[med-svn] [gmap] 12/16: Imported Upstream version 2016-06-09
Alex Mestiashvili
malex-guest at moszumanska.debian.org
Fri Jun 17 13:08:53 UTC 2016
This is an automated email from the git hooks/post-receive script.
malex-guest pushed a commit to branch master
in repository gmap.
commit 8ab5509eea3358e42cfcb811f5d9d0265f77f27f
Author: Alexandre Mestiashvili <alex at biotec.tu-dresden.de>
Date: Mon Jun 13 10:00:01 2016 +0200
Imported Upstream version 2016-06-09
---
ChangeLog | 18 ++++
VERSION | 2 +-
config/ax_ext.m4 | 10 +-
configure | 34 +++----
src/Makefile.am | 10 +-
src/Makefile.in | 268 ++++++++++++++++++++++++++++++------------------------
src/cpuid.c | 34 ++++++-
src/sarray-read.c | 6 +-
src/splice.c | 87 ++++++++++++------
src/splicetrie.c | 4 +-
src/stage3.c | 4 +-
11 files changed, 297 insertions(+), 180 deletions(-)
diff --git a/ChangeLog b/ChangeLog
index ec71e96..e8ec9be 100644
--- a/ChangeLog
+++ b/ChangeLog
@@ -1,3 +1,21 @@
+2016-06-09 twu
+
+ * cpuid.c: Providing more detailed information from standalone program
+
+ * splicetrie.c: Commented out a debugging statement
+
+ * splice.c: Restored check for sufficient splice probabilities on splices
+
+ * sarray-read.c: Restored _pext_u32 command
+
+ * Makefile.gsnaptoo.am, cpuid.c: Added cpuid main program
+
+ * stage3.c: Added comment
+
+2016-06-08 twu
+
+ * ax_ext.m4: Added -mbmi2 flag for avx2
+
2016-06-03 twu
* VERSION: Updated version number
diff --git a/VERSION b/VERSION
index 67c7133..765dd15 100644
--- a/VERSION
+++ b/VERSION
@@ -1 +1 @@
-2016-06-03
\ No newline at end of file
+2016-06-09
\ No newline at end of file
diff --git a/config/ax_ext.m4 b/config/ax_ext.m4
index 534054e..2832615 100644
--- a/config/ax_ext.m4
+++ b/config/ax_ext.m4
@@ -266,11 +266,11 @@ AC_DEFUN([AX_EXT],
if test x"$ax_cv_c_compiler_vendor" = xintel; then
TEST_CFLAGS="-march=core-avx2"
else
- TEST_CFLAGS="$SIMD_SSE4_2_CFLAGS -mavx2"
- SIMD_SSE2_CFLAGS="$SIMD_SSE2_CFLAGS -mno-avx2"
- SIMD_SSSE3_CFLAGS="$SIMD_SSSE3_CFLAGS -mno-avx2"
- SIMD_SSE4_1_CFLAGS="$SIMD_SSE4_1_CFLAGS -mno-avx2"
- SIMD_SSE4_2_CFLAGS="$SIMD_SSE4_2_CFLAGS -mno-avx2"
+ TEST_CFLAGS="$SIMD_SSE4_2_CFLAGS -mavx2 -mbmi2"
+ SIMD_SSE2_CFLAGS="$SIMD_SSE2_CFLAGS -mno-avx2 -mno-bmi2"
+ SIMD_SSSE3_CFLAGS="$SIMD_SSSE3_CFLAGS -mno-avx2 -mno-bmi2"
+ SIMD_SSE4_1_CFLAGS="$SIMD_SSE4_1_CFLAGS -mno-avx2 -mno-bmi2"
+ SIMD_SSE4_2_CFLAGS="$SIMD_SSE4_2_CFLAGS -mno-avx2 -mno-bmi2"
fi
AX_CHECK_COMPILE_FLAG([$TEST_CFLAGS], [ax_cv_compile_avx2_ext=yes], [ax_cv_ext_compile_problem=yes])
if test x"$ax_cv_compile_avx2_ext" != xyes; then
diff --git a/configure b/configure
index 7e36b15..3cd3025 100755
--- a/configure
+++ b/configure
@@ -1,6 +1,6 @@
#! /bin/sh
# Guess values for system-dependent variables and create Makefiles.
-# Generated by GNU Autoconf 2.69 for gmap 2016-06-03.
+# Generated by GNU Autoconf 2.69 for gmap 2016-06-09.
#
# Report bugs to <Thomas Wu <twu at gene.com>>.
#
@@ -590,8 +590,8 @@ MAKEFLAGS=
# Identity of this package.
PACKAGE_NAME='gmap'
PACKAGE_TARNAME='gmap'
-PACKAGE_VERSION='2016-06-03'
-PACKAGE_STRING='gmap 2016-06-03'
+PACKAGE_VERSION='2016-06-09'
+PACKAGE_STRING='gmap 2016-06-09'
PACKAGE_BUGREPORT='Thomas Wu <twu at gene.com>'
PACKAGE_URL=''
@@ -1367,7 +1367,7 @@ if test "$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 gmap 2016-06-03 to adapt to many kinds of systems.
+\`configure' configures gmap 2016-06-09 to adapt to many kinds of systems.
Usage: $0 [OPTION]... [VAR=VALUE]...
@@ -1438,7 +1438,7 @@ fi
if test -n "$ac_init_help"; then
case $ac_init_help in
- short | recursive ) echo "Configuration of gmap 2016-06-03:";;
+ short | recursive ) echo "Configuration of gmap 2016-06-09:";;
esac
cat <<\_ACEOF
@@ -1570,7 +1570,7 @@ fi
test -n "$ac_init_help" && exit $ac_status
if $ac_init_version; then
cat <<\_ACEOF
-gmap configure 2016-06-03
+gmap configure 2016-06-09
generated by GNU Autoconf 2.69
Copyright (C) 2012 Free Software Foundation, Inc.
@@ -2176,7 +2176,7 @@ 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 gmap $as_me 2016-06-03, which was
+It was created by gmap $as_me 2016-06-09, which was
generated by GNU Autoconf 2.69. Invocation command line was
$ $0 $@
@@ -2526,8 +2526,8 @@ ac_compiler_gnu=$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: 2016-06-03" >&5
-$as_echo "2016-06-03" >&6; }
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: 2016-06-09" >&5
+$as_echo "2016-06-09" >&6; }
### Read defaults
@@ -4392,7 +4392,7 @@ fi
# Define the identity of the package.
PACKAGE='gmap'
- VERSION='2016-06-03'
+ VERSION='2016-06-09'
cat >>confdefs.h <<_ACEOF
@@ -18583,11 +18583,11 @@ fi
if test x"$ax_cv_c_compiler_vendor" = xintel; then
TEST_CFLAGS="-march=core-avx2"
else
- TEST_CFLAGS="$SIMD_SSE4_2_CFLAGS -mavx2"
- SIMD_SSE2_CFLAGS="$SIMD_SSE2_CFLAGS -mno-avx2"
- SIMD_SSSE3_CFLAGS="$SIMD_SSSE3_CFLAGS -mno-avx2"
- SIMD_SSE4_1_CFLAGS="$SIMD_SSE4_1_CFLAGS -mno-avx2"
- SIMD_SSE4_2_CFLAGS="$SIMD_SSE4_2_CFLAGS -mno-avx2"
+ TEST_CFLAGS="$SIMD_SSE4_2_CFLAGS -mavx2 -mbmi2"
+ SIMD_SSE2_CFLAGS="$SIMD_SSE2_CFLAGS -mno-avx2 -mno-bmi2"
+ SIMD_SSSE3_CFLAGS="$SIMD_SSSE3_CFLAGS -mno-avx2 -mno-bmi2"
+ SIMD_SSE4_1_CFLAGS="$SIMD_SSE4_1_CFLAGS -mno-avx2 -mno-bmi2"
+ SIMD_SSE4_2_CFLAGS="$SIMD_SSE4_2_CFLAGS -mno-avx2 -mno-bmi2"
fi
as_CACHEVAR=`$as_echo "ax_cv_check_cflags__$TEST_CFLAGS" | $as_tr_sh`
{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether C compiler accepts $TEST_CFLAGS" >&5
@@ -20048,7 +20048,7 @@ cat >>$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 gmap $as_me 2016-06-03, which was
+This file was extended by gmap $as_me 2016-06-09, which was
generated by GNU Autoconf 2.69. Invocation command line was
CONFIG_FILES = $CONFIG_FILES
@@ -20114,7 +20114,7 @@ _ACEOF
cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
ac_cs_config="`$as_echo "$ac_configure_args" | sed 's/^ //; s/[\\""\`\$]/\\\\&/g'`"
ac_cs_version="\\
-gmap config.status 2016-06-03
+gmap config.status 2016-06-09
configured by $0, generated by GNU Autoconf 2.69,
with options \\"\$ac_cs_config\\"
diff --git a/src/Makefile.am b/src/Makefile.am
index c66daf9..c38ec89 100644
--- a/src/Makefile.am
+++ b/src/Makefile.am
@@ -8,7 +8,7 @@ EXTRA_DIST = mpidebug.c mpidebug.h master.c master.h
# get-genome so they can handle both small and large genomes at run
# time
-bin_PROGRAMS = gmap gmapl get-genome gmapindex iit_store iit_get iit_dump \
+bin_PROGRAMS = cpuid gmap gmapl get-genome gmapindex iit_store iit_get iit_dump \
gsnap gsnapl uniqscan uniqscanl snpindex cmetindex atoiindex \
sam_sort
bin_PROGRAMS += gmap.nosimd
@@ -47,6 +47,14 @@ if MAKE_AVX2
endif
+CPUID_FILES = bool.h cpuid.c cpuid.h
+cpuid_CC = $(CC)
+cpuid_CFLAGS = $(AM_CFLAGS) -DMAIN=1
+cpuid_LDFLAGS = $(AM_LDFLAGS)
+cpuid_LDADD =
+dist_cpuid_SOURCES = $(CPUID_FILES)
+
+
GMAP_SELECT_FILES = bool.h cpuid.c cpuid.h gmap_select.c
gmap_CC = $(CC)
gmap_CFLAGS = $(AM_CFLAGS)
diff --git a/src/Makefile.in b/src/Makefile.in
index a3ec2a1..2d51a86 100644
--- a/src/Makefile.in
+++ b/src/Makefile.in
@@ -89,12 +89,12 @@ POST_UNINSTALL = :
build_triplet = @build@
host_triplet = @host@
target_triplet = @target@
