@@ -10,7 +10,7 @@ Description: GSNAP and GMAP are a pair of tools to align short-read

         methods to work with GMAP and GSNAP from within R. In addition,

         it provides methods to tally alignment results on a

         per-nucleotide basis using the bam_tally tool.

-Version: 1.7.3

+Version: 1.7.4

 Depends: R (>= 2.15.0), methods, GenomeInfoDb (>= 1.1.3),

         GenomicRanges (>= 1.17.12)

 Imports: S4Vectors, IRanges, Rsamtools (>= 1.17.8), rtracklayer (>= 1.25.5),

@@ -218,7 +218,7 @@ normArgTRUEorFALSE <- function(x) {

     if (is.unsorted(read_pos_breaks))

       stop("'read_pos_breaks' must be sorted")

   }

-  ptr <- .Call(R_Bamtally_iit, bamreader@.extptr, genome_dir, db, which,

+  .Call(R_Bamtally_iit, bamreader@.extptr, genome_dir, db, which,

         desired_read_group,

         normArgSingleInteger(alloclength),

         normArgSingleInteger(minimum_mapq),

@@ -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

@@ -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.

@@ -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

@@ -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)

@@ -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

@@ -13,29 +13,6 @@ lib_LTLIBRARIES = libgstruct-@LIBGSTRUCT_API_VERSION@.la

-EXON_EXON_JUNCTIONS_FILES = bool.h \

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

- fopen.h types.h littleendian.c littleendian.h bigendian.c bigendian.h \

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

- listdef.h list.c list.h \

- uintlist.c uintlist.h \

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

- genomicpos.c genomicpos.h \

- intlistdef.h intlist.c intlist.h md5.c md5.h \

- chrnum.c chrnum.h \

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

- table.c table.h \

- datadir.c datadir.h \

- exon-exon-junctions.c

-

-exon_exon_junctions_CC = $(PTHREAD_CC)

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

-exon_exon_junctions_LDFLAGS = $(AM_LDFLAGS) $(STATIC_LDFLAG) $(PTHREAD_CFLAGS)

-exon_exon_junctions_LDADD = $(PTHREAD_LIBS) $(ZLIB_LIBS)

-dist_exon_exon_junctions_SOURCES = $(EXON_EXON_JUNCTIONS_FILES)

-

-

-

 BAM_TALLY_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 \

@@ -48,7 +25,8 @@ BAM_TALLY_FILES = fopen.h bool.h types.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 bamtally.c bamtally.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

@@ -72,7 +50,8 @@ LIBGSTRUCT_LA_FILES = config.h fopen.h bool.h types.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 bamtally.c bamtally.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

 # Do not add SAMTOOLS LIBS here

@@ -100,7 +79,8 @@ gstruct_include_HEADERS = config.h fopen.h bool.h types.h \

  chrnum.h \

  bamread.h samread.h parserange.h \

  dynprog.h dynprog_simd.h dynprog_single.h \

- tableuint.h iit-write.h ucharlist.h bamtally.h datadir.h

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

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

 # May want nodist_bamtally_libinclude_HEADERS = ../lib/bamtally.h

 #bamtally_libincludedir = $(libdir)/bamtally-$(LIBGSTRUCT_API_VERSION)/include

@@ -111,28 +91,6 @@ pkgconfig_DATA = ../lib/gstruct-$(LIBGSTRUCT_API_VERSION).pc

-BAM_PILEUP_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 \

- littleendian.c littleendian.h bigendian.c bigendian.h \

- interval.c interval.h uintlist.c uintlist.h \

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

- datadir.c datadir.h \

- getopt.c getopt1.c getopt.h bam_pileup.c

-

-if SAMTOOLS

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

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

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

-dist_bam_pileup_SOURCES = $(BAM_PILEUP_FILES)

-endif

-

-

 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 \

@@ -153,29 +111,6 @@ bam_get_LDADD = $(PTHREAD_LIBS) $(ZLIB_LIBS) $(SAMTOOLS_LIBS)

 dist_bam_get_SOURCES = $(BAM_GET_FILES)

