@@ -79,13 +79,13 @@ build_triplet = @build@

 host_triplet = @host@

 target_triplet = @target@

 subdir = .

-DIST_COMMON = INSTALL NEWS README AUTHORS ChangeLog \

+DIST_COMMON = INSTALL NEWS README AUTHORS ChangeLog COPYING \

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

 	$(top_srcdir)/configure $(am__configure_deps) \

-	$(top_srcdir)/lib/gstruct.pc.in COPYING config/compile \

-	config/config.guess config/config.sub config/depcomp \

-	config/install-sh config/missing config/ltmain.sh \

-	$(top_srcdir)/config/compile $(top_srcdir)/config/config.guess \

+	$(top_srcdir)/lib/gstruct.pc.in config/compile \

+	config/config.guess config/config.sub config/install-sh \

+	config/missing 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

@@ -265,7 +265,6 @@ LIBTOOL = @LIBTOOL@

 LIPO = @LIPO@

 LN_S = @LN_S@

 LTLIBOBJS = @LTLIBOBJS@

-MAINT = @MAINT@

 MAKEINFO = @MAKEINFO@

 MANIFEST_TOOL = @MANIFEST_TOOL@

 MKDIR_P = @MKDIR_P@

@@ -364,7 +363,7 @@ all: all-recursive

 .SUFFIXES:

 am--refresh: Makefile

 	@:

-$(srcdir)/Makefile.in: @MAINTAINER_MODE_TRUE@ $(srcdir)/Makefile.am  $(am__configure_deps)

+$(srcdir)/Makefile.in:  $(srcdir)/Makefile.am  $(am__configure_deps)

 	@for dep in $?; do \

 	  case '$(am__configure_deps)' in \

 	    *$$dep*) \

@@ -391,9 +390,9 @@ Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status

 $(top_builddir)/config.status: $(top_srcdir)/configure $(CONFIG_STATUS_DEPENDENCIES)

 	$(SHELL) ./config.status --recheck

-$(top_srcdir)/configure: @MAINTAINER_MODE_TRUE@ $(am__configure_deps)

+$(top_srcdir)/configure:  $(am__configure_deps)

 	$(am__cd) $(srcdir) && $(AUTOCONF)

-$(ACLOCAL_M4): @MAINTAINER_MODE_TRUE@ $(am__aclocal_m4_deps)

+$(ACLOCAL_M4):  $(am__aclocal_m4_deps)

 	$(am__cd) $(srcdir) && $(ACLOCAL) $(ACLOCAL_AMFLAGS)

 $(am__aclocal_m4_deps):

 lib/gstruct-${LIBGSTRUCT_API_VERSION}.pc: $(top_builddir)/config.status $(top_srcdir)/lib/gstruct.pc.in

@@ -1 +1 @@

-2013-11-15

\ No newline at end of file

+2014-05-20

\ No newline at end of file

@@ -642,42 +642,6 @@ fi

 rmdir .tst 2>/dev/null

 AC_SUBST([am__leading_dot])])

-# Add --enable-maintainer-mode option to configure.         -*- Autoconf -*-

-# From Jim Meyering

-

-# Copyright (C) 1996-2013 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_MAINTAINER_MODE([DEFAULT-MODE])

-# ----------------------------------

-# Control maintainer-specific portions of Makefiles.

-# Default is to disable them, unless 'enable' is passed literally.

-# For symmetry, 'disable' may be passed as well.  Anyway, the user

-# can override the default with the --enable/--disable switch.

-AC_DEFUN([AM_MAINTAINER_MODE],

-[m4_case(m4_default([$1], [disable]),

-       [enable], [m4_define([am_maintainer_other], [disable])],

-       [disable], [m4_define([am_maintainer_other], [enable])],

-       [m4_define([am_maintainer_other], [enable])

-        m4_warn([syntax], [unexpected argument to AM@&t@_MAINTAINER_MODE: $1])])

-AC_MSG_CHECKING([whether to enable maintainer-specific portions of Makefiles])

-  dnl maintainer-mode's default is 'disable' unless 'enable' is passed

-  AC_ARG_ENABLE([maintainer-mode],

-    [AS_HELP_STRING([--]am_maintainer_other[-maintainer-mode],

-      am_maintainer_other[ make rules and dependencies not useful

-      (and sometimes confusing) to the casual installer])],

-    [USE_MAINTAINER_MODE=$enableval],

-    [USE_MAINTAINER_MODE=]m4_if(am_maintainer_other, [enable], [no], [yes]))

-  AC_MSG_RESULT([$USE_MAINTAINER_MODE])

-  AM_CONDITIONAL([MAINTAINER_MODE], [test $USE_MAINTAINER_MODE = yes])

-  MAINT=$MAINTAINER_MODE_TRUE

-  AC_SUBST([MAINT])dnl

-]

-)

-

 # Check to see how 'make' treats includes.	            -*- Autoconf -*-

 # Copyright (C) 2001-2013 Free Software Foundation, Inc.

@@ -1,6 +1,6 @@

 #! /bin/sh

 # Guess values for system-dependent variables and create Makefiles.

-# Generated by GNU Autoconf 2.69 for gstruct 2013-11-15.

+# Generated by GNU Autoconf 2.69 for gstruct 2014-05-20.

 #

 # Report bugs to <Thomas Wu <twu@gene.com>>.

 #

@@ -590,8 +590,8 @@ MAKEFLAGS=

 # Identity of this package.

 PACKAGE_NAME='gstruct'

 PACKAGE_TARNAME='gstruct'

-PACKAGE_VERSION='2013-11-15'

-PACKAGE_STRING='gstruct 2013-11-15'

+PACKAGE_VERSION='2014-05-20'

+PACKAGE_STRING='gstruct 2014-05-20'

 PACKAGE_BUGREPORT='Thomas Wu <twu@gene.com>'

 PACKAGE_URL=''

@@ -685,9 +685,6 @@ MAINTAINER_FALSE

 MAINTAINER_TRUE

 FULLDIST_FALSE

 FULLDIST_TRUE

-MAINT

-MAINTAINER_MODE_FALSE

-MAINTAINER_MODE_TRUE

 AM_BACKSLASH

 AM_DEFAULT_VERBOSITY

 AM_DEFAULT_V

@@ -790,7 +787,6 @@ enable_option_checking

 enable_largefile

 enable_dependency_tracking

 enable_silent_rules

-enable_maintainer_mode

 enable_fulldist

 enable_maintainer

 enable_static_linking

@@ -1360,7 +1356,7 @@ 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 gstruct 2013-11-15 to adapt to many kinds of systems.