-bin_PROGRAMS = gmap$(EXEEXT) gmapl$(EXEEXT) get-genome$(EXEEXT) \
- gmapindex$(EXEEXT) iit_store$(EXEEXT) iit_get$(EXEEXT) \
- iit_dump$(EXEEXT) gsnap$(EXEEXT) gsnapl$(EXEEXT) \
- uniqscan$(EXEEXT) uniqscanl$(EXEEXT) snpindex$(EXEEXT) \
- cmetindex$(EXEEXT) atoiindex$(EXEEXT) sam_sort$(EXEEXT) \
- gmap.nosimd$(EXEEXT) gmapl.nosimd$(EXEEXT) \
+bin_PROGRAMS = cpuid$(EXEEXT) gmap$(EXEEXT) gmapl$(EXEEXT) \
+ get-genome$(EXEEXT) gmapindex$(EXEEXT) iit_store$(EXEEXT) \
+ iit_get$(EXEEXT) iit_dump$(EXEEXT) gsnap$(EXEEXT) \
+ gsnapl$(EXEEXT) uniqscan$(EXEEXT) uniqscanl$(EXEEXT) \
+ snpindex$(EXEEXT) cmetindex$(EXEEXT) atoiindex$(EXEEXT) \
+ sam_sort$(EXEEXT) gmap.nosimd$(EXEEXT) gmapl.nosimd$(EXEEXT) \
gsnap.nosimd$(EXEEXT) gsnapl.nosimd$(EXEEXT) $(am__EXEEXT_1) \
$(am__EXEEXT_2) $(am__EXEEXT_3) $(am__EXEEXT_4) \
$(am__EXEEXT_5)
@@ -224,7 +224,14 @@ cmetindex_DEPENDENCIES = $(am__DEPENDENCIES_1) $(am__DEPENDENCIES_1) \
cmetindex_LINK = $(LIBTOOL) $(AM_V_lt) --tag=CC $(AM_LIBTOOLFLAGS) \
$(LIBTOOLFLAGS) --mode=link $(CCLD) $(cmetindex_CFLAGS) \
$(CFLAGS) $(cmetindex_LDFLAGS) $(LDFLAGS) -o $@
-am__objects_3 = get_genome-except.$(OBJEXT) \
+am__objects_3 = cpuid-cpuid.$(OBJEXT)
+dist_cpuid_OBJECTS = $(am__objects_3)
+cpuid_OBJECTS = $(dist_cpuid_OBJECTS)
+cpuid_DEPENDENCIES =
+cpuid_LINK = $(LIBTOOL) $(AM_V_lt) --tag=CC $(AM_LIBTOOLFLAGS) \
+ $(LIBTOOLFLAGS) --mode=link $(CCLD) $(cpuid_CFLAGS) $(CFLAGS) \
+ $(cpuid_LDFLAGS) $(LDFLAGS) -o $@
+am__objects_4 = get_genome-except.$(OBJEXT) \
get_genome-assert.$(OBJEXT) get_genome-mem.$(OBJEXT) \
get_genome-intlist.$(OBJEXT) get_genome-list.$(OBJEXT) \
get_genome-littleendian.$(OBJEXT) \
@@ -241,21 +248,21 @@ am__objects_3 = get_genome-except.$(OBJEXT) \
get_genome-datadir.$(OBJEXT) get_genome-parserange.$(OBJEXT) \
get_genome-getopt.$(OBJEXT) get_genome-getopt1.$(OBJEXT) \
get_genome-get-genome.$(OBJEXT)
-dist_get_genome_OBJECTS = $(am__objects_3)
+dist_get_genome_OBJECTS = $(am__objects_4)
get_genome_OBJECTS = $(dist_get_genome_OBJECTS)
get_genome_DEPENDENCIES = $(am__DEPENDENCIES_1) $(am__DEPENDENCIES_1) \
$(am__DEPENDENCIES_1)
get_genome_LINK = $(LIBTOOL) $(AM_V_lt) --tag=CC $(AM_LIBTOOLFLAGS) \
$(LIBTOOLFLAGS) --mode=link $(CCLD) $(get_genome_CFLAGS) \
$(CFLAGS) $(get_genome_LDFLAGS) $(LDFLAGS) -o $@
-am__objects_4 = gmap-cpuid.$(OBJEXT) gmap-gmap_select.$(OBJEXT)
-dist_gmap_OBJECTS = $(am__objects_4)
+am__objects_5 = gmap-cpuid.$(OBJEXT) gmap-gmap_select.$(OBJEXT)
+dist_gmap_OBJECTS = $(am__objects_5)
gmap_OBJECTS = $(dist_gmap_OBJECTS)
gmap_DEPENDENCIES =
gmap_LINK = $(LIBTOOL) $(AM_V_lt) --tag=CC $(AM_LIBTOOLFLAGS) \
$(LIBTOOLFLAGS) --mode=link $(CCLD) $(gmap_CFLAGS) $(CFLAGS) \
$(gmap_LDFLAGS) $(LDFLAGS) -o $@
-am__objects_5 = gmap_avx2-except.$(OBJEXT) gmap_avx2-assert.$(OBJEXT) \
+am__objects_6 = gmap_avx2-except.$(OBJEXT) gmap_avx2-assert.$(OBJEXT) \
gmap_avx2-mem.$(OBJEXT) gmap_avx2-intlist.$(OBJEXT) \
gmap_avx2-list.$(OBJEXT) gmap_avx2-littleendian.$(OBJEXT) \
gmap_avx2-bigendian.$(OBJEXT) gmap_avx2-univinterval.$(OBJEXT) \
@@ -303,14 +310,14 @@ am__objects_5 = gmap_avx2-except.$(OBJEXT) gmap_avx2-assert.$(OBJEXT) \
gmap_avx2-chimera.$(OBJEXT) gmap_avx2-datadir.$(OBJEXT) \
gmap_avx2-parserange.$(OBJEXT) gmap_avx2-getopt.$(OBJEXT) \
gmap_avx2-getopt1.$(OBJEXT) gmap_avx2-gmap.$(OBJEXT)
-dist_gmap_avx2_OBJECTS = $(am__objects_5)
+dist_gmap_avx2_OBJECTS = $(am__objects_6)
gmap_avx2_OBJECTS = $(dist_gmap_avx2_OBJECTS)
gmap_avx2_DEPENDENCIES = $(am__DEPENDENCIES_1) $(am__DEPENDENCIES_1) \
$(am__DEPENDENCIES_1)
gmap_avx2_LINK = $(LIBTOOL) $(AM_V_lt) --tag=CC $(AM_LIBTOOLFLAGS) \
$(LIBTOOLFLAGS) --mode=link $(CCLD) $(gmap_avx2_CFLAGS) \
$(CFLAGS) $(gmap_avx2_LDFLAGS) $(LDFLAGS) -o $@
-am__objects_6 = gmap_nosimd-except.$(OBJEXT) \
+am__objects_7 = gmap_nosimd-except.$(OBJEXT) \
gmap_nosimd-assert.$(OBJEXT) gmap_nosimd-mem.$(OBJEXT) \
gmap_nosimd-intlist.$(OBJEXT) gmap_nosimd-list.$(OBJEXT) \
gmap_nosimd-littleendian.$(OBJEXT) \
@@ -368,14 +375,14 @@ am__objects_6 = gmap_nosimd-except.$(OBJEXT) \
gmap_nosimd-datadir.$(OBJEXT) gmap_nosimd-parserange.$(OBJEXT) \
gmap_nosimd-getopt.$(OBJEXT) gmap_nosimd-getopt1.$(OBJEXT) \
gmap_nosimd-gmap.$(OBJEXT)
-dist_gmap_nosimd_OBJECTS = $(am__objects_6)
+dist_gmap_nosimd_OBJECTS = $(am__objects_7)
gmap_nosimd_OBJECTS = $(dist_gmap_nosimd_OBJECTS)
gmap_nosimd_DEPENDENCIES = $(am__DEPENDENCIES_1) $(am__DEPENDENCIES_1) \
$(am__DEPENDENCIES_1)
gmap_nosimd_LINK = $(LIBTOOL) $(AM_V_lt) --tag=CC $(AM_LIBTOOLFLAGS) \
$(LIBTOOLFLAGS) --mode=link $(CCLD) $(gmap_nosimd_CFLAGS) \
$(CFLAGS) $(gmap_nosimd_LDFLAGS) $(LDFLAGS) -o $@
-am__objects_7 = gmap_sse2-except.$(OBJEXT) gmap_sse2-assert.$(OBJEXT) \
+am__objects_8 = gmap_sse2-except.$(OBJEXT) gmap_sse2-assert.$(OBJEXT) \
gmap_sse2-mem.$(OBJEXT) gmap_sse2-intlist.$(OBJEXT) \
gmap_sse2-list.$(OBJEXT) gmap_sse2-littleendian.$(OBJEXT) \
gmap_sse2-bigendian.$(OBJEXT) gmap_sse2-univinterval.$(OBJEXT) \
@@ -423,14 +430,14 @@ am__objects_7 = gmap_sse2-except.$(OBJEXT) gmap_sse2-assert.$(OBJEXT) \
gmap_sse2-chimera.$(OBJEXT) gmap_sse2-datadir.$(OBJEXT) \
gmap_sse2-parserange.$(OBJEXT) gmap_sse2-getopt.$(OBJEXT) \
gmap_sse2-getopt1.$(OBJEXT) gmap_sse2-gmap.$(OBJEXT)
-dist_gmap_sse2_OBJECTS = $(am__objects_7)
+dist_gmap_sse2_OBJECTS = $(am__objects_8)
gmap_sse2_OBJECTS = $(dist_gmap_sse2_OBJECTS)
gmap_sse2_DEPENDENCIES = $(am__DEPENDENCIES_1) $(am__DEPENDENCIES_1) \
$(am__DEPENDENCIES_1)
gmap_sse2_LINK = $(LIBTOOL) $(AM_V_lt) --tag=CC $(AM_LIBTOOLFLAGS) \
$(LIBTOOLFLAGS) --mode=link $(CCLD) $(gmap_sse2_CFLAGS) \
$(CFLAGS) $(gmap_sse2_LDFLAGS) $(LDFLAGS) -o $@
-am__objects_8 = gmap_sse41-except.$(OBJEXT) \
+am__objects_9 = gmap_sse41-except.$(OBJEXT) \
gmap_sse41-assert.$(OBJEXT) gmap_sse41-mem.$(OBJEXT) \
gmap_sse41-intlist.$(OBJEXT) gmap_sse41-list.$(OBJEXT) \
gmap_sse41-littleendian.$(OBJEXT) \
@@ -483,14 +490,14 @@ am__objects_8 = gmap_sse41-except.$(OBJEXT) \
gmap_sse41-chimera.$(OBJEXT) gmap_sse41-datadir.$(OBJEXT) \
gmap_sse41-parserange.$(OBJEXT) gmap_sse41-getopt.$(OBJEXT) \
gmap_sse41-getopt1.$(OBJEXT) gmap_sse41-gmap.$(OBJEXT)
-dist_gmap_sse41_OBJECTS = $(am__objects_8)
+dist_gmap_sse41_OBJECTS = $(am__objects_9)
gmap_sse41_OBJECTS = $(dist_gmap_sse41_OBJECTS)
gmap_sse41_DEPENDENCIES = $(am__DEPENDENCIES_1) $(am__DEPENDENCIES_1) \
$(am__DEPENDENCIES_1)
gmap_sse41_LINK = $(LIBTOOL) $(AM_V_lt) --tag=CC $(AM_LIBTOOLFLAGS) \
$(LIBTOOLFLAGS) --mode=link $(CCLD) $(gmap_sse41_CFLAGS) \
$(CFLAGS) $(gmap_sse41_LDFLAGS) $(LDFLAGS) -o $@
-am__objects_9 = gmap_sse42-except.$(OBJEXT) \
+am__objects_10 = gmap_sse42-except.$(OBJEXT) \
gmap_sse42-assert.$(OBJEXT) gmap_sse42-mem.$(OBJEXT) \
gmap_sse42-intlist.$(OBJEXT) gmap_sse42-list.$(OBJEXT) \
gmap_sse42-littleendian.$(OBJEXT) \
@@ -543,14 +550,14 @@ am__objects_9 = gmap_sse42-except.$(OBJEXT) \
gmap_sse42-chimera.$(OBJEXT) gmap_sse42-datadir.$(OBJEXT) \
gmap_sse42-parserange.$(OBJEXT) gmap_sse42-getopt.$(OBJEXT) \
gmap_sse42-getopt1.$(OBJEXT) gmap_sse42-gmap.$(OBJEXT)
-dist_gmap_sse42_OBJECTS = $(am__objects_9)
+dist_gmap_sse42_OBJECTS = $(am__objects_10)
gmap_sse42_OBJECTS = $(dist_gmap_sse42_OBJECTS)
gmap_sse42_DEPENDENCIES = $(am__DEPENDENCIES_1) $(am__DEPENDENCIES_1) \