-BAM_PRINT_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 \

- littleendian.c littleendian.h bigendian.c bigendian.h \

- interval.c interval.h uintlist.c uintlist.h \

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

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

- orderstat.c orderstat.h lgamma.c lgamma.h tally.c tally.h \

- tableint.c tableint.h splice.c splice.h maxent_hr.c maxent_hr.h gstruct.c gstruct.h \

- datadir.c datadir.h parserange.c parserange.h \

- getopt.c getopt1.c getopt.h bam_print.c

-

-bam_print_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) $(SAMTOOLS_CFLAGS) -DTARGET=\"$(target)\" -DGMAPDB=\"$(GMAPDB)\" -DBAM_INPUT=1

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

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

-dist_bam_print_SOURCES = $(BAM_PRINT_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 \

@@ -197,104 +132,3 @@ dist_bam_fastq_SOURCES = $(BAM_FASTQ_FILES)

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

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

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

- listdef.h list.c list.h \

- genomicpos.c genomicpos.h \

- chrom.c chrom.h \

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

- orderstat.c orderstat.h lgamma.c lgamma.h tally.c tally.h \

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

- getopt.c getopt1.c getopt.h spliceclean.c

-

-spliceclean_CFLAGS = $(AM_CFLAGS)  $(PTHREAD_CFLAGS)

-spliceclean_LDFLAGS = $(AM_LDFLAGS) $(STATIC_LDFLAG) $(PTHREAD_CFLAGS)

-spliceclean_LDADD = $(PTHREAD_LIBS)

-dist_spliceclean_SOURCES = $(SPLICECLEAN_FILES)

-

-

-

-#SPLICEGENE_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 \

-# littleendian.c littleendian.h bigendian.c bigendian.h \

-# interval.c interval.h uintlist.c uintlist.h \

-# stopwatch.c stopwatch.h access.c access.h iitdef.h iit-read.c iit-read.h \

-# uinttable.c uinttable.h genomicpos.c genomicpos.h \

-# getopt.c getopt1.c getopt.h splicegene.c

-#

-#splicegene_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) -DTARGET=\"$(target)\" -DGMAPDB=\"$(GMAPDB)\"

-#splicegene_LDFLAGS = $(AM_LDFLAGS) $(STATIC_LDFLAG) $(PTHREAD_CFLAGS)

-#splicegene_LDADD = $(PTHREAD_LIBS) $(ZLIB_LIBS)

-#dist_splicegene_SOURCES = $(SPLICEGENE_FILES)

-

-

-#SAM_GSTRUCT_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 \

-# littleendian.c littleendian.h bigendian.c bigendian.h \

-# interval.c interval.h uintlist.c uintlist.h \

-# stopwatch.c stopwatch.h access.c access.h iitdef.h iit-read.c iit-read.h \

-# complement.h chrom.c chrom.h genomicpos.c genomicpos.h \

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

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

-# samflags.h samread.c samread.h \

-# orderstat.c orderstat.h lgamma.c lgamma.h tally.c tally.h \

-# iit-write.c iit-write.h ucharlist.c ucharlist.h bamtally.c bamtally.h \

-# splice.c splice.h gstruct.c gstruct.h cappaths.c cappaths.h splicegraph.c splicegraph.h \

-# datadir.c datadir.h parserange.c parserange.h \

-# getopt.c getopt1.c getopt.h gstruct_main.c

-#

-#sam_gstruct_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) -DTARGET=\"$(target)\" -DGMAPDB=\"$(GMAPDB)\"

-#sam_gstruct_LDFLAGS = $(AM_LDFLAGS) $(STATIC_LDFLAG) $(PTHREAD_CFLAGS)

-#sam_gstruct_LDADD = $(PTHREAD_LIBS) $(ZLIB_LIBS)

-#dist_sam_gstruct_SOURCES = $(SAM_GSTRUCT_FILES)

-

-

-BAM_SINGLEMAP_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 \

- littleendian.c littleendian.h bigendian.c bigendian.h \

- interval.c interval.h uintlist.c uintlist.h \

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

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

- chrnum.c chrnum.h \

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

- orderstat.c orderstat.h lgamma.c lgamma.h tally.c tally.h \

- tableint.c tableint.h tableuint.c tableuint.h \

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

- datadir.c datadir.h \

- getopt.c getopt1.c getopt.h singlemap.c

-bam_singlemap_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) $(SAMTOOLS_CFLAGS) -DTARGET=\"$(target)\" -DGMAPDB=\"$(GMAPDB)\" -DBAM_INPUT=1