+\`configure' configures gstruct 2014-05-20 to adapt to many kinds of systems.

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

@@ -1431,7 +1427,7 @@ fi

 if test -n "$ac_init_help"; then

   case $ac_init_help in

-     short | recursive ) echo "Configuration of gstruct 2013-11-15:";;

+     short | recursive ) echo "Configuration of gstruct 2014-05-20:";;

    esac

   cat <<\_ACEOF

@@ -1446,9 +1442,6 @@ Optional Features:

                           speeds up one-time build

   --enable-silent-rules   less verbose build output (undo: "make V=1")

   --disable-silent-rules  verbose build output (undo: "make V=0")

-  --disable-maintainer-mode

-                          disable make rules and dependencies not useful (and

-                          sometimes confusing) to the casual installer

   --enable-fulldist       For use by program maintainer

   --enable-maintainer     For use by program maintainer

   --enable-static-linking Link binaries statically (default=no)

@@ -1559,7 +1552,7 @@ fi

 test -n "$ac_init_help" && exit $ac_status

 if $ac_init_version; then

   cat <<\_ACEOF

-gstruct configure 2013-11-15

+gstruct configure 2014-05-20

 generated by GNU Autoconf 2.69

 Copyright (C) 2012 Free Software Foundation, Inc.

@@ -2165,7 +2158,7 @@ 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 gstruct $as_me 2013-11-15, which was

+It was created by gstruct $as_me 2014-05-20, which was

 generated by GNU Autoconf 2.69.  Invocation command line was

   $ $0 $@

@@ -2515,8 +2508,8 @@ ac_compiler_gnu=$ac_cv_c_compiler_gnu

 { $as_echo "$as_me:${as_lineno-$LINENO}: checking package version" >&5

 $as_echo_n "checking package version... " >&6; }

-{ $as_echo "$as_me:${as_lineno-$LINENO}: result: 2013-11-15" >&5

-$as_echo "2013-11-15" >&6; }

+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: 2014-05-20" >&5

+$as_echo "2014-05-20" >&6; }

 ### Read defaults

 { $as_echo "$as_me:${as_lineno-$LINENO}: checking CONFIG_SITE" >&5

@@ -4331,7 +4324,7 @@ fi

 # Define the identity of the package.

  PACKAGE=gstruct

- VERSION=2013-11-15

+ VERSION=2014-05-20

 cat >>confdefs.h <<_ACEOF

@@ -4552,29 +4545,6 @@ END

   fi

 fi

-{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether to enable maintainer-specific portions of Makefiles" >&5

-$as_echo_n "checking whether to enable maintainer-specific portions of Makefiles... " >&6; }

-    # Check whether --enable-maintainer-mode was given.

-if test "${enable_maintainer_mode+set}" = set; then :

-  enableval=$enable_maintainer_mode; USE_MAINTAINER_MODE=$enableval

-else

-  USE_MAINTAINER_MODE=yes

-fi

-

-  { $as_echo "$as_me:${as_lineno-$LINENO}: result: $USE_MAINTAINER_MODE" >&5

-$as_echo "$USE_MAINTAINER_MODE" >&6; }

-   if test $USE_MAINTAINER_MODE = yes; then

-  MAINTAINER_MODE_TRUE=

-  MAINTAINER_MODE_FALSE='#'

-else

-  MAINTAINER_MODE_TRUE='#'

-  MAINTAINER_MODE_FALSE=

-fi

-

-  MAINT=$MAINTAINER_MODE_TRUE

-

-

-

  if test "x$enable_fulldist" = xyes; then

   FULLDIST_TRUE=

   FULLDIST_FALSE='#'

@@ -18008,10 +17978,6 @@ else

   am__EXEEXT_FALSE=

 fi

-if test -z "${MAINTAINER_MODE_TRUE}" && test -z "${MAINTAINER_MODE_FALSE}"; then

-  as_fn_error $? "conditional \"MAINTAINER_MODE\" was never defined.

-Usually this means the macro was only invoked conditionally." "$LINENO" 5

-fi

 if test -z "${FULLDIST_TRUE}" && test -z "${FULLDIST_FALSE}"; then

   as_fn_error $? "conditional \"FULLDIST\" was never defined.

 Usually this means the macro was only invoked conditionally." "$LINENO" 5

@@ -18426,7 +18392,7 @@ cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1

 # report actual input values of CONFIG_FILES etc. instead of their

 # values after options handling.

 ac_log="

-This file was extended by gstruct $as_me 2013-11-15, which was

+This file was extended by gstruct $as_me 2014-05-20, which was

 generated by GNU Autoconf 2.69.  Invocation command line was

   CONFIG_FILES    = $CONFIG_FILES

@@ -18492,7 +18458,7 @@ _ACEOF

 cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1

 ac_cs_config="`$as_echo "$ac_configure_args" | sed 's/^ //; s/[\\""\`\$]/\\\\&/g'`"

 ac_cs_version="\\

-gstruct config.status 2013-11-15

+gstruct config.status 2014-05-20

 configured by $0, generated by GNU Autoconf 2.69,

   with options \\"\$ac_cs_config\\"

@@ -64,7 +64,6 @@ AC_ARG_PROGRAM

 #AM_INIT_AUTOMAKE([no-dependencies])

 AM_INIT_AUTOMAKE(AC_PACKAGE_NAME, AC_PACKAGE_VERSION)

-AM_MAINTAINER_MODE([enable])