$(am__DEPENDENCIES_1)
gmap_sse42_LINK = $(LIBTOOL) $(AM_V_lt) --tag=CC $(AM_LIBTOOLFLAGS) \
$(LIBTOOLFLAGS) --mode=link $(CCLD) $(gmap_sse42_CFLAGS) \
$(CFLAGS) $(gmap_sse42_LDFLAGS) $(LDFLAGS) -o $@
-am__objects_10 = gmap_ssse3-except.$(OBJEXT) \
+am__objects_11 = gmap_ssse3-except.$(OBJEXT) \
gmap_ssse3-assert.$(OBJEXT) gmap_ssse3-mem.$(OBJEXT) \
gmap_ssse3-intlist.$(OBJEXT) gmap_ssse3-list.$(OBJEXT) \
gmap_ssse3-littleendian.$(OBJEXT) \
@@ -603,14 +610,14 @@ am__objects_10 = gmap_ssse3-except.$(OBJEXT) \
gmap_ssse3-chimera.$(OBJEXT) gmap_ssse3-datadir.$(OBJEXT) \
gmap_ssse3-parserange.$(OBJEXT) gmap_ssse3-getopt.$(OBJEXT) \
gmap_ssse3-getopt1.$(OBJEXT) gmap_ssse3-gmap.$(OBJEXT)
-dist_gmap_ssse3_OBJECTS = $(am__objects_10)
+dist_gmap_ssse3_OBJECTS = $(am__objects_11)
gmap_ssse3_OBJECTS = $(dist_gmap_ssse3_OBJECTS)
gmap_ssse3_DEPENDENCIES = $(am__DEPENDENCIES_1) $(am__DEPENDENCIES_1) \
$(am__DEPENDENCIES_1)
gmap_ssse3_LINK = $(LIBTOOL) $(AM_V_lt) --tag=CC $(AM_LIBTOOLFLAGS) \
$(LIBTOOLFLAGS) --mode=link $(CCLD) $(gmap_ssse3_CFLAGS) \
$(CFLAGS) $(gmap_ssse3_LDFLAGS) $(LDFLAGS) -o $@
-am__objects_11 = gmapindex-except.$(OBJEXT) gmapindex-assert.$(OBJEXT) \
+am__objects_12 = gmapindex-except.$(OBJEXT) gmapindex-assert.$(OBJEXT) \
gmapindex-mem.$(OBJEXT) gmapindex-intlist.$(OBJEXT) \
gmapindex-list.$(OBJEXT) gmapindex-littleendian.$(OBJEXT) \
gmapindex-bigendian.$(OBJEXT) gmapindex-univinterval.$(OBJEXT) \
@@ -638,21 +645,21 @@ am__objects_11 = gmapindex-except.$(OBJEXT) gmapindex-assert.$(OBJEXT) \
gmapindex-bytecoding.$(OBJEXT) \
gmapindex-sarray-write.$(OBJEXT) \
gmapindex-parserange.$(OBJEXT) gmapindex-gmapindex.$(OBJEXT)
-dist_gmapindex_OBJECTS = $(am__objects_11)
+dist_gmapindex_OBJECTS = $(am__objects_12)
gmapindex_OBJECTS = $(dist_gmapindex_OBJECTS)
gmapindex_DEPENDENCIES = $(am__DEPENDENCIES_1) $(am__DEPENDENCIES_1) \
$(am__DEPENDENCIES_1)
gmapindex_LINK = $(LIBTOOL) $(AM_V_lt) --tag=CC $(AM_LIBTOOLFLAGS) \
$(LIBTOOLFLAGS) --mode=link $(CCLD) $(gmapindex_CFLAGS) \
$(CFLAGS) $(gmapindex_LDFLAGS) $(LDFLAGS) -o $@
-am__objects_12 = gmapl-cpuid.$(OBJEXT) gmapl-gmapl_select.$(OBJEXT)
-dist_gmapl_OBJECTS = $(am__objects_12)
+am__objects_13 = gmapl-cpuid.$(OBJEXT) gmapl-gmapl_select.$(OBJEXT)
+dist_gmapl_OBJECTS = $(am__objects_13)
gmapl_OBJECTS = $(dist_gmapl_OBJECTS)
gmapl_DEPENDENCIES =
gmapl_LINK = $(LIBTOOL) $(AM_V_lt) --tag=CC $(AM_LIBTOOLFLAGS) \
$(LIBTOOLFLAGS) --mode=link $(CCLD) $(gmapl_CFLAGS) $(CFLAGS) \
$(gmapl_LDFLAGS) $(LDFLAGS) -o $@
-am__objects_13 = gmapl_avx2-except.$(OBJEXT) \
+am__objects_14 = gmapl_avx2-except.$(OBJEXT) \
gmapl_avx2-assert.$(OBJEXT) gmapl_avx2-mem.$(OBJEXT) \
gmapl_avx2-intlist.$(OBJEXT) gmapl_avx2-list.$(OBJEXT) \
gmapl_avx2-littleendian.$(OBJEXT) \
@@ -705,14 +712,14 @@ am__objects_13 = gmapl_avx2-except.$(OBJEXT) \
gmapl_avx2-chimera.$(OBJEXT) gmapl_avx2-datadir.$(OBJEXT) \
gmapl_avx2-parserange.$(OBJEXT) gmapl_avx2-getopt.$(OBJEXT) \
gmapl_avx2-getopt1.$(OBJEXT) gmapl_avx2-gmap.$(OBJEXT)
-dist_gmapl_avx2_OBJECTS = $(am__objects_13)
+dist_gmapl_avx2_OBJECTS = $(am__objects_14)
gmapl_avx2_OBJECTS = $(dist_gmapl_avx2_OBJECTS)
gmapl_avx2_DEPENDENCIES = $(am__DEPENDENCIES_1) $(am__DEPENDENCIES_1) \
$(am__DEPENDENCIES_1)
gmapl_avx2_LINK = $(LIBTOOL) $(AM_V_lt) --tag=CC $(AM_LIBTOOLFLAGS) \
$(LIBTOOLFLAGS) --mode=link $(CCLD) $(gmapl_avx2_CFLAGS) \
$(CFLAGS) $(gmapl_avx2_LDFLAGS) $(LDFLAGS) -o $@
-am__objects_14 = gmapl_nosimd-except.$(OBJEXT) \
+am__objects_15 = gmapl_nosimd-except.$(OBJEXT) \
gmapl_nosimd-assert.$(OBJEXT) gmapl_nosimd-mem.$(OBJEXT) \
gmapl_nosimd-intlist.$(OBJEXT) gmapl_nosimd-list.$(OBJEXT) \
gmapl_nosimd-littleendian.$(OBJEXT) \
@@ -777,14 +784,14 @@ am__objects_14 = gmapl_nosimd-except.$(OBJEXT) \
gmapl_nosimd-parserange.$(OBJEXT) \
gmapl_nosimd-getopt.$(OBJEXT) gmapl_nosimd-getopt1.$(OBJEXT) \
gmapl_nosimd-gmap.$(OBJEXT)
-dist_gmapl_nosimd_OBJECTS = $(am__objects_14)
+dist_gmapl_nosimd_OBJECTS = $(am__objects_15)
gmapl_nosimd_OBJECTS = $(dist_gmapl_nosimd_OBJECTS)
gmapl_nosimd_DEPENDENCIES = $(am__DEPENDENCIES_1) \
$(am__DEPENDENCIES_1) $(am__DEPENDENCIES_1)
gmapl_nosimd_LINK = $(LIBTOOL) $(AM_V_lt) --tag=CC $(AM_LIBTOOLFLAGS) \
$(LIBTOOLFLAGS) --mode=link $(CCLD) $(gmapl_nosimd_CFLAGS) \
$(CFLAGS) $(gmapl_nosimd_LDFLAGS) $(LDFLAGS) -o $@
-am__objects_15 = gmapl_sse2-except.$(OBJEXT) \
+am__objects_16 = gmapl_sse2-except.$(OBJEXT) \
gmapl_sse2-assert.$(OBJEXT) gmapl_sse2-mem.$(OBJEXT) \
gmapl_sse2-intlist.$(OBJEXT) gmapl_sse2-list.$(OBJEXT) \
gmapl_sse2-littleendian.$(OBJEXT) \
@@ -837,14 +844,14 @@ am__objects_15 = gmapl_sse2-except.$(OBJEXT) \
gmapl_sse2-chimera.$(OBJEXT) gmapl_sse2-datadir.$(OBJEXT) \
gmapl_sse2-parserange.$(OBJEXT) gmapl_sse2-getopt.$(OBJEXT) \
gmapl_sse2-getopt1.$(OBJEXT) gmapl_sse2-gmap.$(OBJEXT)
-dist_gmapl_sse2_OBJECTS = $(am__objects_15)
+dist_gmapl_sse2_OBJECTS = $(am__objects_16)
gmapl_sse2_OBJECTS = $(dist_gmapl_sse2_OBJECTS)
gmapl_sse2_DEPENDENCIES = $(am__DEPENDENCIES_1) $(am__DEPENDENCIES_1) \
$(am__DEPENDENCIES_1)
gmapl_sse2_LINK = $(LIBTOOL) $(AM_V_lt) --tag=CC $(AM_LIBTOOLFLAGS) \
$(LIBTOOLFLAGS) --mode=link $(CCLD) $(gmapl_sse2_CFLAGS) \
$(CFLAGS) $(gmapl_sse2_LDFLAGS) $(LDFLAGS) -o $@
-am__objects_16 = gmapl_sse41-except.$(OBJEXT) \
+am__objects_17 = gmapl_sse41-except.$(OBJEXT) \
gmapl_sse41-assert.$(OBJEXT) gmapl_sse41-mem.$(OBJEXT) \
gmapl_sse41-intlist.$(OBJEXT) gmapl_sse41-list.$(OBJEXT) \
gmapl_sse41-littleendian.$(OBJEXT) \
@@ -902,14 +909,14 @@ am__objects_16 = gmapl_sse41-except.$(OBJEXT) \
gmapl_sse41-datadir.$(OBJEXT) gmapl_sse41-parserange.$(OBJEXT) \
gmapl_sse41-getopt.$(OBJEXT) gmapl_sse41-getopt1.$(OBJEXT) \
gmapl_sse41-gmap.$(OBJEXT)
-dist_gmapl_sse41_OBJECTS = $(am__objects_16)
+dist_gmapl_sse41_OBJECTS = $(am__objects_17)
gmapl_sse41_OBJECTS = $(dist_gmapl_sse41_OBJECTS)
gmapl_sse41_DEPENDENCIES = $(am__DEPENDENCIES_1) $(am__DEPENDENCIES_1) \
$(am__DEPENDENCIES_1)
gmapl_sse41_LINK = $(LIBTOOL) $(AM_V_lt) --tag=CC $(AM_LIBTOOLFLAGS) \
$(LIBTOOLFLAGS) --mode=link $(CCLD) $(gmapl_sse41_CFLAGS) \
$(CFLAGS) $(gmapl_sse41_LDFLAGS) $(LDFLAGS) -o $@
-am__objects_17 = gmapl_sse42-except.$(OBJEXT) \
+am__objects_18 = gmapl_sse42-except.$(OBJEXT) \
gmapl_sse42-assert.$(OBJEXT) gmapl_sse42-mem.$(OBJEXT) \
gmapl_sse42-intlist.$(OBJEXT) gmapl_sse42-list.$(OBJEXT) \
gmapl_sse42-littleendian.$(OBJEXT) \
@@ -967,14 +974,14 @@ am__objects_17 = gmapl_sse42-except.$(OBJEXT) \
gmapl_sse42-datadir.$(OBJEXT) gmapl_sse42-parserange.$(OBJEXT) \
gmapl_sse42-getopt.$(OBJEXT) gmapl_sse42-getopt1.$(OBJEXT) \
gmapl_sse42-gmap.$(OBJEXT)
-dist_gmapl_sse42_OBJECTS = $(am__objects_17)
+dist_gmapl_sse42_OBJECTS = $(am__objects_18)
gmapl_sse42_OBJECTS = $(dist_gmapl_sse42_OBJECTS)
gmapl_sse42_DEPENDENCIES = $(am__DEPENDENCIES_1) $(am__DEPENDENCIES_1) \
$(am__DEPENDENCIES_1)
gmapl_sse42_LINK = $(LIBTOOL) $(AM_V_lt) --tag=CC $(AM_LIBTOOLFLAGS) \
$(LIBTOOLFLAGS) --mode=link $(CCLD) $(gmapl_sse42_CFLAGS) \
$(CFLAGS) $(gmapl_sse42_LDFLAGS) $(LDFLAGS) -o $@
-am__objects_18 = gmapl_ssse3-except.$(OBJEXT) \
+am__objects_19 = gmapl_ssse3-except.$(OBJEXT) \