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

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

-dist_bam_singlemap_SOURCES = $(BAM_SINGLEMAP_FILES)

-

-

-BAM_GSTRUCT_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 \

- littleendian.c littleendian.h bigendian.c bigendian.h \

- interval.c interval.h uintlist.c uintlist.h \

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

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

- chrnum.c chrnum.h \

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

- orderstat.c orderstat.h lgamma.c lgamma.h tally.c tally.h \

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

- tableint.c tableint.h splice.c splice.h maxent_hr.c maxent_hr.h gstruct.c gstruct.h \

- cappaths.c cappaths.h splicegraph.c splicegraph.h \

- datadir.c datadir.h parserange.c parserange.h \

- getopt.c getopt1.c getopt.h gstruct_main.c

-

-bam_gstruct_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) $(SAMTOOLS_CFLAGS) -DTARGET=\"$(target)\" -DGMAPDB=\"$(GMAPDB)\" -DBAM_INPUT=1

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

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

-dist_bam_gstruct_SOURCES = $(BAM_GSTRUCT_FILES)

-

-

@@ -160,7 +160,9 @@ am__dist_libgstruct_@LIBGSTRUCT_API_VERSION@_la_SOURCES_DIST =  \

 	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 \

-	bamtally.c bamtally.h datadir.c datadir.h

+	matchdef.h matchpool.c matchpool.h mismatchdef.h \

+	mismatchpool.c mismatchpool.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 \

@@ -190,6 +192,8 @@ am__objects_1 = libgstruct_@LIBGSTRUCT_API_VERSION@_la-except.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-bamtally.lo \

 	libgstruct_@LIBGSTRUCT_API_VERSION@_la-datadir.lo

 @SAMTOOLS_TRUE@dist_libgstruct_@LIBGSTRUCT_API_VERSION@_la_OBJECTS =  \

@@ -256,9 +260,10 @@ am__dist_bam_tally_SOURCES_DIST = fopen.h bool.h types.h except.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 bamtally.c bamtally.h \

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

-	bamtally_main.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) \

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

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

@@ -274,7 +279,8 @@ am__objects_4 = bam_tally-except.$(OBJEXT) bam_tally-assert.$(OBJEXT) \

 	bam_tally-dynprog_simd.$(OBJEXT) \

 	bam_tally-dynprog_single.$(OBJEXT) \

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

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

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

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

@@ -402,7 +408,6 @@ LIBTOOL = @LIBTOOL@

 LIPO = @LIPO@

 LN_S = @LN_S@

 LTLIBOBJS = @LTLIBOBJS@

-MAINT = @MAINT@

 MAKEINFO = @MAKEINFO@

 MANIFEST_TOOL = @MANIFEST_TOOL@

 MKDIR_P = @MKDIR_P@

@@ -493,26 +498,6 @@ top_build_prefix = @top_build_prefix@

 top_builddir = @top_builddir@

 top_srcdir = @top_srcdir@

 lib_LTLIBRARIES = libgstruct-@LIBGSTRUCT_API_VERSION@.la

-EXON_EXON_JUNCTIONS_FILES = bool.h \

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

- fopen.h types.h littleendian.c littleendian.h bigendian.c bigendian.h \

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

- listdef.h list.c list.h \

- uintlist.c uintlist.h \

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

- genomicpos.c genomicpos.h \

- intlistdef.h intlist.c intlist.h md5.c md5.h \

- chrnum.c chrnum.h \

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

- table.c table.h \

- datadir.c datadir.h \

- exon-exon-junctions.c

-

-exon_exon_junctions_CC = $(PTHREAD_CC)

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

-exon_exon_junctions_LDFLAGS = $(AM_LDFLAGS) $(STATIC_LDFLAG) $(PTHREAD_CFLAGS)

-exon_exon_junctions_LDADD = $(PTHREAD_LIBS) $(ZLIB_LIBS)

-dist_exon_exon_junctions_SOURCES = $(EXON_EXON_JUNCTIONS_FILES)

 BAM_TALLY_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 \

@@ -525,7 +510,8 @@ BAM_TALLY_FILES = fopen.h bool.h types.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 bamtally.c bamtally.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