 AM_CONDITIONAL(FULLDIST,test "x$enable_fulldist" = xyes)

 AC_ARG_ENABLE([fulldist],

@@ -3,7 +3,7 @@ if MAKE_BINARIES

 bin_PROGRAMS = 

 if SAMTOOLS

-bin_PROGRAMS += bam_tally bam_get bam_fastq

+bin_PROGRAMS += bam_tally

 endif

 endif

@@ -24,9 +24,8 @@ BAM_TALLY_FILES = fopen.h bool.h types.h \

  uinttable.c uinttable.h table.c table.h \

  chrnum.c chrnum.h \

  bamread.c bamread.h samread.c samread.h parserange.c parserange.h \

- dynprog.c dynprog.h dynprog_simd.c dynprog_simd.h dynprog_single.c dynprog_single.h \

  tableuint.c tableuint.h iit-write.c iit-write.h ucharlist.c ucharlist.h \

- matchdef.h matchpool.c matchpool.h mismatchdef.h mismatchpool.c mismatchpool.h bamtally.c bamtally.h \

+ matchdef.h matchpool.c matchpool.h mismatchdef.h mismatchpool.c mismatchpool.h tally.c tally.h bamtally.c bamtally.h \

  datadir.c datadir.h \

  getopt.c getopt1.c getopt.h bamtally_main.c

@@ -49,9 +48,8 @@ LIBGSTRUCT_LA_FILES = config.h fopen.h bool.h types.h \

  uinttable.c uinttable.h table.c table.h \

  chrnum.c chrnum.h \

  bamread.c bamread.h samread.c samread.h parserange.c parserange.h \

- dynprog.c dynprog.h dynprog_simd.c dynprog_simd.h dynprog_single.c dynprog_single.h \

  tableuint.c tableuint.h iit-write.c iit-write.h ucharlist.c ucharlist.h \

- matchdef.h matchpool.c matchpool.h mismatchdef.h mismatchpool.c mismatchpool.h bamtally.c bamtally.h \

+ matchdef.h matchpool.c matchpool.h mismatchdef.h mismatchpool.c mismatchpool.h tally.c tally.h bamtally.c bamtally.h \

  datadir.c datadir.h

 # Do not add SAMTOOLS LIBS here

@@ -78,7 +76,7 @@ gstruct_include_HEADERS = config.h fopen.h bool.h types.h \

  uinttable.h table.h \

  chrnum.h \

  bamread.h samread.h parserange.h \

- dynprog.h dynprog_simd.h dynprog_single.h \

+ dynprog.h dynprog_simd.h dynprog_cigar.h dynprog_single.h \

  tableuint.h iit-write.h ucharlist.h \

  matchdef.h matchpool.h mismatchdef.h mismatchpool.h bamtally.h datadir.h

@@ -91,44 +89,3 @@ pkgconfig_DATA = ../lib/gstruct-$(LIBGSTRUCT_API_VERSION).pc

-BAM_GET_FILES = fopen.h bool.h types.h \

- except.c except.h assert.c assert.h mem.c mem.h \

- intlistdef.h intlist.c intlist.h listdef.h list.c list.h \

- uintlist.c uintlist.h \

- stopwatch.c stopwatch.h access.c access.h \

- interval.c interval.h iitdef.h iit-read.c iit-read.h \

- chrom.c chrom.h genomicpos.c genomicpos.h \

- md5.c md5.h complement.h sequence.c sequence.h genome.c genome.h \

- uinttable.c uinttable.h table.c table.h \

- chrnum.c chrnum.h \

- bamread.c bamread.h samread.c samread.h \

- parserange.c parserange.h \

- getopt.c getopt1.c getopt.h bam_get.c

-

-bam_get_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) $(SAMTOOLS_CFLAGS) -DTARGET=\"$(target)\" -DBAM_INPUT=1

-bam_get_LDFLAGS = $(AM_LDFLAGS) $(STATIC_LDFLAG) $(PTHREAD_CFLAGS) $(SAMTOOLS_LDFLAGS)

-bam_get_LDADD = $(PTHREAD_LIBS) $(ZLIB_LIBS) $(SAMTOOLS_LIBS)

-dist_bam_get_SOURCES = $(BAM_GET_FILES)

-

-

-BAM_FASTQ_FILES = fopen.h bool.h types.h \

- except.c except.h assert.c assert.h mem.c mem.h \

- listdef.h list.c list.h \

- genomicpos.c genomicpos.h complement.h \

- intlistdef.h intlist.c intlist.h uintlist.c uintlist.h \

- stopwatch.c stopwatch.h access.c access.h \

- md5.c md5.h sequence.c sequence.h \

- genome.c genome.h chrom.c chrom.h \

- uinttable.c uinttable.h \

- interval.c interval.h iit-read.c iit-read.h \

- bamread.c bamread.h samread.c samread.h \

- table.c table.h \

- getopt.c getopt1.c getopt.h bam_fastq.c

-

-bam_fastq_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) $(SAMTOOLS_CFLAGS) -DTARGET=\"$(target)\" -DGMAPDB=\"$(GMAPDB)\"

-bam_fastq_LDFLAGS = $(AM_LDFLAGS) $(STATIC_LDFLAG) $(PTHREAD_CFLAGS) $(SAMTOOLS_LDFLAGS)

-bam_fastq_LDADD = $(PTHREAD_LIBS) $(ZLIB_LIBS) $(SAMTOOLS_LIBS)

-dist_bam_fastq_SOURCES = $(BAM_FASTQ_FILES)

-

-

-

@@ -83,7 +83,7 @@ build_triplet = @build@

 host_triplet = @host@

 target_triplet = @target@

 @MAKE_BINARIES_TRUE@bin_PROGRAMS = $(am__EXEEXT_1)