gmapl_ssse3-assert.$(OBJEXT) gmapl_ssse3-mem.$(OBJEXT) \
gmapl_ssse3-intlist.$(OBJEXT) gmapl_ssse3-list.$(OBJEXT) \
gmapl_ssse3-littleendian.$(OBJEXT) \
@@ -1032,21 +1039,21 @@ am__objects_18 = gmapl_ssse3-except.$(OBJEXT) \
gmapl_ssse3-datadir.$(OBJEXT) gmapl_ssse3-parserange.$(OBJEXT) \
gmapl_ssse3-getopt.$(OBJEXT) gmapl_ssse3-getopt1.$(OBJEXT) \
gmapl_ssse3-gmap.$(OBJEXT)
-dist_gmapl_ssse3_OBJECTS = $(am__objects_18)
+dist_gmapl_ssse3_OBJECTS = $(am__objects_19)
gmapl_ssse3_OBJECTS = $(dist_gmapl_ssse3_OBJECTS)
gmapl_ssse3_DEPENDENCIES = $(am__DEPENDENCIES_1) $(am__DEPENDENCIES_1) \
$(am__DEPENDENCIES_1)
gmapl_ssse3_LINK = $(LIBTOOL) $(AM_V_lt) --tag=CC $(AM_LIBTOOLFLAGS) \
$(LIBTOOLFLAGS) --mode=link $(CCLD) $(gmapl_ssse3_CFLAGS) \
$(CFLAGS) $(gmapl_ssse3_LDFLAGS) $(LDFLAGS) -o $@
-am__objects_19 = gsnap-cpuid.$(OBJEXT) gsnap-gsnap_select.$(OBJEXT)
-dist_gsnap_OBJECTS = $(am__objects_19)
+am__objects_20 = gsnap-cpuid.$(OBJEXT) gsnap-gsnap_select.$(OBJEXT)
+dist_gsnap_OBJECTS = $(am__objects_20)
gsnap_OBJECTS = $(dist_gsnap_OBJECTS)
gsnap_DEPENDENCIES =
gsnap_LINK = $(LIBTOOL) $(AM_V_lt) --tag=CC $(AM_LIBTOOLFLAGS) \
$(LIBTOOLFLAGS) --mode=link $(CCLD) $(gsnap_CFLAGS) $(CFLAGS) \
$(gsnap_LDFLAGS) $(LDFLAGS) -o $@
-am__objects_20 = gsnap_avx2-except.$(OBJEXT) \
+am__objects_21 = gsnap_avx2-except.$(OBJEXT) \
gsnap_avx2-assert.$(OBJEXT) gsnap_avx2-mem.$(OBJEXT) \
gsnap_avx2-intlist.$(OBJEXT) gsnap_avx2-list.$(OBJEXT) \
gsnap_avx2-littleendian.$(OBJEXT) \
@@ -1100,14 +1107,14 @@ am__objects_20 = gsnap_avx2-except.$(OBJEXT) \
gsnap_avx2-datadir.$(OBJEXT) gsnap_avx2-parserange.$(OBJEXT) \
gsnap_avx2-getopt.$(OBJEXT) gsnap_avx2-getopt1.$(OBJEXT) \
gsnap_avx2-gsnap.$(OBJEXT)
-dist_gsnap_avx2_OBJECTS = $(am__objects_20)
+dist_gsnap_avx2_OBJECTS = $(am__objects_21)
gsnap_avx2_OBJECTS = $(dist_gsnap_avx2_OBJECTS)
gsnap_avx2_DEPENDENCIES = $(am__DEPENDENCIES_1) $(am__DEPENDENCIES_1) \
$(am__DEPENDENCIES_1)
gsnap_avx2_LINK = $(LIBTOOL) $(AM_V_lt) --tag=CC $(AM_LIBTOOLFLAGS) \
$(LIBTOOLFLAGS) --mode=link $(CCLD) $(gsnap_avx2_CFLAGS) \
$(CFLAGS) $(gsnap_avx2_LDFLAGS) $(LDFLAGS) -o $@
-am__objects_21 = gsnap_nosimd-except.$(OBJEXT) \
+am__objects_22 = gsnap_nosimd-except.$(OBJEXT) \
gsnap_nosimd-assert.$(OBJEXT) gsnap_nosimd-mem.$(OBJEXT) \
gsnap_nosimd-intlist.$(OBJEXT) gsnap_nosimd-list.$(OBJEXT) \
gsnap_nosimd-littleendian.$(OBJEXT) \
@@ -1175,14 +1182,14 @@ am__objects_21 = gsnap_nosimd-except.$(OBJEXT) \
gsnap_nosimd-parserange.$(OBJEXT) \
gsnap_nosimd-getopt.$(OBJEXT) gsnap_nosimd-getopt1.$(OBJEXT) \
gsnap_nosimd-gsnap.$(OBJEXT)
-dist_gsnap_nosimd_OBJECTS = $(am__objects_21)
+dist_gsnap_nosimd_OBJECTS = $(am__objects_22)
gsnap_nosimd_OBJECTS = $(dist_gsnap_nosimd_OBJECTS)
gsnap_nosimd_DEPENDENCIES = $(am__DEPENDENCIES_1) \
$(am__DEPENDENCIES_1) $(am__DEPENDENCIES_1)
gsnap_nosimd_LINK = $(LIBTOOL) $(AM_V_lt) --tag=CC $(AM_LIBTOOLFLAGS) \
$(LIBTOOLFLAGS) --mode=link $(CCLD) $(gsnap_nosimd_CFLAGS) \
$(CFLAGS) $(gsnap_nosimd_LDFLAGS) $(LDFLAGS) -o $@
-am__objects_22 = gsnap_sse2-except.$(OBJEXT) \
+am__objects_23 = gsnap_sse2-except.$(OBJEXT) \
gsnap_sse2-assert.$(OBJEXT) gsnap_sse2-mem.$(OBJEXT) \
gsnap_sse2-intlist.$(OBJEXT) gsnap_sse2-list.$(OBJEXT) \
gsnap_sse2-littleendian.$(OBJEXT) \
@@ -1236,14 +1243,14 @@ am__objects_22 = gsnap_sse2-except.$(OBJEXT) \
gsnap_sse2-datadir.$(OBJEXT) gsnap_sse2-parserange.$(OBJEXT) \
gsnap_sse2-getopt.$(OBJEXT) gsnap_sse2-getopt1.$(OBJEXT) \
gsnap_sse2-gsnap.$(OBJEXT)
-dist_gsnap_sse2_OBJECTS = $(am__objects_22)
+dist_gsnap_sse2_OBJECTS = $(am__objects_23)
gsnap_sse2_OBJECTS = $(dist_gsnap_sse2_OBJECTS)
gsnap_sse2_DEPENDENCIES = $(am__DEPENDENCIES_1) $(am__DEPENDENCIES_1) \
$(am__DEPENDENCIES_1)
gsnap_sse2_LINK = $(LIBTOOL) $(AM_V_lt) --tag=CC $(AM_LIBTOOLFLAGS) \
$(LIBTOOLFLAGS) --mode=link $(CCLD) $(gsnap_sse2_CFLAGS) \
$(CFLAGS) $(gsnap_sse2_LDFLAGS) $(LDFLAGS) -o $@
-am__objects_23 = gsnap_sse41-except.$(OBJEXT) \
+am__objects_24 = gsnap_sse41-except.$(OBJEXT) \
gsnap_sse41-assert.$(OBJEXT) gsnap_sse41-mem.$(OBJEXT) \
gsnap_sse41-intlist.$(OBJEXT) gsnap_sse41-list.$(OBJEXT) \
gsnap_sse41-littleendian.$(OBJEXT) \
@@ -1302,14 +1309,14 @@ am__objects_23 = gsnap_sse41-except.$(OBJEXT) \
gsnap_sse41-outbuffer.$(OBJEXT) gsnap_sse41-datadir.$(OBJEXT) \
gsnap_sse41-parserange.$(OBJEXT) gsnap_sse41-getopt.$(OBJEXT) \
gsnap_sse41-getopt1.$(OBJEXT) gsnap_sse41-gsnap.$(OBJEXT)
-dist_gsnap_sse41_OBJECTS = $(am__objects_23)
+dist_gsnap_sse41_OBJECTS = $(am__objects_24)
gsnap_sse41_OBJECTS = $(dist_gsnap_sse41_OBJECTS)
gsnap_sse41_DEPENDENCIES = $(am__DEPENDENCIES_1) $(am__DEPENDENCIES_1) \
$(am__DEPENDENCIES_1)
gsnap_sse41_LINK = $(LIBTOOL) $(AM_V_lt) --tag=CC $(AM_LIBTOOLFLAGS) \
$(LIBTOOLFLAGS) --mode=link $(CCLD) $(gsnap_sse41_CFLAGS) \
$(CFLAGS) $(gsnap_sse41_LDFLAGS) $(LDFLAGS) -o $@
-am__objects_24 = gsnap_sse42-except.$(OBJEXT) \
+am__objects_25 = gsnap_sse42-except.$(OBJEXT) \
gsnap_sse42-assert.$(OBJEXT) gsnap_sse42-mem.$(OBJEXT) \
gsnap_sse42-intlist.$(OBJEXT) gsnap_sse42-list.$(OBJEXT) \
gsnap_sse42-littleendian.$(OBJEXT) \
@@ -1368,14 +1375,14 @@ am__objects_24 = gsnap_sse42-except.$(OBJEXT) \
gsnap_sse42-outbuffer.$(OBJEXT) gsnap_sse42-datadir.$(OBJEXT) \
gsnap_sse42-parserange.$(OBJEXT) gsnap_sse42-getopt.$(OBJEXT) \
gsnap_sse42-getopt1.$(OBJEXT) gsnap_sse42-gsnap.$(OBJEXT)
-dist_gsnap_sse42_OBJECTS = $(am__objects_24)
+dist_gsnap_sse42_OBJECTS = $(am__objects_25)
gsnap_sse42_OBJECTS = $(dist_gsnap_sse42_OBJECTS)
gsnap_sse42_DEPENDENCIES = $(am__DEPENDENCIES_1) $(am__DEPENDENCIES_1) \
$(am__DEPENDENCIES_1)
gsnap_sse42_LINK = $(LIBTOOL) $(AM_V_lt) --tag=CC $(AM_LIBTOOLFLAGS) \
$(LIBTOOLFLAGS) --mode=link $(CCLD) $(gsnap_sse42_CFLAGS) \
$(CFLAGS) $(gsnap_sse42_LDFLAGS) $(LDFLAGS) -o $@
-am__objects_25 = gsnap_ssse3-except.$(OBJEXT) \
+am__objects_26 = gsnap_ssse3-except.$(OBJEXT) \
gsnap_ssse3-assert.$(OBJEXT) gsnap_ssse3-mem.$(OBJEXT) \
gsnap_ssse3-intlist.$(OBJEXT) gsnap_ssse3-list.$(OBJEXT) \
gsnap_ssse3-littleendian.$(OBJEXT) \
@@ -1434,21 +1441,21 @@ am__objects_25 = gsnap_ssse3-except.$(OBJEXT) \
gsnap_ssse3-outbuffer.$(OBJEXT) gsnap_ssse3-datadir.$(OBJEXT) \
gsnap_ssse3-parserange.$(OBJEXT) gsnap_ssse3-getopt.$(OBJEXT) \
gsnap_ssse3-getopt1.$(OBJEXT) gsnap_ssse3-gsnap.$(OBJEXT)
-dist_gsnap_ssse3_OBJECTS = $(am__objects_25)
+dist_gsnap_ssse3_OBJECTS = $(am__objects_26)
gsnap_ssse3_OBJECTS = $(dist_gsnap_ssse3_OBJECTS)
gsnap_ssse3_DEPENDENCIES = $(am__DEPENDENCIES_1) $(am__DEPENDENCIES_1) \
$(am__DEPENDENCIES_1)
gsnap_ssse3_LINK = $(LIBTOOL) $(AM_V_lt) --tag=CC $(AM_LIBTOOLFLAGS) \
$(LIBTOOLFLAGS) --mode=link $(CCLD) $(gsnap_ssse3_CFLAGS) \
$(CFLAGS) $(gsnap_ssse3_LDFLAGS) $(LDFLAGS) -o $@
-am__objects_26 = gsnapl-cpuid.$(OBJEXT) gsnapl-gsnapl_select.$(OBJEXT)
-dist_gsnapl_OBJECTS = $(am__objects_26)
+am__objects_27 = gsnapl-cpuid.$(OBJEXT) gsnapl-gsnapl_select.$(OBJEXT)
+dist_gsnapl_OBJECTS = $(am__objects_27)
gsnapl_OBJECTS = $(dist_gsnapl_OBJECTS)
gsnapl_DEPENDENCIES =
gsnapl_LINK = $(LIBTOOL) $(AM_V_lt) --tag=CC $(AM_LIBTOOLFLAGS) \
$(LIBTOOLFLAGS) --mode=link $(CCLD) $(gsnapl_CFLAGS) $(CFLAGS) \
$(gsnapl_LDFLAGS) $(LDFLAGS) -o $@