@@ -545,7 +531,8 @@ LIBGSTRUCT_LA_FILES = config.h fopen.h bool.h types.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 bamtally.c bamtally.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

@@ -570,7 +557,8 @@ gstruct_include_HEADERS = config.h fopen.h bool.h types.h \

  chrnum.h \

  bamread.h samread.h parserange.h \

  dynprog.h dynprog_simd.h dynprog_single.h \

- tableuint.h iit-write.h ucharlist.h bamtally.h datadir.h

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

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

 # May want nodist_bamtally_libinclude_HEADERS = ../lib/bamtally.h

@@ -578,24 +566,6 @@ 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_PILEUP_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 \

- littleendian.c littleendian.h bigendian.c bigendian.h \

- interval.c interval.h uintlist.c uintlist.h \

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

- datadir.c datadir.h \

- getopt.c getopt1.c getopt.h bam_pileup.c

-

-@SAMTOOLS_TRUE@bam_pileup_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) $(SAMTOOLS_CFLAGS) -DTARGET=\"$(target)\" -DGMAPDB=\"$(GMAPDB)\"

-@SAMTOOLS_TRUE@bam_pileup_LDFLAGS = $(AM_LDFLAGS) $(STATIC_LDFLAG) $(PTHREAD_CFLAGS) $(SAMTOOLS_LDFLAGS)

-@SAMTOOLS_TRUE@bam_pileup_LDADD = $(PTHREAD_LIBS) $(ZLIB_LIBS) $(SAMTOOLS_LIBS)

-@SAMTOOLS_TRUE@dist_bam_pileup_SOURCES = $(BAM_PILEUP_FILES)

 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 \

@@ -614,27 +584,6 @@ bam_get_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) $(SAMTOOLS_CFLAGS) -DTARGET=\"$(

 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_PRINT_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 \

- littleendian.c littleendian.h bigendian.c bigendian.h \

- interval.c interval.h uintlist.c uintlist.h \

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

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

- orderstat.c orderstat.h lgamma.c lgamma.h tally.c tally.h \

- tableint.c tableint.h splice.c splice.h maxent_hr.c maxent_hr.h gstruct.c gstruct.h \

- datadir.c datadir.h parserange.c parserange.h \

- getopt.c getopt1.c getopt.h bam_print.c

-

-bam_print_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) $(SAMTOOLS_CFLAGS) -DTARGET=\"$(target)\" -DGMAPDB=\"$(GMAPDB)\" -DBAM_INPUT=1

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

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

-dist_bam_print_SOURCES = $(BAM_PRINT_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 \

@@ -653,105 +602,12 @@ bam_fastq_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) $(SAMTOOLS_CFLAGS) -DTARGET=\"

 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)

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

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

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

- listdef.h list.c list.h \

- genomicpos.c genomicpos.h \

- chrom.c chrom.h \

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

- orderstat.c orderstat.h lgamma.c lgamma.h tally.c tally.h \

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

- getopt.c getopt1.c getopt.h spliceclean.c

-

-spliceclean_CFLAGS = $(AM_CFLAGS)  $(PTHREAD_CFLAGS)

-spliceclean_LDFLAGS = $(AM_LDFLAGS) $(STATIC_LDFLAG) $(PTHREAD_CFLAGS)

-spliceclean_LDADD = $(PTHREAD_LIBS)

-dist_spliceclean_SOURCES = $(SPLICECLEAN_FILES)

-

-#SPLICEGENE_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 \

-# littleendian.c littleendian.h bigendian.c bigendian.h \

-# interval.c interval.h uintlist.c uintlist.h \

-# stopwatch.c stopwatch.h access.c access.h iitdef.h iit-read.c iit-read.h \

-# uinttable.c uinttable.h genomicpos.c genomicpos.h \

-# getopt.c getopt1.c getopt.h splicegene.c

-#

-#splicegene_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) -DTARGET=\"$(target)\" -DGMAPDB=\"$(GMAPDB)\"

-#splicegene_LDFLAGS = $(AM_LDFLAGS) $(STATIC_LDFLAG) $(PTHREAD_CFLAGS)

-#splicegene_LDADD = $(PTHREAD_LIBS) $(ZLIB_LIBS)