-@MAKE_BINARIES_TRUE@@SAMTOOLS_TRUE@am__append_1 = bam_tally bam_get bam_fastq

+@MAKE_BINARIES_TRUE@@SAMTOOLS_TRUE@am__append_1 = bam_tally

 subdir = src

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

 	$(srcdir)/config.h.in $(top_srcdir)/config/depcomp \

@@ -157,12 +157,10 @@ am__dist_libgstruct_@LIBGSTRUCT_API_VERSION@_la_SOURCES_DIST =  \

 	genomicpos.c genomicpos.h md5.c md5.h sequence.c sequence.h \

 	genome.c genome.h uinttable.c uinttable.h table.c table.h \

 	chrnum.c chrnum.h bamread.c bamread.h samread.c samread.h \

-	parserange.c parserange.h dynprog.c dynprog.h dynprog_simd.c \

-	dynprog_simd.h dynprog_single.c dynprog_single.h tableuint.c \

-	tableuint.h iit-write.c iit-write.h ucharlist.c ucharlist.h \

-	matchdef.h matchpool.c matchpool.h mismatchdef.h \

-	mismatchpool.c mismatchpool.h bamtally.c bamtally.h datadir.c \

-	datadir.h

+	parserange.c parserange.h tableuint.c tableuint.h iit-write.c \

+	iit-write.h ucharlist.c ucharlist.h matchdef.h matchpool.c \

+	matchpool.h mismatchdef.h mismatchpool.c mismatchpool.h \

+	tally.c tally.h bamtally.c bamtally.h datadir.c datadir.h

 am__objects_1 = libgstruct_@LIBGSTRUCT_API_VERSION@_la-except.lo \

 	libgstruct_@LIBGSTRUCT_API_VERSION@_la-assert.lo \

 	libgstruct_@LIBGSTRUCT_API_VERSION@_la-mem.lo \

@@ -186,14 +184,12 @@ am__objects_1 = libgstruct_@LIBGSTRUCT_API_VERSION@_la-except.lo \

 	libgstruct_@LIBGSTRUCT_API_VERSION@_la-bamread.lo \

 	libgstruct_@LIBGSTRUCT_API_VERSION@_la-samread.lo \

 	libgstruct_@LIBGSTRUCT_API_VERSION@_la-parserange.lo \

-	libgstruct_@LIBGSTRUCT_API_VERSION@_la-dynprog.lo \

-	libgstruct_@LIBGSTRUCT_API_VERSION@_la-dynprog_simd.lo \

-	libgstruct_@LIBGSTRUCT_API_VERSION@_la-dynprog_single.lo \

 	libgstruct_@LIBGSTRUCT_API_VERSION@_la-tableuint.lo \

 	libgstruct_@LIBGSTRUCT_API_VERSION@_la-iit-write.lo \

 	libgstruct_@LIBGSTRUCT_API_VERSION@_la-ucharlist.lo \

 	libgstruct_@LIBGSTRUCT_API_VERSION@_la-matchpool.lo \

 	libgstruct_@LIBGSTRUCT_API_VERSION@_la-mismatchpool.lo \

+	libgstruct_@LIBGSTRUCT_API_VERSION@_la-tally.lo \

 	libgstruct_@LIBGSTRUCT_API_VERSION@_la-bamtally.lo \

 	libgstruct_@LIBGSTRUCT_API_VERSION@_la-datadir.lo

 @SAMTOOLS_TRUE@dist_libgstruct_@LIBGSTRUCT_API_VERSION@_la_OBJECTS =  \

@@ -209,45 +205,8 @@ libgstruct_@LIBGSTRUCT_API_VERSION@_la_LINK = $(LIBTOOL) $(AM_V_lt) \

 	$(CCLD) $(libgstruct_@LIBGSTRUCT_API_VERSION@_la_CFLAGS) \

 	$(CFLAGS) $(libgstruct_@LIBGSTRUCT_API_VERSION@_la_LDFLAGS) \

 	$(LDFLAGS) -o $@

-@MAKE_BINARIES_TRUE@@SAMTOOLS_TRUE@am__EXEEXT_1 = bam_tally$(EXEEXT) \

-@MAKE_BINARIES_TRUE@@SAMTOOLS_TRUE@	bam_get$(EXEEXT) \

-@MAKE_BINARIES_TRUE@@SAMTOOLS_TRUE@	bam_fastq$(EXEEXT)

+@MAKE_BINARIES_TRUE@@SAMTOOLS_TRUE@am__EXEEXT_1 = bam_tally$(EXEEXT)

 PROGRAMS = $(bin_PROGRAMS)

-am__objects_2 = bam_fastq-except.$(OBJEXT) bam_fastq-assert.$(OBJEXT) \

-	bam_fastq-mem.$(OBJEXT) bam_fastq-list.$(OBJEXT) \

-	bam_fastq-genomicpos.$(OBJEXT) bam_fastq-intlist.$(OBJEXT) \

-	bam_fastq-uintlist.$(OBJEXT) bam_fastq-stopwatch.$(OBJEXT) \

-	bam_fastq-access.$(OBJEXT) bam_fastq-md5.$(OBJEXT) \

-	bam_fastq-sequence.$(OBJEXT) bam_fastq-genome.$(OBJEXT) \

-	bam_fastq-chrom.$(OBJEXT) bam_fastq-uinttable.$(OBJEXT) \

-	bam_fastq-interval.$(OBJEXT) bam_fastq-iit-read.$(OBJEXT) \

-	bam_fastq-bamread.$(OBJEXT) bam_fastq-samread.$(OBJEXT) \

-	bam_fastq-table.$(OBJEXT) bam_fastq-getopt.$(OBJEXT) \

-	bam_fastq-getopt1.$(OBJEXT) bam_fastq-bam_fastq.$(OBJEXT)

-dist_bam_fastq_OBJECTS = $(am__objects_2)

-bam_fastq_OBJECTS = $(dist_bam_fastq_OBJECTS)

-bam_fastq_DEPENDENCIES = $(am__DEPENDENCIES_1) $(am__DEPENDENCIES_1)