-am__objects_27 = gsnapl_avx2-except.$(OBJEXT) \
+am__objects_28 = gsnapl_avx2-except.$(OBJEXT) \
gsnapl_avx2-assert.$(OBJEXT) gsnapl_avx2-mem.$(OBJEXT) \
gsnapl_avx2-intlist.$(OBJEXT) gsnapl_avx2-list.$(OBJEXT) \
gsnapl_avx2-littleendian.$(OBJEXT) \
@@ -1505,14 +1512,14 @@ am__objects_27 = gsnapl_avx2-except.$(OBJEXT) \
gsnapl_avx2-outbuffer.$(OBJEXT) gsnapl_avx2-datadir.$(OBJEXT) \
gsnapl_avx2-parserange.$(OBJEXT) gsnapl_avx2-getopt.$(OBJEXT) \
gsnapl_avx2-getopt1.$(OBJEXT) gsnapl_avx2-gsnap.$(OBJEXT)
-dist_gsnapl_avx2_OBJECTS = $(am__objects_27)
+dist_gsnapl_avx2_OBJECTS = $(am__objects_28)
gsnapl_avx2_OBJECTS = $(dist_gsnapl_avx2_OBJECTS)
gsnapl_avx2_DEPENDENCIES = $(am__DEPENDENCIES_1) $(am__DEPENDENCIES_1) \
$(am__DEPENDENCIES_1)
gsnapl_avx2_LINK = $(LIBTOOL) $(AM_V_lt) --tag=CC $(AM_LIBTOOLFLAGS) \
$(LIBTOOLFLAGS) --mode=link $(CCLD) $(gsnapl_avx2_CFLAGS) \
$(CFLAGS) $(gsnapl_avx2_LDFLAGS) $(LDFLAGS) -o $@
-am__objects_28 = gsnapl_nosimd-except.$(OBJEXT) \
+am__objects_29 = gsnapl_nosimd-except.$(OBJEXT) \
gsnapl_nosimd-assert.$(OBJEXT) gsnapl_nosimd-mem.$(OBJEXT) \
gsnapl_nosimd-intlist.$(OBJEXT) gsnapl_nosimd-list.$(OBJEXT) \
gsnapl_nosimd-littleendian.$(OBJEXT) \
@@ -1585,14 +1592,14 @@ am__objects_28 = gsnapl_nosimd-except.$(OBJEXT) \
gsnapl_nosimd-parserange.$(OBJEXT) \
gsnapl_nosimd-getopt.$(OBJEXT) gsnapl_nosimd-getopt1.$(OBJEXT) \
gsnapl_nosimd-gsnap.$(OBJEXT)
-dist_gsnapl_nosimd_OBJECTS = $(am__objects_28)
+dist_gsnapl_nosimd_OBJECTS = $(am__objects_29)
gsnapl_nosimd_OBJECTS = $(dist_gsnapl_nosimd_OBJECTS)
gsnapl_nosimd_DEPENDENCIES = $(am__DEPENDENCIES_1) \
$(am__DEPENDENCIES_1) $(am__DEPENDENCIES_1)
gsnapl_nosimd_LINK = $(LIBTOOL) $(AM_V_lt) --tag=CC $(AM_LIBTOOLFLAGS) \
$(LIBTOOLFLAGS) --mode=link $(CCLD) $(gsnapl_nosimd_CFLAGS) \
$(CFLAGS) $(gsnapl_nosimd_LDFLAGS) $(LDFLAGS) -o $@
-am__objects_29 = gsnapl_sse2-except.$(OBJEXT) \
+am__objects_30 = gsnapl_sse2-except.$(OBJEXT) \
gsnapl_sse2-assert.$(OBJEXT) gsnapl_sse2-mem.$(OBJEXT) \
gsnapl_sse2-intlist.$(OBJEXT) gsnapl_sse2-list.$(OBJEXT) \
gsnapl_sse2-littleendian.$(OBJEXT) \
@@ -1649,14 +1656,14 @@ am__objects_29 = gsnapl_sse2-except.$(OBJEXT) \
gsnapl_sse2-outbuffer.$(OBJEXT) gsnapl_sse2-datadir.$(OBJEXT) \
gsnapl_sse2-parserange.$(OBJEXT) gsnapl_sse2-getopt.$(OBJEXT) \
gsnapl_sse2-getopt1.$(OBJEXT) gsnapl_sse2-gsnap.$(OBJEXT)
-dist_gsnapl_sse2_OBJECTS = $(am__objects_29)
+dist_gsnapl_sse2_OBJECTS = $(am__objects_30)
gsnapl_sse2_OBJECTS = $(dist_gsnapl_sse2_OBJECTS)
gsnapl_sse2_DEPENDENCIES = $(am__DEPENDENCIES_1) $(am__DEPENDENCIES_1) \
$(am__DEPENDENCIES_1)
gsnapl_sse2_LINK = $(LIBTOOL) $(AM_V_lt) --tag=CC $(AM_LIBTOOLFLAGS) \
$(LIBTOOLFLAGS) --mode=link $(CCLD) $(gsnapl_sse2_CFLAGS) \
$(CFLAGS) $(gsnapl_sse2_LDFLAGS) $(LDFLAGS) -o $@
-am__objects_30 = gsnapl_sse41-except.$(OBJEXT) \
+am__objects_31 = gsnapl_sse41-except.$(OBJEXT) \
gsnapl_sse41-assert.$(OBJEXT) gsnapl_sse41-mem.$(OBJEXT) \
gsnapl_sse41-intlist.$(OBJEXT) gsnapl_sse41-list.$(OBJEXT) \
gsnapl_sse41-littleendian.$(OBJEXT) \
@@ -1722,14 +1729,14 @@ am__objects_30 = gsnapl_sse41-except.$(OBJEXT) \
gsnapl_sse41-parserange.$(OBJEXT) \
gsnapl_sse41-getopt.$(OBJEXT) gsnapl_sse41-getopt1.$(OBJEXT) \
gsnapl_sse41-gsnap.$(OBJEXT)
-dist_gsnapl_sse41_OBJECTS = $(am__objects_30)
+dist_gsnapl_sse41_OBJECTS = $(am__objects_31)
gsnapl_sse41_OBJECTS = $(dist_gsnapl_sse41_OBJECTS)
gsnapl_sse41_DEPENDENCIES = $(am__DEPENDENCIES_1) \
$(am__DEPENDENCIES_1) $(am__DEPENDENCIES_1)
gsnapl_sse41_LINK = $(LIBTOOL) $(AM_V_lt) --tag=CC $(AM_LIBTOOLFLAGS) \
$(LIBTOOLFLAGS) --mode=link $(CCLD) $(gsnapl_sse41_CFLAGS) \
$(CFLAGS) $(gsnapl_sse41_LDFLAGS) $(LDFLAGS) -o $@
-am__objects_31 = gsnapl_sse42-except.$(OBJEXT) \
+am__objects_32 = gsnapl_sse42-except.$(OBJEXT) \
gsnapl_sse42-assert.$(OBJEXT) gsnapl_sse42-mem.$(OBJEXT) \
gsnapl_sse42-intlist.$(OBJEXT) gsnapl_sse42-list.$(OBJEXT) \
gsnapl_sse42-littleendian.$(OBJEXT) \
@@ -1795,14 +1802,14 @@ am__objects_31 = gsnapl_sse42-except.$(OBJEXT) \
gsnapl_sse42-parserange.$(OBJEXT) \
gsnapl_sse42-getopt.$(OBJEXT) gsnapl_sse42-getopt1.$(OBJEXT) \
gsnapl_sse42-gsnap.$(OBJEXT)
-dist_gsnapl_sse42_OBJECTS = $(am__objects_31)
+dist_gsnapl_sse42_OBJECTS = $(am__objects_32)
gsnapl_sse42_OBJECTS = $(dist_gsnapl_sse42_OBJECTS)
gsnapl_sse42_DEPENDENCIES = $(am__DEPENDENCIES_1) \
$(am__DEPENDENCIES_1) $(am__DEPENDENCIES_1)
gsnapl_sse42_LINK = $(LIBTOOL) $(AM_V_lt) --tag=CC $(AM_LIBTOOLFLAGS) \
$(LIBTOOLFLAGS) --mode=link $(CCLD) $(gsnapl_sse42_CFLAGS) \
$(CFLAGS) $(gsnapl_sse42_LDFLAGS) $(LDFLAGS) -o $@
-am__objects_32 = gsnapl_ssse3-except.$(OBJEXT) \
+am__objects_33 = gsnapl_ssse3-except.$(OBJEXT) \
gsnapl_ssse3-assert.$(OBJEXT) gsnapl_ssse3-mem.$(OBJEXT) \
gsnapl_ssse3-intlist.$(OBJEXT) gsnapl_ssse3-list.$(OBJEXT) \
gsnapl_ssse3-littleendian.$(OBJEXT) \
@@ -1868,14 +1875,14 @@ am__objects_32 = gsnapl_ssse3-except.$(OBJEXT) \
gsnapl_ssse3-parserange.$(OBJEXT) \
gsnapl_ssse3-getopt.$(OBJEXT) gsnapl_ssse3-getopt1.$(OBJEXT) \
gsnapl_ssse3-gsnap.$(OBJEXT)
-dist_gsnapl_ssse3_OBJECTS = $(am__objects_32)
+dist_gsnapl_ssse3_OBJECTS = $(am__objects_33)
gsnapl_ssse3_OBJECTS = $(dist_gsnapl_ssse3_OBJECTS)
gsnapl_ssse3_DEPENDENCIES = $(am__DEPENDENCIES_1) \
$(am__DEPENDENCIES_1) $(am__DEPENDENCIES_1)
gsnapl_ssse3_LINK = $(LIBTOOL) $(AM_V_lt) --tag=CC $(AM_LIBTOOLFLAGS) \
$(LIBTOOLFLAGS) --mode=link $(CCLD) $(gsnapl_ssse3_CFLAGS) \
$(CFLAGS) $(gsnapl_ssse3_LDFLAGS) $(LDFLAGS) -o $@
-am__objects_33 = iit_dump-except.$(OBJEXT) iit_dump-assert.$(OBJEXT) \
+am__objects_34 = iit_dump-except.$(OBJEXT) iit_dump-assert.$(OBJEXT) \
iit_dump-mem.$(OBJEXT) iit_dump-littleendian.$(OBJEXT) \
iit_dump-bigendian.$(OBJEXT) iit_dump-intlist.$(OBJEXT) \
iit_dump-list.$(OBJEXT) iit_dump-univinterval.$(OBJEXT) \
@@ -1885,13 +1892,13 @@ am__objects_33 = iit_dump-except.$(OBJEXT) iit_dump-assert.$(OBJEXT) \
iit_dump-iit-read-univ.$(OBJEXT) iit_dump-iit-read.$(OBJEXT) \
iit_dump-parserange.$(OBJEXT) iit_dump-getopt.$(OBJEXT) \
iit_dump-getopt1.$(OBJEXT) iit_dump-iit_dump.$(OBJEXT)
-dist_iit_dump_OBJECTS = $(am__objects_33)
+dist_iit_dump_OBJECTS = $(am__objects_34)
iit_dump_OBJECTS = $(dist_iit_dump_OBJECTS)
iit_dump_DEPENDENCIES = $(am__DEPENDENCIES_1)
iit_dump_LINK = $(LIBTOOL) $(AM_V_lt) --tag=CC $(AM_LIBTOOLFLAGS) \
$(LIBTOOLFLAGS) --mode=link $(CCLD) $(iit_dump_CFLAGS) \
$(CFLAGS) $(iit_dump_LDFLAGS) $(LDFLAGS) -o $@
-am__objects_34 = iit_get-except.$(OBJEXT) iit_get-assert.$(OBJEXT) \
+am__objects_35 = iit_get-except.$(OBJEXT) iit_get-assert.$(OBJEXT) \
iit_get-mem.$(OBJEXT) iit_get-intlist.$(OBJEXT) \
iit_get-list.$(OBJEXT) iit_get-littleendian.$(OBJEXT) \
iit_get-bigendian.$(OBJEXT) iit_get-univinterval.$(OBJEXT) \
@@ -1901,13 +1908,13 @@ am__objects_34 = iit_get-except.$(OBJEXT) iit_get-assert.$(OBJEXT) \
iit_get-iit-read-univ.$(OBJEXT) iit_get-iit-read.$(OBJEXT) \
iit_get-parserange.$(OBJEXT) iit_get-getopt.$(OBJEXT) \
iit_get-getopt1.$(OBJEXT) iit_get-iit_get.$(OBJEXT)
-dist_iit_get_OBJECTS = $(am__objects_34)
+dist_iit_get_OBJECTS = $(am__objects_35)
iit_get_OBJECTS = $(dist_iit_get_OBJECTS)
iit_get_DEPENDENCIES = $(am__DEPENDENCIES_1)
iit_get_LINK = $(LIBTOOL) $(AM_V_lt) --tag=CC $(AM_LIBTOOLFLAGS) \