-#dist_splicegene_SOURCES = $(SPLICEGENE_FILES)

-

-#SAM_GSTRUCT_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 \

-# littleendian.c littleendian.h bigendian.c bigendian.h \

-# interval.c interval.h uintlist.c uintlist.h \

-# stopwatch.c stopwatch.h access.c access.h iitdef.h iit-read.c iit-read.h \

-# complement.h chrom.c chrom.h genomicpos.c genomicpos.h \

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

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

-# samflags.h samread.c samread.h \

-# orderstat.c orderstat.h lgamma.c lgamma.h tally.c tally.h \

-# iit-write.c iit-write.h ucharlist.c ucharlist.h bamtally.c bamtally.h \

-# splice.c splice.h gstruct.c gstruct.h cappaths.c cappaths.h splicegraph.c splicegraph.h \

-# datadir.c datadir.h parserange.c parserange.h \

-# getopt.c getopt1.c getopt.h gstruct_main.c

-#

-#sam_gstruct_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) -DTARGET=\"$(target)\" -DGMAPDB=\"$(GMAPDB)\"

-#sam_gstruct_LDFLAGS = $(AM_LDFLAGS) $(STATIC_LDFLAG) $(PTHREAD_CFLAGS)

-#sam_gstruct_LDADD = $(PTHREAD_LIBS) $(ZLIB_LIBS)

-#dist_sam_gstruct_SOURCES = $(SAM_GSTRUCT_FILES)

-BAM_SINGLEMAP_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 \

- littleendian.c littleendian.h bigendian.c bigendian.h \

- interval.c interval.h uintlist.c uintlist.h \

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

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

- chrnum.c chrnum.h \

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

- orderstat.c orderstat.h lgamma.c lgamma.h tally.c tally.h \

- tableint.c tableint.h tableuint.c tableuint.h \

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

- datadir.c datadir.h \

- getopt.c getopt1.c getopt.h singlemap.c

-

-bam_singlemap_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) $(SAMTOOLS_CFLAGS) -DTARGET=\"$(target)\" -DGMAPDB=\"$(GMAPDB)\" -DBAM_INPUT=1

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

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

-dist_bam_singlemap_SOURCES = $(BAM_SINGLEMAP_FILES)

-BAM_GSTRUCT_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 \

- littleendian.c littleendian.h bigendian.c bigendian.h \

- interval.c interval.h uintlist.c uintlist.h \

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

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

- chrnum.c chrnum.h \

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

- orderstat.c orderstat.h lgamma.c lgamma.h tally.c tally.h \

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

- tableint.c tableint.h splice.c splice.h maxent_hr.c maxent_hr.h gstruct.c gstruct.h \

- cappaths.c cappaths.h splicegraph.c splicegraph.h \

- datadir.c datadir.h parserange.c parserange.h \

- getopt.c getopt1.c getopt.h gstruct_main.c

-

-bam_gstruct_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) $(SAMTOOLS_CFLAGS) -DTARGET=\"$(target)\" -DGMAPDB=\"$(GMAPDB)\" -DBAM_INPUT=1

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

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

-dist_bam_gstruct_SOURCES = $(BAM_GSTRUCT_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*) \

@@ -776,9 +632,9 @@ 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):

@@ -789,7 +645,7 @@ 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 $@

@@ -971,8 +827,10 @@ distclean-compile:

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

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

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

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

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

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

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

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

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

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

@@ -1002,8 +860,10 @@ distclean-compile:

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

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

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

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

 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libgstruct_@LIBGSTRUCT_API_VERSION@_la-md5.Plo@am__quote@

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

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

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

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

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

@@ -1238,6 +1098,20 @@ libgstruct_@LIBGSTRUCT_API_VERSION@_la-ucharlist.lo: ucharlist.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) $(CFLAGS) -c -o libgstruct_@LIBGSTRUCT_API_VERSION@_la-ucharlist.lo `test -f 'ucharlist.c' || echo '$(srcdir)/'`ucharlist.c

+libgstruct_@LIBGSTRUCT_API_VERSION@_la-matchpool.lo: matchpool.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-matchpool.lo -MD -MP -MF $(DEPDIR)/libgstruct_@LIBGSTRUCT_API_VERSION@_la-matchpool.Tpo -c -o libgstruct_@LIBGSTRUCT_API_VERSION@_la-matchpool.lo `test -f 'matchpool.c' || echo '$(srcdir)/'`matchpool.c