-bam_fastq_LINK = $(LIBTOOL) $(AM_V_lt) --tag=CC $(AM_LIBTOOLFLAGS) \

-	$(LIBTOOLFLAGS) --mode=link $(CCLD) $(bam_fastq_CFLAGS) \

-	$(CFLAGS) $(bam_fastq_LDFLAGS) $(LDFLAGS) -o $@

-am__objects_3 = bam_get-except.$(OBJEXT) bam_get-assert.$(OBJEXT) \

-	bam_get-mem.$(OBJEXT) bam_get-intlist.$(OBJEXT) \

-	bam_get-list.$(OBJEXT) bam_get-uintlist.$(OBJEXT) \

-	bam_get-stopwatch.$(OBJEXT) bam_get-access.$(OBJEXT) \

-	bam_get-interval.$(OBJEXT) bam_get-iit-read.$(OBJEXT) \

-	bam_get-chrom.$(OBJEXT) bam_get-genomicpos.$(OBJEXT) \

-	bam_get-md5.$(OBJEXT) bam_get-sequence.$(OBJEXT) \

-	bam_get-genome.$(OBJEXT) bam_get-uinttable.$(OBJEXT) \

-	bam_get-table.$(OBJEXT) bam_get-chrnum.$(OBJEXT) \

-	bam_get-bamread.$(OBJEXT) bam_get-samread.$(OBJEXT) \

-	bam_get-parserange.$(OBJEXT) bam_get-getopt.$(OBJEXT) \

-	bam_get-getopt1.$(OBJEXT) bam_get-bam_get.$(OBJEXT)

-dist_bam_get_OBJECTS = $(am__objects_3)

-bam_get_OBJECTS = $(dist_bam_get_OBJECTS)

-bam_get_DEPENDENCIES = $(am__DEPENDENCIES_1) $(am__DEPENDENCIES_1)

-bam_get_LINK = $(LIBTOOL) $(AM_V_lt) --tag=CC $(AM_LIBTOOLFLAGS) \

-	$(LIBTOOLFLAGS) --mode=link $(CCLD) $(bam_get_CFLAGS) \

-	$(CFLAGS) $(bam_get_LDFLAGS) $(LDFLAGS) -o $@

 am__dist_bam_tally_SOURCES_DIST = fopen.h bool.h types.h except.c \

 	except.h assert.c assert.h mem.c mem.h intlistdef.h intlist.c \

 	intlist.h listdef.h list.c list.h littleendian.c \

@@ -257,14 +216,12 @@ am__dist_bam_tally_SOURCES_DIST = fopen.h bool.h types.h except.c \

 	genomicpos.c genomicpos.h md5.c md5.h complement.h sequence.c \

 	sequence.h genome.c genome.h uinttable.c uinttable.h table.c \

 	table.h chrnum.c chrnum.h bamread.c bamread.h samread.c \

-	samread.h parserange.c parserange.h dynprog.c dynprog.h \

-	dynprog_simd.c dynprog_simd.h dynprog_single.c \

-	dynprog_single.h tableuint.c tableuint.h iit-write.c \

-	iit-write.h ucharlist.c ucharlist.h matchdef.h matchpool.c \

-	matchpool.h mismatchdef.h mismatchpool.c mismatchpool.h \

-	bamtally.c bamtally.h datadir.c datadir.h getopt.c getopt1.c \

-	getopt.h bamtally_main.c

-am__objects_4 = bam_tally-except.$(OBJEXT) bam_tally-assert.$(OBJEXT) \

+	samread.h parserange.c parserange.h tableuint.c tableuint.h \

+	iit-write.c iit-write.h ucharlist.c ucharlist.h matchdef.h \

+	matchpool.c matchpool.h mismatchdef.h mismatchpool.c \

+	mismatchpool.h tally.c tally.h bamtally.c bamtally.h datadir.c \

+	datadir.h getopt.c getopt1.c getopt.h bamtally_main.c

+am__objects_2 = bam_tally-except.$(OBJEXT) bam_tally-assert.$(OBJEXT) \

 	bam_tally-mem.$(OBJEXT) bam_tally-intlist.$(OBJEXT) \

 	bam_tally-list.$(OBJEXT) bam_tally-littleendian.$(OBJEXT) \

 	bam_tally-bigendian.$(OBJEXT) bam_tally-interval.$(OBJEXT) \

@@ -275,15 +232,13 @@ am__objects_4 = bam_tally-except.$(OBJEXT) bam_tally-assert.$(OBJEXT) \

 	bam_tally-genome.$(OBJEXT) bam_tally-uinttable.$(OBJEXT) \

 	bam_tally-table.$(OBJEXT) bam_tally-chrnum.$(OBJEXT) \

 	bam_tally-bamread.$(OBJEXT) bam_tally-samread.$(OBJEXT) \

-	bam_tally-parserange.$(OBJEXT) bam_tally-dynprog.$(OBJEXT) \

-	bam_tally-dynprog_simd.$(OBJEXT) \

-	bam_tally-dynprog_single.$(OBJEXT) \

-	bam_tally-tableuint.$(OBJEXT) bam_tally-iit-write.$(OBJEXT) \

-	bam_tally-ucharlist.$(OBJEXT) bam_tally-matchpool.$(OBJEXT) \

-	bam_tally-mismatchpool.$(OBJEXT) bam_tally-bamtally.$(OBJEXT) \

+	bam_tally-parserange.$(OBJEXT) bam_tally-tableuint.$(OBJEXT) \

+	bam_tally-iit-write.$(OBJEXT) bam_tally-ucharlist.$(OBJEXT) \

+	bam_tally-matchpool.$(OBJEXT) bam_tally-mismatchpool.$(OBJEXT) \

+	bam_tally-tally.$(OBJEXT) bam_tally-bamtally.$(OBJEXT) \

 	bam_tally-datadir.$(OBJEXT) bam_tally-getopt.$(OBJEXT) \

 	bam_tally-getopt1.$(OBJEXT) bam_tally-bamtally_main.$(OBJEXT)

-@SAMTOOLS_TRUE@dist_bam_tally_OBJECTS = $(am__objects_4)

+@SAMTOOLS_TRUE@dist_bam_tally_OBJECTS = $(am__objects_2)

 bam_tally_OBJECTS = $(dist_bam_tally_OBJECTS)