$(LIBTOOLFLAGS) --mode=link $(CCLD) $(iit_get_CFLAGS) \
$(CFLAGS) $(iit_get_LDFLAGS) $(LDFLAGS) -o $@
-am__objects_35 = iit_store-except.$(OBJEXT) iit_store-assert.$(OBJEXT) \
+am__objects_36 = iit_store-except.$(OBJEXT) iit_store-assert.$(OBJEXT) \
iit_store-mem.$(OBJEXT) iit_store-intlist.$(OBJEXT) \
iit_store-list.$(OBJEXT) iit_store-littleendian.$(OBJEXT) \
iit_store-bigendian.$(OBJEXT) iit_store-univinterval.$(OBJEXT) \
@@ -1919,13 +1926,13 @@ am__objects_35 = iit_store-except.$(OBJEXT) iit_store-assert.$(OBJEXT) \
iit_store-table.$(OBJEXT) iit_store-chrom.$(OBJEXT) \
iit_store-getopt.$(OBJEXT) iit_store-getopt1.$(OBJEXT) \
iit_store-iit_store.$(OBJEXT)
-dist_iit_store_OBJECTS = $(am__objects_35)
+dist_iit_store_OBJECTS = $(am__objects_36)
iit_store_OBJECTS = $(dist_iit_store_OBJECTS)
iit_store_DEPENDENCIES = $(am__DEPENDENCIES_1)
iit_store_LINK = $(LIBTOOL) $(AM_V_lt) --tag=CC $(AM_LIBTOOLFLAGS) \
$(LIBTOOLFLAGS) --mode=link $(CCLD) $(iit_store_CFLAGS) \
$(CFLAGS) $(iit_store_LDFLAGS) $(LDFLAGS) -o $@
-am__objects_36 = sam_sort-except.$(OBJEXT) sam_sort-assert.$(OBJEXT) \
+am__objects_37 = sam_sort-except.$(OBJEXT) sam_sort-assert.$(OBJEXT) \
sam_sort-mem.$(OBJEXT) sam_sort-littleendian.$(OBJEXT) \
sam_sort-bigendian.$(OBJEXT) sam_sort-intlist.$(OBJEXT) \
sam_sort-list.$(OBJEXT) sam_sort-stopwatch.$(OBJEXT) \
@@ -1937,13 +1944,13 @@ am__objects_36 = sam_sort-except.$(OBJEXT) sam_sort-assert.$(OBJEXT) \
sam_sort-samread.$(OBJEXT) sam_sort-datadir.$(OBJEXT) \
sam_sort-getopt.$(OBJEXT) sam_sort-getopt1.$(OBJEXT) \
sam_sort-sam_sort.$(OBJEXT)
-dist_sam_sort_OBJECTS = $(am__objects_36)
+dist_sam_sort_OBJECTS = $(am__objects_37)
sam_sort_OBJECTS = $(dist_sam_sort_OBJECTS)
sam_sort_DEPENDENCIES = $(am__DEPENDENCIES_1)
sam_sort_LINK = $(LIBTOOL) $(AM_V_lt) --tag=CC $(AM_LIBTOOLFLAGS) \
$(LIBTOOLFLAGS) --mode=link $(CCLD) $(sam_sort_CFLAGS) \
$(CFLAGS) $(sam_sort_LDFLAGS) $(LDFLAGS) -o $@
-am__objects_37 = snpindex-except.$(OBJEXT) snpindex-assert.$(OBJEXT) \
+am__objects_38 = snpindex-except.$(OBJEXT) snpindex-assert.$(OBJEXT) \
snpindex-mem.$(OBJEXT) snpindex-intlist.$(OBJEXT) \
snpindex-list.$(OBJEXT) snpindex-littleendian.$(OBJEXT) \
snpindex-bigendian.$(OBJEXT) snpindex-univinterval.$(OBJEXT) \
@@ -1965,14 +1972,14 @@ am__objects_37 = snpindex-except.$(OBJEXT) snpindex-assert.$(OBJEXT) \
snpindex-datadir.$(OBJEXT) snpindex-parserange.$(OBJEXT) \
snpindex-getopt.$(OBJEXT) snpindex-getopt1.$(OBJEXT) \
snpindex-snpindex.$(OBJEXT)
-dist_snpindex_OBJECTS = $(am__objects_37)
+dist_snpindex_OBJECTS = $(am__objects_38)
snpindex_OBJECTS = $(dist_snpindex_OBJECTS)
snpindex_DEPENDENCIES = $(am__DEPENDENCIES_1) $(am__DEPENDENCIES_1) \
$(am__DEPENDENCIES_1)
snpindex_LINK = $(LIBTOOL) $(AM_V_lt) --tag=CC $(AM_LIBTOOLFLAGS) \
$(LIBTOOLFLAGS) --mode=link $(CCLD) $(snpindex_CFLAGS) \
$(CFLAGS) $(snpindex_LDFLAGS) $(LDFLAGS) -o $@
-am__objects_38 = uniqscan-except.$(OBJEXT) uniqscan-assert.$(OBJEXT) \
+am__objects_39 = uniqscan-except.$(OBJEXT) uniqscan-assert.$(OBJEXT) \
uniqscan-mem.$(OBJEXT) uniqscan-intlist.$(OBJEXT) \
uniqscan-list.$(OBJEXT) uniqscan-littleendian.$(OBJEXT) \
uniqscan-bigendian.$(OBJEXT) uniqscan-univinterval.$(OBJEXT) \
@@ -2017,14 +2024,14 @@ am__objects_38 = uniqscan-except.$(OBJEXT) uniqscan-assert.$(OBJEXT) \
uniqscan-resulthr.$(OBJEXT) uniqscan-datadir.$(OBJEXT) \
uniqscan-parserange.$(OBJEXT) uniqscan-getopt.$(OBJEXT) \
uniqscan-getopt1.$(OBJEXT) uniqscan-uniqscan.$(OBJEXT)
-dist_uniqscan_OBJECTS = $(am__objects_38)
+dist_uniqscan_OBJECTS = $(am__objects_39)
uniqscan_OBJECTS = $(dist_uniqscan_OBJECTS)
uniqscan_DEPENDENCIES = $(am__DEPENDENCIES_1) $(am__DEPENDENCIES_1) \
$(am__DEPENDENCIES_1)
uniqscan_LINK = $(LIBTOOL) $(AM_V_lt) --tag=CC $(AM_LIBTOOLFLAGS) \
$(LIBTOOLFLAGS) --mode=link $(CCLD) $(uniqscan_CFLAGS) \
$(CFLAGS) $(uniqscan_LDFLAGS) $(LDFLAGS) -o $@
-am__objects_39 = uniqscanl-except.$(OBJEXT) uniqscanl-assert.$(OBJEXT) \
+am__objects_40 = uniqscanl-except.$(OBJEXT) uniqscanl-assert.$(OBJEXT) \
uniqscanl-mem.$(OBJEXT) uniqscanl-intlist.$(OBJEXT) \
uniqscanl-list.$(OBJEXT) uniqscanl-littleendian.$(OBJEXT) \
uniqscanl-bigendian.$(OBJEXT) uniqscanl-univinterval.$(OBJEXT) \
@@ -2072,7 +2079,7 @@ am__objects_39 = uniqscanl-except.$(OBJEXT) uniqscanl-assert.$(OBJEXT) \
uniqscanl-datadir.$(OBJEXT) uniqscanl-parserange.$(OBJEXT) \
uniqscanl-getopt.$(OBJEXT) uniqscanl-getopt1.$(OBJEXT) \
uniqscanl-uniqscan.$(OBJEXT)
-dist_uniqscanl_OBJECTS = $(am__objects_39)
+dist_uniqscanl_OBJECTS = $(am__objects_40)
uniqscanl_OBJECTS = $(dist_uniqscanl_OBJECTS)
uniqscanl_DEPENDENCIES = $(am__DEPENDENCIES_1) $(am__DEPENDENCIES_1) \
$(am__DEPENDENCIES_1)
@@ -2114,45 +2121,45 @@ am__v_CCLD_ = $(am__v_CCLD_ at AM_DEFAULT_V@)
am__v_CCLD_0 = @echo " CCLD " $@;
am__v_CCLD_1 =
SOURCES = $(dist_atoiindex_SOURCES) $(dist_cmetindex_SOURCES) \
- $(dist_get_genome_SOURCES) $(dist_gmap_SOURCES) \
- $(dist_gmap_avx2_SOURCES) $(dist_gmap_nosimd_SOURCES) \
- $(dist_gmap_sse2_SOURCES) $(dist_gmap_sse41_SOURCES) \
- $(dist_gmap_sse42_SOURCES) $(dist_gmap_ssse3_SOURCES) \
- $(dist_gmapindex_SOURCES) $(dist_gmapl_SOURCES) \
- $(dist_gmapl_avx2_SOURCES) $(dist_gmapl_nosimd_SOURCES) \
- $(dist_gmapl_sse2_SOURCES) $(dist_gmapl_sse41_SOURCES) \
- $(dist_gmapl_sse42_SOURCES) $(dist_gmapl_ssse3_SOURCES) \
- $(dist_gsnap_SOURCES) $(dist_gsnap_avx2_SOURCES) \
- $(dist_gsnap_nosimd_SOURCES) $(dist_gsnap_sse2_SOURCES) \
- $(dist_gsnap_sse41_SOURCES) $(dist_gsnap_sse42_SOURCES) \
- $(dist_gsnap_ssse3_SOURCES) $(dist_gsnapl_SOURCES) \
- $(dist_gsnapl_avx2_SOURCES) $(dist_gsnapl_nosimd_SOURCES) \
- $(dist_gsnapl_sse2_SOURCES) $(dist_gsnapl_sse41_SOURCES) \
- $(dist_gsnapl_sse42_SOURCES) $(dist_gsnapl_ssse3_SOURCES) \
- $(dist_iit_dump_SOURCES) $(dist_iit_get_SOURCES) \
- $(dist_iit_store_SOURCES) $(dist_sam_sort_SOURCES) \
- $(dist_snpindex_SOURCES) $(dist_uniqscan_SOURCES) \
- $(dist_uniqscanl_SOURCES)
+ $(dist_cpuid_SOURCES) $(dist_get_genome_SOURCES) \
+ $(dist_gmap_SOURCES) $(dist_gmap_avx2_SOURCES) \
+ $(dist_gmap_nosimd_SOURCES) $(dist_gmap_sse2_SOURCES) \
+ $(dist_gmap_sse41_SOURCES) $(dist_gmap_sse42_SOURCES) \
+ $(dist_gmap_ssse3_SOURCES) $(dist_gmapindex_SOURCES) \
+ $(dist_gmapl_SOURCES) $(dist_gmapl_avx2_SOURCES) \
+ $(dist_gmapl_nosimd_SOURCES) $(dist_gmapl_sse2_SOURCES) \
+ $(dist_gmapl_sse41_SOURCES) $(dist_gmapl_sse42_SOURCES) \
+ $(dist_gmapl_ssse3_SOURCES) $(dist_gsnap_SOURCES) \
+ $(dist_gsnap_avx2_SOURCES) $(dist_gsnap_nosimd_SOURCES) \
+ $(dist_gsnap_sse2_SOURCES) $(dist_gsnap_sse41_SOURCES) \
+ $(dist_gsnap_sse42_SOURCES) $(dist_gsnap_ssse3_SOURCES) \
+ $(dist_gsnapl_SOURCES) $(dist_gsnapl_avx2_SOURCES) \
+ $(dist_gsnapl_nosimd_SOURCES) $(dist_gsnapl_sse2_SOURCES) \
+ $(dist_gsnapl_sse41_SOURCES) $(dist_gsnapl_sse42_SOURCES) \
+ $(dist_gsnapl_ssse3_SOURCES) $(dist_iit_dump_SOURCES) \
+ $(dist_iit_get_SOURCES) $(dist_iit_store_SOURCES) \
+ $(dist_sam_sort_SOURCES) $(dist_snpindex_SOURCES) \
+ $(dist_uniqscan_SOURCES) $(dist_uniqscanl_SOURCES)
DIST_SOURCES = $(dist_atoiindex_SOURCES) $(dist_cmetindex_SOURCES) \
- $(dist_get_genome_SOURCES) $(dist_gmap_SOURCES) \