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

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

+@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) $(CFLAGS) -c -o libgstruct_@LIBGSTRUCT_API_VERSION@_la-matchpool.lo `test -f 'matchpool.c' || echo '$(srcdir)/'`matchpool.c

+

+libgstruct_@LIBGSTRUCT_API_VERSION@_la-mismatchpool.lo: mismatchpool.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-mismatchpool.lo -MD -MP -MF $(DEPDIR)/libgstruct_@LIBGSTRUCT_API_VERSION@_la-mismatchpool.Tpo -c -o libgstruct_@LIBGSTRUCT_API_VERSION@_la-mismatchpool.lo `test -f 'mismatchpool.c' || echo '$(srcdir)/'`mismatchpool.c

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

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

+@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) $(CFLAGS) -c -o libgstruct_@LIBGSTRUCT_API_VERSION@_la-mismatchpool.lo `test -f 'mismatchpool.c' || echo '$(srcdir)/'`mismatchpool.c

+

 libgstruct_@LIBGSTRUCT_API_VERSION@_la-bamtally.lo: bamtally.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-bamtally.lo -MD -MP -MF $(DEPDIR)/libgstruct_@LIBGSTRUCT_API_VERSION@_la-bamtally.Tpo -c -o libgstruct_@LIBGSTRUCT_API_VERSION@_la-bamtally.lo `test -f 'bamtally.c' || echo '$(srcdir)/'`bamtally.c

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

@@ -2302,6 +2176,34 @@ bam_tally-ucharlist.obj: ucharlist.c

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

 @am__fastdepCC_FALSE@	$(AM_V_CC@am__nodep@)$(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(bam_tally_CFLAGS) $(CFLAGS) -c -o bam_tally-ucharlist.obj `if test -f 'ucharlist.c'; then $(CYGPATH_W) 'ucharlist.c'; else $(CYGPATH_W) '$(srcdir)/ucharlist.c'; fi`

+bam_tally-matchpool.o: matchpool.c

+@am__fastdepCC_TRUE@	$(AM_V_CC)$(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(bam_tally_CFLAGS) $(CFLAGS) -MT bam_tally-matchpool.o -MD -MP -MF $(DEPDIR)/bam_tally-matchpool.Tpo -c -o bam_tally-matchpool.o `test -f 'matchpool.c' || echo '$(srcdir)/'`matchpool.c

+@am__fastdepCC_TRUE@	$(AM_V_at)$(am__mv) $(DEPDIR)/bam_tally-matchpool.Tpo $(DEPDIR)/bam_tally-matchpool.Po

+@AMDEP_TRUE@@am__fastdepCC_FALSE@	$(AM_V_CC)source='matchpool.c' object='bam_tally-matchpool.o' libtool=no @AMDEPBACKSLASH@

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

+@am__fastdepCC_FALSE@	$(AM_V_CC@am__nodep@)$(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(bam_tally_CFLAGS) $(CFLAGS) -c -o bam_tally-matchpool.o `test -f 'matchpool.c' || echo '$(srcdir)/'`matchpool.c

+

+bam_tally-matchpool.obj: matchpool.c

+@am__fastdepCC_TRUE@	$(AM_V_CC)$(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(bam_tally_CFLAGS) $(CFLAGS) -MT bam_tally-matchpool.obj -MD -MP -MF $(DEPDIR)/bam_tally-matchpool.Tpo -c -o bam_tally-matchpool.obj `if test -f 'matchpool.c'; then $(CYGPATH_W) 'matchpool.c'; else $(CYGPATH_W) '$(srcdir)/matchpool.c'; fi`

+@am__fastdepCC_TRUE@	$(AM_V_at)$(am__mv) $(DEPDIR)/bam_tally-matchpool.Tpo $(DEPDIR)/bam_tally-matchpool.Po

+@AMDEP_TRUE@@am__fastdepCC_FALSE@	$(AM_V_CC)source='matchpool.c' object='bam_tally-matchpool.obj' libtool=no @AMDEPBACKSLASH@