 @SAMTOOLS_TRUE@bam_tally_DEPENDENCIES = $(am__DEPENDENCIES_1) \

 @SAMTOOLS_TRUE@	$(am__DEPENDENCIES_1)

@@ -325,10 +280,8 @@ am__v_CCLD_ = $(am__v_CCLD_@AM_DEFAULT_V@)

 am__v_CCLD_0 = @echo "  CCLD    " $@;

 am__v_CCLD_1 = 

 SOURCES = $(dist_libgstruct_@LIBGSTRUCT_API_VERSION@_la_SOURCES) \

-	$(dist_bam_fastq_SOURCES) $(dist_bam_get_SOURCES) \

 	$(dist_bam_tally_SOURCES)

 DIST_SOURCES = $(am__dist_libgstruct_@LIBGSTRUCT_API_VERSION@_la_SOURCES_DIST) \

-	$(dist_bam_fastq_SOURCES) $(dist_bam_get_SOURCES) \

 	$(am__dist_bam_tally_SOURCES_DIST)

 am__can_run_installinfo = \

   case $$AM_UPDATE_INFO_DIR in \

@@ -408,7 +361,6 @@ LIBTOOL = @LIBTOOL@

 LIPO = @LIPO@

 LN_S = @LN_S@

 LTLIBOBJS = @LTLIBOBJS@

-MAINT = @MAINT@

 MAKEINFO = @MAKEINFO@

 MANIFEST_TOOL = @MANIFEST_TOOL@

 MKDIR_P = @MKDIR_P@

@@ -510,9 +462,8 @@ BAM_TALLY_FILES = fopen.h bool.h types.h \

  uinttable.c uinttable.h table.c table.h \

  chrnum.c chrnum.h \

  bamread.c bamread.h samread.c samread.h parserange.c parserange.h \

- dynprog.c dynprog.h dynprog_simd.c dynprog_simd.h dynprog_single.c dynprog_single.h \

  tableuint.c tableuint.h iit-write.c iit-write.h ucharlist.c ucharlist.h \

- matchdef.h matchpool.c matchpool.h mismatchdef.h mismatchpool.c mismatchpool.h bamtally.c bamtally.h \

+ matchdef.h matchpool.c matchpool.h mismatchdef.h mismatchpool.c mismatchpool.h tally.c tally.h bamtally.c bamtally.h \

  datadir.c datadir.h \

  getopt.c getopt1.c getopt.h bamtally_main.c

@@ -531,9 +482,8 @@ LIBGSTRUCT_LA_FILES = config.h fopen.h bool.h types.h \

  uinttable.c uinttable.h table.c table.h \

  chrnum.c chrnum.h \

  bamread.c bamread.h samread.c samread.h parserange.c parserange.h \

- dynprog.c dynprog.h dynprog_simd.c dynprog_simd.h dynprog_single.c dynprog_single.h \

  tableuint.c tableuint.h iit-write.c iit-write.h ucharlist.c ucharlist.h \

- matchdef.h matchpool.c matchpool.h mismatchdef.h mismatchpool.c mismatchpool.h bamtally.c bamtally.h \

+ matchdef.h matchpool.c matchpool.h mismatchdef.h mismatchpool.c mismatchpool.h tally.c tally.h bamtally.c bamtally.h \

  datadir.c datadir.h

@@ -557,7 +507,7 @@ gstruct_include_HEADERS = config.h fopen.h bool.h types.h \

  uinttable.h table.h \

  chrnum.h \

  bamread.h samread.h parserange.h \

- dynprog.h dynprog_simd.h dynprog_single.h \

+ dynprog.h dynprog_simd.h dynprog_cigar.h dynprog_single.h \

  tableuint.h iit-write.h ucharlist.h \

  matchdef.h matchpool.h mismatchdef.h mismatchpool.h bamtally.h datadir.h

@@ -567,48 +517,12 @@ gstruct_include_HEADERS = config.h fopen.h bool.h types.h \

 #nodist_bamtally_libinclude_HEADERS = bamtally-config.h

 pkgconfigdir = $(libdir)/pkgconfig

 pkgconfig_DATA = ../lib/gstruct-$(LIBGSTRUCT_API_VERSION).pc

-BAM_GET_FILES = fopen.h bool.h types.h \

- except.c except.h assert.c assert.h mem.c mem.h \

- intlistdef.h intlist.c intlist.h listdef.h list.c list.h \

- uintlist.c uintlist.h \

- stopwatch.c stopwatch.h access.c access.h \

- interval.c interval.h iitdef.h iit-read.c iit-read.h \

- chrom.c chrom.h genomicpos.c genomicpos.h \

- md5.c md5.h complement.h sequence.c sequence.h genome.c genome.h \

- uinttable.c uinttable.h table.c table.h \

- chrnum.c chrnum.h \

- bamread.c bamread.h samread.c samread.h \

- parserange.c parserange.h \

- getopt.c getopt1.c getopt.h bam_get.c

-

-bam_get_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) $(SAMTOOLS_CFLAGS) -DTARGET=\"$(target)\" -DBAM_INPUT=1

-bam_get_LDFLAGS = $(AM_LDFLAGS) $(STATIC_LDFLAG) $(PTHREAD_CFLAGS) $(SAMTOOLS_LDFLAGS)

-bam_get_LDADD = $(PTHREAD_LIBS) $(ZLIB_LIBS) $(SAMTOOLS_LIBS)

-dist_bam_get_SOURCES = $(BAM_GET_FILES)

-BAM_FASTQ_FILES = fopen.h bool.h types.h \

- except.c except.h assert.c assert.h mem.c mem.h \

- listdef.h list.c list.h \

- genomicpos.c genomicpos.h complement.h \

- intlistdef.h intlist.c intlist.h uintlist.c uintlist.h \

- stopwatch.c stopwatch.h access.c access.h \

- md5.c md5.h sequence.c sequence.h \

- genome.c genome.h chrom.c chrom.h \

- uinttable.c uinttable.h \

- interval.c interval.h iit-read.c iit-read.h \

- bamread.c bamread.h samread.c samread.h \

- table.c table.h \

- getopt.c getopt1.c getopt.h bam_fastq.c

-

-bam_fastq_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) $(SAMTOOLS_CFLAGS) -DTARGET=\"$(target)\" -DGMAPDB=\"$(GMAPDB)\"