- $(dist_gmap_avx2_SOURCES) $(dist_gmap_nosimd_SOURCES) \
- $(dist_gmap_sse2_SOURCES) $(dist_gmap_sse41_SOURCES) \
- $(dist_gmap_sse42_SOURCES) $(dist_gmap_ssse3_SOURCES) \
- $(dist_gmapindex_SOURCES) $(dist_gmapl_SOURCES) \
- $(dist_gmapl_avx2_SOURCES) $(dist_gmapl_nosimd_SOURCES) \
- $(dist_gmapl_sse2_SOURCES) $(dist_gmapl_sse41_SOURCES) \
- $(dist_gmapl_sse42_SOURCES) $(dist_gmapl_ssse3_SOURCES) \
- $(dist_gsnap_SOURCES) $(dist_gsnap_avx2_SOURCES) \
- $(dist_gsnap_nosimd_SOURCES) $(dist_gsnap_sse2_SOURCES) \
- $(dist_gsnap_sse41_SOURCES) $(dist_gsnap_sse42_SOURCES) \
- $(dist_gsnap_ssse3_SOURCES) $(dist_gsnapl_SOURCES) \
- $(dist_gsnapl_avx2_SOURCES) $(dist_gsnapl_nosimd_SOURCES) \
- $(dist_gsnapl_sse2_SOURCES) $(dist_gsnapl_sse41_SOURCES) \
- $(dist_gsnapl_sse42_SOURCES) $(dist_gsnapl_ssse3_SOURCES) \
- $(dist_iit_dump_SOURCES) $(dist_iit_get_SOURCES) \
- $(dist_iit_store_SOURCES) $(dist_sam_sort_SOURCES) \
- $(dist_snpindex_SOURCES) $(dist_uniqscan_SOURCES) \
- $(dist_uniqscanl_SOURCES)
+ $(dist_cpuid_SOURCES) $(dist_get_genome_SOURCES) \
+ $(dist_gmap_SOURCES) $(dist_gmap_avx2_SOURCES) \
+ $(dist_gmap_nosimd_SOURCES) $(dist_gmap_sse2_SOURCES) \
+ $(dist_gmap_sse41_SOURCES) $(dist_gmap_sse42_SOURCES) \
+ $(dist_gmap_ssse3_SOURCES) $(dist_gmapindex_SOURCES) \
+ $(dist_gmapl_SOURCES) $(dist_gmapl_avx2_SOURCES) \
+ $(dist_gmapl_nosimd_SOURCES) $(dist_gmapl_sse2_SOURCES) \
+ $(dist_gmapl_sse41_SOURCES) $(dist_gmapl_sse42_SOURCES) \
+ $(dist_gmapl_ssse3_SOURCES) $(dist_gsnap_SOURCES) \
+ $(dist_gsnap_avx2_SOURCES) $(dist_gsnap_nosimd_SOURCES) \
+ $(dist_gsnap_sse2_SOURCES) $(dist_gsnap_sse41_SOURCES) \
+ $(dist_gsnap_sse42_SOURCES) $(dist_gsnap_ssse3_SOURCES) \
+ $(dist_gsnapl_SOURCES) $(dist_gsnapl_avx2_SOURCES) \
+ $(dist_gsnapl_nosimd_SOURCES) $(dist_gsnapl_sse2_SOURCES) \
+ $(dist_gsnapl_sse41_SOURCES) $(dist_gsnapl_sse42_SOURCES) \
+ $(dist_gsnapl_ssse3_SOURCES) $(dist_iit_dump_SOURCES) \
+ $(dist_iit_get_SOURCES) $(dist_iit_store_SOURCES) \
+ $(dist_sam_sort_SOURCES) $(dist_snpindex_SOURCES) \
+ $(dist_uniqscan_SOURCES) $(dist_uniqscanl_SOURCES)
am__can_run_installinfo = \
case $$AM_UPDATE_INFO_DIR in \
n|no|NO) false;; \
@@ -2326,6 +2333,12 @@ CLEANFILES = fa_coords gmap_process
# Include master.c and master.h, so they get included in distribution
EXTRA_DIST = mpidebug.c mpidebug.h master.c master.h
+CPUID_FILES = bool.h cpuid.c cpuid.h
+cpuid_CC = $(CC)
+cpuid_CFLAGS = $(AM_CFLAGS) -DMAIN=1
+cpuid_LDFLAGS = $(AM_LDFLAGS)
+cpuid_LDADD =
+dist_cpuid_SOURCES = $(CPUID_FILES)
GMAP_SELECT_FILES = bool.h cpuid.c cpuid.h gmap_select.c
gmap_CC = $(CC)
gmap_CFLAGS = $(AM_CFLAGS)
@@ -3013,6 +3026,10 @@ cmetindex$(EXEEXT): $(cmetindex_OBJECTS) $(cmetindex_DEPENDENCIES) $(EXTRA_cmeti
@rm -f cmetindex$(EXEEXT)
$(AM_V_CCLD)$(cmetindex_LINK) $(cmetindex_OBJECTS) $(cmetindex_LDADD) $(LIBS)
+cpuid$(EXEEXT): $(cpuid_OBJECTS) $(cpuid_DEPENDENCIES) $(EXTRA_cpuid_DEPENDENCIES)
+ @rm -f cpuid$(EXEEXT)
+ $(AM_V_CCLD)$(cpuid_LINK) $(cpuid_OBJECTS) $(cpuid_LDADD) $(LIBS)
+
get-genome$(EXEEXT): $(get_genome_OBJECTS) $(get_genome_DEPENDENCIES) $(EXTRA_get_genome_DEPENDENCIES)
@rm -f get-genome$(EXEEXT)
$(AM_V_CCLD)$(get_genome_LINK) $(get_genome_OBJECTS) $(get_genome_LDADD) $(LIBS)
@@ -3251,6 +3268,7 @@ distclean-compile:
@AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/cmetindex-uint8list.Po at am__quote@
@AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/cmetindex-uintlist.Po at am__quote@
@AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/cmetindex-univinterval.Po at am__quote@
+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/cpuid-cpuid.Po at am__quote@
@AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/get_genome-access.Po at am__quote@
@AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/get_genome-assert.Po at am__quote@
@AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/get_genome-bigendian.Po at am__quote@
@@ -6894,6 +6912,20 @@ cmetindex-cmetindex.obj: cmetindex.c
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(AM_V_CC at am__nodep@)$(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(cmetindex_CFLAGS) $(CFLAGS) -c -o cmetindex-cmetindex.obj `if test -f 'cmetindex.c'; then $(CYGPATH_W) 'cmetindex.c'; else $(CYGPATH_W) '$(srcdir)/cmetindex.c'; fi`
+cpuid-cpuid.o: cpuid.c
+ at am__fastdepCC_TRUE@ $(AM_V_CC)$(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(cpuid_CFLAGS) $(CFLAGS) -MT cpuid-cpuid.o -MD -MP -MF $(DEPDIR)/cpuid-cpuid.Tpo -c -o cpuid-cpuid.o `test -f 'cpuid.c' || echo '$(srcdir)/'`cpuid.c
+ at am__fastdepCC_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/cpuid-cpuid.Tpo $(DEPDIR)/cpuid-cpuid.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ $(AM_V_CC)source='cpuid.c' object='cpuid-cpuid.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(AM_V_CC at am__nodep@)$(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(cpuid_CFLAGS) $(CFLAGS) -c -o cpuid-cpuid.o `test -f 'cpuid.c' || echo '$(srcdir)/'`cpuid.c
+
+cpuid-cpuid.obj: cpuid.c
+ at am__fastdepCC_TRUE@ $(AM_V_CC)$(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(cpuid_CFLAGS) $(CFLAGS) -MT cpuid-cpuid.obj -MD -MP -MF $(DEPDIR)/cpuid-cpuid.Tpo -c -o cpuid-cpuid.obj `if test -f 'cpuid.c'; then $(CYGPATH_W) 'cpuid.c'; else $(CYGPATH_W) '$(srcdir)/cpuid.c'; fi`
+ at am__fastdepCC_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/cpuid-cpuid.Tpo $(DEPDIR)/cpuid-cpuid.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ $(AM_V_CC)source='cpuid.c' object='cpuid-cpuid.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(AM_V_CC at am__nodep@)$(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(cpuid_CFLAGS) $(CFLAGS) -c -o cpuid-cpuid.obj `if test -f 'cpuid.c'; then $(CYGPATH_W) 'cpuid.c'; else $(CYGPATH_W) '$(srcdir)/cpuid.c'; fi`
+
get_genome-except.o: except.c
@am__fastdepCC_TRUE@ $(AM_V_CC)$(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(get_genome_CFLAGS) $(CFLAGS) -MT get_genome-except.o -MD -MP -MF $(DEPDIR)/get_genome-except.Tpo -c -o get_genome-except.o `test -f 'except.c' || echo '$(srcdir)/'`except.c
@am__fastdepCC_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/get_genome-except.Tpo $(DEPDIR)/get_genome-except.Po
diff --git a/src/cpuid.c b/src/cpuid.c
index e533604..45d722e 100644
--- a/src/cpuid.c
+++ b/src/cpuid.c
@@ -1,4 +1,4 @@
-static char rcsid[] = "$Id: cpuid.c 190435 2016-05-24 21:33:24Z twu $";
+static char rcsid[] = "$Id: cpuid.c 191640 2016-06-09 22:32:52Z twu $";
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
@@ -93,6 +93,10 @@ CPUID_support (bool *sse2_support_p, bool *ssse3_support_p, bool *sse4_1_support
run_cpuid(1, 0, abcd);
+#ifdef MAIN
+ printf("CPUID 1, 0 returns %08X %08X %08X %08X\n",abcd[EAX],abcd[EBX],abcd[ECX],abcd[EDX]);
+#endif
+
*sse2_support_p = ((abcd[EDX] & sse2_mask) == sse2_mask) ? true : false;
*ssse3_support_p = ((abcd[ECX] & ssse3_mask) == ssse3_mask) ? true : false;
*sse4_1_support_p = ((abcd[ECX] & sse4_1_mask) == sse4_1_mask) ? true : false;
@@ -105,10 +109,18 @@ CPUID_support (bool *sse2_support_p, bool *ssse3_support_p, bool *sse4_1_support
*avx2_support_p = false;
} else {