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

+@am__fastdepCC_FALSE@	$(AM_V_CC@am__nodep@)$(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(bam_tally_CFLAGS) $(CFLAGS) -c -o bam_tally-matchpool.obj `if test -f 'matchpool.c'; then $(CYGPATH_W) 'matchpool.c'; else $(CYGPATH_W) '$(srcdir)/matchpool.c'; fi`

+

+bam_tally-mismatchpool.o: mismatchpool.c

+@am__fastdepCC_TRUE@	$(AM_V_CC)$(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(bam_tally_CFLAGS) $(CFLAGS) -MT bam_tally-mismatchpool.o -MD -MP -MF $(DEPDIR)/bam_tally-mismatchpool.Tpo -c -o bam_tally-mismatchpool.o `test -f 'mismatchpool.c' || echo '$(srcdir)/'`mismatchpool.c

+@am__fastdepCC_TRUE@	$(AM_V_at)$(am__mv) $(DEPDIR)/bam_tally-mismatchpool.Tpo $(DEPDIR)/bam_tally-mismatchpool.Po

+@AMDEP_TRUE@@am__fastdepCC_FALSE@	$(AM_V_CC)source='mismatchpool.c' object='bam_tally-mismatchpool.o' libtool=no @AMDEPBACKSLASH@

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

+@am__fastdepCC_FALSE@	$(AM_V_CC@am__nodep@)$(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(bam_tally_CFLAGS) $(CFLAGS) -c -o bam_tally-mismatchpool.o `test -f 'mismatchpool.c' || echo '$(srcdir)/'`mismatchpool.c

+

+bam_tally-mismatchpool.obj: mismatchpool.c

+@am__fastdepCC_TRUE@	$(AM_V_CC)$(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(bam_tally_CFLAGS) $(CFLAGS) -MT bam_tally-mismatchpool.obj -MD -MP -MF $(DEPDIR)/bam_tally-mismatchpool.Tpo -c -o bam_tally-mismatchpool.obj `if test -f 'mismatchpool.c'; then $(CYGPATH_W) 'mismatchpool.c'; else $(CYGPATH_W) '$(srcdir)/mismatchpool.c'; fi`

+@am__fastdepCC_TRUE@	$(AM_V_at)$(am__mv) $(DEPDIR)/bam_tally-mismatchpool.Tpo $(DEPDIR)/bam_tally-mismatchpool.Po

+@AMDEP_TRUE@@am__fastdepCC_FALSE@	$(AM_V_CC)source='mismatchpool.c' object='bam_tally-mismatchpool.obj' libtool=no @AMDEPBACKSLASH@

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

+@am__fastdepCC_FALSE@	$(AM_V_CC@am__nodep@)$(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(bam_tally_CFLAGS) $(CFLAGS) -c -o bam_tally-mismatchpool.obj `if test -f 'mismatchpool.c'; then $(CYGPATH_W) 'mismatchpool.c'; else $(CYGPATH_W) '$(srcdir)/mismatchpool.c'; fi`

+

 bam_tally-bamtally.o: bamtally.c

 @am__fastdepCC_TRUE@	$(AM_V_CC)$(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(bam_tally_CFLAGS) $(CFLAGS) -MT bam_tally-bamtally.o -MD -MP -MF $(DEPDIR)/bam_tally-bamtally.Tpo -c -o bam_tally-bamtally.o `test -f 'bamtally.c' || echo '$(srcdir)/'`bamtally.c

 @am__fastdepCC_TRUE@	$(AM_V_at)$(am__mv) $(DEPDIR)/bam_tally-bamtally.Tpo $(DEPDIR)/bam_tally-bamtally.Po

@@ -1,4 +1,4 @@

-static char rcsid[] = "$Id: bam_fastq.c 121683 2013-12-17 02:52:04Z twu $";

+static char rcsid[] = "$Id: bam_fastq.c 134975 2014-05-03 01:13:55Z twu $";

 #ifdef HAVE_CONFIG_H

 #include <config.h>

 #endif

@@ -1147,7 +1147,7 @@ print_fastq_paired (FILE *fp1, FILE *fp2, char *acc, T read1, T read2) {

 static void

-parse_bam_input (FILE *fp1, FILE *fp2, Bamreader_T bamreader, Table_T read_table1, Table_T read_table2) {

