    open(WHITE, "<" . $white_list) 
-	or die("Unable to open white list file '$white_list': $!\n");
-
-    my $line   = "";
-
-    while ($line = <WHITE>) {
-	chomp $line;
-
-	next if (length($line) == 0);
-
-	push(@{$wl}, $line);
-    }
-
-    close(WHITE);
-}
-
-sub parse_command_line {
-    while (@ARGV) {
-	$_ = shift @ARGV;
-	if    ($_ =~ /^-s$/) { $single_path = shift @ARGV; }
-	elsif ($_ =~ /^-p$/) { $paired_path = shift @ARGV; }
-	elsif ($_ =~ /^-l$/) { $sanger_path = shift @ARGV; }
-	elsif ($_ =~ /^-o$/) { $out_path    = shift @ARGV; }
-	elsif ($_ =~ /^-c$/) { $collate++; }
-	elsif ($_ =~ /^-W$/) { $white_list  = shift @ARGV; }
-	elsif ($_ =~ /^-I$/) { $insert_len  = shift @ARGV; }
-	elsif ($_ =~ /^-C$/) { $exp_cov     = shift @ARGV; }
-	elsif ($_ =~ /^-T$/) { $cov_cut     = shift @ARGV; }
-	elsif ($_ =~ /^-R$/) { $read_trk    = shift @ARGV; }
-	elsif ($_ =~ /^-M$/) { $min_len     = shift @ARGV; }
-	elsif ($_ =~ /^-H$/) { $hash_len    = shift @ARGV; }
-	elsif ($_ =~ /^-P$/) { $paired++; }
-	elsif ($_ =~ /^-L$/) { $clean    = 0; }
-	elsif ($_ =~ /^-e$/) { $exe_path = shift @ARGV; }
-	elsif ($_ =~ /^-v$/) { version(); exit(); }
-	elsif ($_ =~ /^-d$/) { $debug++; }
-	elsif ($_ =~ /^-h$/) { usage(); }
-	else {
-	    print STDERR "Unknown command line option '$_'\n";
-	    usage();
-	}
-    }
-
-    $single_path = substr($single_path,  0, -1) if (substr($single_path, -1)  eq "/");
-    $paired_path = substr($paired_path,  0, -1) if (substr($paired_path, -1)  eq "/");
-    $out_path    = substr($out_path, 0, -1)     if (substr($out_path, -1)     eq "/");
-    $exe_path    = substr($exe_path, 0, -1)     if (substr($exe_path, -1)     eq "/");
-}
-
-sub version {
-    print STDERR "exec_velvet.pl ", stacks_version, "\n";
-}
-
-sub usage {
-    version();
-
-    print STDERR <<EOQ; 
-exec_velvet.pl -p path -s path [-l path] -o path [-c] [-H len] [-P] [-I len] [-C exp_cov] [-T cov_cut]
-              [-W file_white_list] [-w marker_white_list] [-L] [-e path] [-d] [-h]
-  p: path to the paired-end FASTA files to assemble.
-  s: path to the single-end FASTA files to assemble.
-  l: path to long, sanger-style reads to assemble.
-  o: path to output the assembled files.
-  c: collate the resulting velvet runs into a single FASTA file, clean velvet directories.
-  W: a white list of files to process in the input path.
-  H: length of overlap required for reads (hash length, default 27).
-  P: process paired-end reads.
-  I: insert length (for paired-end reads; see velvet documentation).
-  C: expected coverage (for paired-end reads).
-  T: coverage cutoff.
-  M: minimum contig length, discard contigs shorter than this value.
-  R: turn on velvet's read tracking (uses additional memory).
-  L: leave velvet's intermediate files behind.
-  e: executable path, location of velvet programs.
-  h: display this help message.
-  d: turn on debug output.
-
-EOQ
-
-  exit(0);
-}
--- a/scripts/export_sql.pl
+++ b/scripts/export_sql.pl
--- a/scripts/index_radtags.pl
+++ b/scripts/index_radtags.pl