-bam_fastq_LDFLAGS = $(AM_LDFLAGS) $(STATIC_LDFLAG) $(PTHREAD_CFLAGS) $(SAMTOOLS_LDFLAGS)

-bam_fastq_LDADD = $(PTHREAD_LIBS) $(ZLIB_LIBS) $(SAMTOOLS_LIBS)

-dist_bam_fastq_SOURCES = $(BAM_FASTQ_FILES)

 all: config.h

 	$(MAKE) $(AM_MAKEFLAGS) all-am

 .SUFFIXES:

 .SUFFIXES: .c .lo .o .obj

-$(srcdir)/Makefile.in: @MAINTAINER_MODE_TRUE@ $(srcdir)/Makefile.am  $(am__configure_deps)

+$(srcdir)/Makefile.in:  $(srcdir)/Makefile.am  $(am__configure_deps)

 	@for dep in $?; do \

 	  case '$(am__configure_deps)' in \

 	    *$$dep*) \

@@ -633,9 +547,9 @@ Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status

 $(top_builddir)/config.status: $(top_srcdir)/configure $(CONFIG_STATUS_DEPENDENCIES)

 	cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh

-$(top_srcdir)/configure: @MAINTAINER_MODE_TRUE@ $(am__configure_deps)

+$(top_srcdir)/configure:  $(am__configure_deps)

 	cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh

-$(ACLOCAL_M4): @MAINTAINER_MODE_TRUE@ $(am__aclocal_m4_deps)

+$(ACLOCAL_M4):  $(am__aclocal_m4_deps)

 	cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh

 $(am__aclocal_m4_deps):

@@ -646,7 +560,7 @@ config.h: stamp-h1

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

 	@rm -f stamp-h1

 	cd $(top_builddir) && $(SHELL) ./config.status src/config.h

-$(srcdir)/config.h.in: @MAINTAINER_MODE_TRUE@ $(am__configure_deps) 

+$(srcdir)/config.h.in:  $(am__configure_deps) 

 	($(am__cd) $(top_srcdir) && $(AUTOHEADER))

 	rm -f stamp-h1

 	touch $@

@@ -741,14 +655,6 @@ clean-binPROGRAMS:

 	echo " rm -f" $$list; \

 	rm -f $$list

-bam_fastq$(EXEEXT): $(bam_fastq_OBJECTS) $(bam_fastq_DEPENDENCIES) $(EXTRA_bam_fastq_DEPENDENCIES) 

-	@rm -f bam_fastq$(EXEEXT)

-	$(AM_V_CCLD)$(bam_fastq_LINK) $(bam_fastq_OBJECTS) $(bam_fastq_LDADD) $(LIBS)

-

-bam_get$(EXEEXT): $(bam_get_OBJECTS) $(bam_get_DEPENDENCIES) $(EXTRA_bam_get_DEPENDENCIES) 

-	@rm -f bam_get$(EXEEXT)

-	$(AM_V_CCLD)$(bam_get_LINK) $(bam_get_OBJECTS) $(bam_get_LDADD) $(LIBS)

-

 bam_tally$(EXEEXT): $(bam_tally_OBJECTS) $(bam_tally_DEPENDENCIES) $(EXTRA_bam_tally_DEPENDENCIES) 

 	@rm -f bam_tally$(EXEEXT)

 	$(AM_V_CCLD)$(bam_tally_LINK) $(bam_tally_OBJECTS) $(bam_tally_LDADD) $(LIBS)

@@ -759,52 +665,6 @@ mostlyclean-compile:

 distclean-compile:

 	-rm -f *.tab.c

-@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/bam_fastq-access.Po@am__quote@

-@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/bam_fastq-assert.Po@am__quote@

-@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/bam_fastq-bam_fastq.Po@am__quote@

-@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/bam_fastq-bamread.Po@am__quote@

-@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/bam_fastq-chrom.Po@am__quote@

-@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/bam_fastq-except.Po@am__quote@

-@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/bam_fastq-genome.Po@am__quote@

-@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/bam_fastq-genomicpos.Po@am__quote@

-@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/bam_fastq-getopt.Po@am__quote@

-@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/bam_fastq-getopt1.Po@am__quote@

-@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/bam_fastq-iit-read.Po@am__quote@

-@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/bam_fastq-interval.Po@am__quote@

-@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/bam_fastq-intlist.Po@am__quote@

-@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/bam_fastq-list.Po@am__quote@

-@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/bam_fastq-md5.Po@am__quote@

-@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/bam_fastq-mem.Po@am__quote@

-@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/bam_fastq-samread.Po@am__quote@

-@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/bam_fastq-sequence.Po@am__quote@

-@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/bam_fastq-stopwatch.Po@am__quote@

-@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/bam_fastq-table.Po@am__quote@

-@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/bam_fastq-uintlist.Po@am__quote@

-@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/bam_fastq-uinttable.Po@am__quote@

-@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/bam_get-access.Po@am__quote@

-@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/bam_get-assert.Po@am__quote@

-@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/bam_get-bam_get.Po@am__quote@

-@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/bam_get-bamread.Po@am__quote@

-@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/bam_get-chrnum.Po@am__quote@

-@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/bam_get-chrom.Po@am__quote@

-@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/bam_get-except.Po@am__quote@

-@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/bam_get-genome.Po@am__quote@

-@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/bam_get-genomicpos.Po@am__quote@

-@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/bam_get-getopt.Po@am__quote@

-@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/bam_get-getopt1.Po@am__quote@

-@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/bam_get-iit-read.Po@am__quote@

-@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/bam_get-interval.Po@am__quote@

-@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/bam_get-intlist.Po@am__quote@

-@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/bam_get-list.Po@am__quote@