+parse_bam_input (FILE *fp0, FILE *fp1, FILE *fp2, Bamreader_T bamreader, Table_T read_table1, Table_T read_table2) {

   Bamline_T bamline;

   char *acc, *acc_copy;

   Read_T read1, read2;

@@ -1169,9 +1169,9 @@ parse_bam_input (FILE *fp1, FILE *fp2, Bamreader_T bamreader, Table_T read_table

 	Table_put(read_table1,found1p ? acc : string_copy(acc),read1);

       } else {

 	if (fastap == true) {

-	  print_fasta_single(fp1,acc,read1);

+	  print_fasta_single(fp0,acc,read1);

 	} else {

-	  print_fastq_single(fp1,acc,read1);

+	  print_fastq_single(fp0,acc,read1);

 	}

 	if (found1p == true) {

 	  acc_copy = Table_remove(read_table1,acc);

@@ -1390,7 +1390,7 @@ empty_table (FILE *fp, Table_T read_table, char *suffix) {

 int

 main (int argc, char *argv[]) {

-  FILE *fp1, *fp2 = NULL, *err1 = NULL, *err2 = NULL;

+  FILE *fp0, *fp1, *fp2 = NULL, *err1 = NULL, *err2 = NULL;

   char *filename;

   Bamreader_T bamreader;

   Table_T read_table1, read_table2;

@@ -1488,6 +1488,11 @@ main (int argc, char *argv[]) {

       fp1 = stdout;

     } else {

+      filename = (char *) CALLOC(strlen(output_root) + strlen(".fq") + 1,sizeof(char));

+      sprintf(filename,"%s.fq",output_root);

+      fp0 = fopen(filename,"w");

+      FREE(filename);

+

       filename = (char *) CALLOC(strlen(output_root) + strlen("_1.fq") + 1,sizeof(char));

       sprintf(filename,"%s_1.fq",output_root);

       fp1 = fopen(filename,"w");

@@ -1507,7 +1512,7 @@ main (int argc, char *argv[]) {

       read_table2 = Table_new(1000000,Table_string_compare,Table_string_hash);

       bamreader = Bamread_new(argv[i]);

-      parse_bam_input(fp1,fp2,bamreader,read_table1,read_table2);

+      parse_bam_input(fp0,fp1,fp2,bamreader,read_table1,read_table2);

       Bamread_free(&bamreader);

     }

   }

@@ -1561,6 +1566,7 @@ main (int argc, char *argv[]) {

   }

   if (fastap == false) {

     fclose(fp1);

+    fclose(fp0);

   }

   if (fastap == false) {

@@ -1,4 +1,4 @@

-static char rcsid[] = "$Id: bamtally.c 134416 2014-04-25 22:12:58Z twu $";

+static char rcsid[] = "$Id: bamtally.c 134973 2014-05-03 01:11:47Z twu $";

 #ifdef HAVE_CONFIG_H

 #include <config.h>

 #endif

@@ -32,6 +32,12 @@ static char rcsid[] = "$Id: bamtally.c 134416 2014-04-25 22:12:58Z twu $";

 #include "dynprog.h"

 #include "dynprog_single.h"

+#include "matchdef.h"

+#include "matchpool.h"

+#include "mismatchdef.h"

+#include "mismatchpool.h"

+

+

 /* Specific to BAM */

 #include "samflags.h"		/* For flags */

@@ -86,15 +92,11 @@ typedef struct T *T;

 typedef enum {FIRST, SECOND} Pairend_T;

+#define USE_MATCHPOOL 1

+#define USE_MISMATCHPOOL 1

-typedef struct Match_T *Match_T;

-struct Match_T {

-  int shift;			/* Used to record shifts */

-  int mapq;

-  char quality;

-  long int count;

-};

+#ifndef USE_MATCHPOOL

 static Match_T

 Match_new (int shift, int mapq, char quality) {

   Match_T new = (Match_T) MALLOC(sizeof(*new));

@@ -112,6 +114,9 @@ Match_free (Match_T *old) {

   FREE(*old);

   return;

 }

+#endif

+

+

 static Match_T

 find_match_byshift (List_T matches, int shift) {

@@ -206,21 +211,7 @@ Match_mapq_cmp (const void *a, const void *b) {

 }

-typedef struct Mismatch_T *Mismatch_T;