-@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/bam_get-md5.Po@am__quote@

-@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/bam_get-mem.Po@am__quote@

-@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/bam_get-parserange.Po@am__quote@

-@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/bam_get-samread.Po@am__quote@

-@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/bam_get-sequence.Po@am__quote@

-@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/bam_get-stopwatch.Po@am__quote@

-@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/bam_get-table.Po@am__quote@

-@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/bam_get-uintlist.Po@am__quote@

-@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/bam_get-uinttable.Po@am__quote@

 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/bam_tally-access.Po@am__quote@

 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/bam_tally-assert.Po@am__quote@

 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/bam_tally-bamread.Po@am__quote@

@@ -814,9 +674,6 @@ distclean-compile:

 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/bam_tally-chrnum.Po@am__quote@

 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/bam_tally-chrom.Po@am__quote@

 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/bam_tally-datadir.Po@am__quote@

-@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/bam_tally-dynprog.Po@am__quote@

-@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/bam_tally-dynprog_simd.Po@am__quote@

-@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/bam_tally-dynprog_single.Po@am__quote@

 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/bam_tally-except.Po@am__quote@

 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/bam_tally-genome.Po@am__quote@

 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/bam_tally-genomicpos.Po@am__quote@

@@ -838,6 +695,7 @@ distclean-compile:

 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/bam_tally-stopwatch.Po@am__quote@

 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/bam_tally-table.Po@am__quote@

 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/bam_tally-tableuint.Po@am__quote@

+@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/bam_tally-tally.Po@am__quote@

 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/bam_tally-ucharlist.Po@am__quote@

 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/bam_tally-uintlist.Po@am__quote@

 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/bam_tally-uinttable.Po@am__quote@

@@ -849,9 +707,6 @@ distclean-compile:

 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libgstruct_@LIBGSTRUCT_API_VERSION@_la-chrnum.Plo@am__quote@

 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libgstruct_@LIBGSTRUCT_API_VERSION@_la-chrom.Plo@am__quote@

 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libgstruct_@LIBGSTRUCT_API_VERSION@_la-datadir.Plo@am__quote@

-@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libgstruct_@LIBGSTRUCT_API_VERSION@_la-dynprog.Plo@am__quote@

-@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libgstruct_@LIBGSTRUCT_API_VERSION@_la-dynprog_simd.Plo@am__quote@

-@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libgstruct_@LIBGSTRUCT_API_VERSION@_la-dynprog_single.Plo@am__quote@

 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libgstruct_@LIBGSTRUCT_API_VERSION@_la-except.Plo@am__quote@

 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libgstruct_@LIBGSTRUCT_API_VERSION@_la-genome.Plo@am__quote@

 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libgstruct_@LIBGSTRUCT_API_VERSION@_la-genomicpos.Plo@am__quote@

@@ -871,6 +726,7 @@ distclean-compile:

 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libgstruct_@LIBGSTRUCT_API_VERSION@_la-stopwatch.Plo@am__quote@

 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libgstruct_@LIBGSTRUCT_API_VERSION@_la-table.Plo@am__quote@

 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libgstruct_@LIBGSTRUCT_API_VERSION@_la-tableuint.Plo@am__quote@

+@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libgstruct_@LIBGSTRUCT_API_VERSION@_la-tally.Plo@am__quote@

 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libgstruct_@LIBGSTRUCT_API_VERSION@_la-ucharlist.Plo@am__quote@

 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libgstruct_@LIBGSTRUCT_API_VERSION@_la-uintlist.Plo@am__quote@

 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libgstruct_@LIBGSTRUCT_API_VERSION@_la-uinttable.Plo@am__quote@

@@ -1057,27 +913,6 @@ libgstruct_@LIBGSTRUCT_API_VERSION@_la-parserange.lo: parserange.c

 @AMDEP_TRUE@@am__fastdepCC_FALSE@	DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@

 @am__fastdepCC_FALSE@	$(AM_V_CC@am__nodep@)$(LIBTOOL) $(AM_V_lt) --tag=CC $(AM_LIBTOOLFLAGS) $(LIBTOOLFLAGS) --mode=compile $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(libgstruct_@LIBGSTRUCT_API_VERSION@_la_CFLAGS) $(CFLAGS) -c -o libgstruct_@LIBGSTRUCT_API_VERSION@_la-parserange.lo `test -f 'parserange.c' || echo '$(srcdir)/'`parserange.c

-libgstruct_@LIBGSTRUCT_API_VERSION@_la-dynprog.lo: dynprog.c

-@am__fastdepCC_TRUE@	$(AM_V_CC)$(LIBTOOL) $(AM_V_lt) --tag=CC $(AM_LIBTOOLFLAGS) $(LIBTOOLFLAGS) --mode=compile $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(libgstruct_@LIBGSTRUCT_API_VERSION@_la_CFLAGS) $(CFLAGS) -MT libgstruct_@LIBGSTRUCT_API_VERSION@_la-dynprog.lo -MD -MP -MF $(DEPDIR)/libgstruct_@LIBGSTRUCT_API_VERSION@_la-dynprog.Tpo -c -o libgstruct_@LIBGSTRUCT_API_VERSION@_la-dynprog.lo `test -f 'dynprog.c' || echo '$(srcdir)/'`dynprog.c

-@am__fastdepCC_TRUE@	$(AM_V_at)$(am__mv) $(DEPDIR)/libgstruct_@LIBGSTRUCT_API_VERSION@_la-dynprog.Tpo $(DEPDIR)/libgstruct_@LIBGSTRUCT_API_VERSION@_la-dynprog.Plo

-@AMDEP_TRUE@@am__fastdepCC_FALSE@	$(AM_V_CC)source='dynprog.c' object='libgstruct_@LIBGSTRUCT_API_VERSION@_la-dynprog.lo' libtool=yes @AMDEPBACKSLASH@

-@AMDEP_TRUE@@am__fastdepCC_FALSE@	DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@

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 libgstruct_@LIBGSTRUCT_API_VERSION@_la-bamtally.lo: bamtally.c

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