run_cpuid(7, 0, abcd);
+#ifdef MAIN
+ printf("CPUID 7, 0 returns %08X %08X %08X %08X\n",abcd[EAX],abcd[EBX],abcd[ECX],abcd[EDX]);
+#endif
+
if ((abcd[EBX] & avx2_bmi12_mask) != avx2_bmi12_mask) {
*avx2_support_p = false;
} else {
run_cpuid(0x80000001, 0, abcd);
+#ifdef MAIN
+ printf("CPUID 0x80000001, 0 returns %08X %08X %08X %08X\n",abcd[EAX],abcd[EBX],abcd[ECX],abcd[EDX]);
+#endif
+
if ((abcd[ECX] & lzcnt_mask) != lzcnt_mask) {
*avx2_support_p = false;
} else {
@@ -123,3 +135,23 @@ CPUID_support (bool *sse2_support_p, bool *ssse3_support_p, bool *sse4_1_support
#endif /* non-Intel compiler */
+#ifdef MAIN
+int
+main (int argc, char *argv[]) {
+ bool sse2_support_p;
+ bool ssse3_support_p;
+ bool sse4_1_support_p;
+ bool sse4_2_support_p;
+ bool avx2_support_p;
+
+ CPUID_support(&sse2_support_p,&ssse3_support_p,&sse4_1_support_p,&sse4_2_support_p,&avx2_support_p);
+
+ printf("sse2 support: %d\n",sse2_support_p);
+ printf("ssse3 support: %d\n",ssse3_support_p);
+ printf("sse4.1 support: %d\n",sse4_1_support_p);
+ printf("sse4.2 support: %d\n",sse4_2_support_p);
+ printf("avx2 support: %d\n",avx2_support_p);
+
+ return 0;
+}
+#endif
diff --git a/src/sarray-read.c b/src/sarray-read.c
index b55b8fa..321510b 100644
--- a/src/sarray-read.c
+++ b/src/sarray-read.c
@@ -1,4 +1,4 @@
-static char rcsid[] = "$Id: sarray-read.c 191132 2016-06-03 17:24:03Z twu $";
+static char rcsid[] = "$Id: sarray-read.c 191632 2016-06-09 22:02:23Z twu $";
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
@@ -2292,7 +2292,7 @@ fill_positions_std (int *npositions, Univcoord_T low_adj, Univcoord_T high_adj,
#ifdef HAVE_ALLOCA
-#if 0 && defined(HAVE_AVX2) && !defined(WORDS_BIGENDIAN)
+#if defined(HAVE_AVX2) && !defined(WORDS_BIGENDIAN)
/* Using pext method, because _mm256_shuffle_epi32 doesn't work well
because it works only within lanes, and MASTER_CONTROL does not extend
@@ -2406,7 +2406,7 @@ fill_positions_filtered_first (Elt_T this, T sarray, Univcoord_T low, Univcoord_
if (mask) {
adjusted = _mm256_sub_epi32(values,adj);
- selector = _pext_u32(univ_selector,mask);
+ selector = _pext_u32(univ_selector,mask); /* Requires compilation with -mbmi2 */
/* 01110110 01010100 00110010 00010000 (32-bit int, univ_selector) */
/* 00000000 00000000 01110101 00110001 (32-bit int, selector), equiv to 0x00007531 */
debug7b(printf("selector: %08X\n",selector));
diff --git a/src/splice.c b/src/splice.c
index 8b9b15e..d08bd47 100644
--- a/src/splice.c
+++ b/src/splice.c
@@ -1,4 +1,4 @@
-static char rcsid[] = "$Id: splice.c 188752 2016-05-01 17:28:22Z twu $";
+static char rcsid[] = "$Id: splice.c 191633 2016-06-09 22:03:28Z twu $";
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
@@ -63,6 +63,30 @@ Splice_setup (int min_shortend_in) {
+#if 0
+/* Copied from stage3.c Used also in splice.c */
+static int
+sufficient_splice_prob_local (int support, int nmatches, int nmismatches, double distal_spliceprob,
+ double medial_spliceprob) {
+ debug3(printf("Checking for sufficient splice prob, based on %d matches, %d mismatches, and support %d\n",
+ nmatches,nmismatches,support));
+ nmatches -= 2*nmismatches;
+ if (nmatches < 0) {
+ return (int) false;
+ } else if (nmatches < 7) {
+ return (distal_spliceprob > 0.95 && medial_spliceprob > 0.90);
+ } else if (nmatches < 11) {
+ return (distal_spliceprob > 0.90 && medial_spliceprob > 0.85);
+ } else if (nmatches < 15) {
+ return (distal_spliceprob > 0.85 && medial_spliceprob > 0.80);
+ } else if (nmatches < 19) {
+ return (distal_spliceprob > 0.50 /*&& medial_spliceprob > 0.50*/);
+ } else {
+ return (int) true;
+ }
+}
+#endif
+
/* Do not compare against true or false */
/* Loosest criterion */
static int
@@ -81,6 +105,8 @@ sufficient_splice_prob_local (int support, int nmismatches, double spliceprob) {
+
+
/* Note: knowni holds joffset + j + 1, so 0 represents no known site
and values greater than 0 represent a known site. Need to subtract
1 to obtain joffset + j. */
@@ -107,6 +133,7 @@ Splice_resolve_sense (int *best_knowni_i, int *best_knowni_j,
int best_nmismatches, nmismatches;
int segmenti_nmismatches, segmentj_nmismatches;
double best_prob, probi, probj;
+ bool sufficient1p, sufficient2p;
int donori_nsites, acceptorj_nsites, antiacceptori_nsites, antidonorj_nsites;
int *donori_positions, *acceptorj_positions, *antiacceptori_positions, *antidonorj_positions;
@@ -210,14 +237,18 @@ Splice_resolve_sense (int *best_knowni_i, int *best_knowni_j,
debug1(printf("nmismatches %d + %d <= best_nmismatches %d\n",segmenti_nmismatches,segmentj_nmismatches,best_nmismatches));
if (donori_knowni[i] >= 0) {
probi = 1.0; /* Needs to be 1.0 for output */
+ sufficient1p = true;
} else {
probi = Maxent_hr_donor_prob(segmenti_left + splice_pos,segmenti_chroffset);
+ sufficient1p = sufficient_splice_prob_local(/*support*/splice_pos,segmenti_nmismatches,probi);
}
if (acceptorj_knowni[j] >= 0) {
probj = 1.0; /* Needs to be 1.0 for output */
+ sufficient2p = true;
} else {
probj = Maxent_hr_acceptor_prob(segmentj_left + splice_pos,segmentj_chroffset);
+ sufficient2p = sufficient_splice_prob_local(/*support*/querylength - splice_pos,segmentj_nmismatches,probj);
}
debug1(
@@ -227,13 +258,7 @@ Splice_resolve_sense (int *best_knowni_i, int *best_knowni_j,
printf("minus antisense splice_pos %d, i.donor %f, j.acceptor %f\n",splice_pos,probi,probj);
});
-
-#if 0
- sufficient1p = sufficient_splice_prob_local(/*support*/splice_pos,segmenti_nmismatches,probi);
- sufficient2p = sufficient_splice_prob_local(/*support*/querylength - splice_pos,segmentj_nmismatches,probj);
-#endif
-
- /* if (sufficient1p && sufficient2p) { */
+ if (sufficient1p && sufficient2p) {
if (nmismatches < best_nmismatches ||
(nmismatches == best_nmismatches && probi + probj > best_prob)) {
/* Success */
@@ -250,7 +275,7 @@ Splice_resolve_sense (int *best_knowni_i, int *best_knowni_j,
*best_nmismatches_i = segmenti_nmismatches;
*best_nmismatches_j = segmentj_nmismatches;
}
- /* } */
+ }
}
i++;
j++;
@@ -329,14 +354,18 @@ Splice_resolve_sense (int *best_knowni_i, int *best_knowni_j,
debug1(printf("nmismatches %d + %d <= best_nmismatches %d\n",segmenti_nmismatches,segmentj_nmismatches,best_nmismatches));
if (antiacceptori_knowni[i] >= 0) {
probi = 1.0; /* Needs to be 1.0 for output */
+ sufficient1p = true;
} else {
probi = Maxent_hr_antiacceptor_prob(segmenti_left + splice_pos,segmenti_chroffset);
+ sufficient1p = sufficient_splice_prob_local(/*support*/splice_pos,segmenti_nmismatches,probi);
}
if (antidonorj_knowni[j] >= 0) {
probj = 1.0; /* Needs to be 1.0 for output */
+ sufficient2p = true;
} else {
probj = Maxent_hr_antidonor_prob(segmentj_left + splice_pos,segmentj_chroffset);
+ sufficient2p = sufficient_splice_prob_local(/*support*/querylength - splice_pos,segmentj_nmismatches,probj);
}
debug1(
@@ -346,12 +375,7 @@ Splice_resolve_sense (int *best_knowni_i, int *best_knowni_j,
printf("minus sense splice_pos %d, j.donor %f, i.acceptor %f\n",splice_pos,probj,probi);
});
-#if 0
- sufficient1p = sufficient_splice_prob_local(/*support*/splice_pos,segmenti_nmismatches,probi);
- sufficient2p = sufficient_splice_prob_local(/*support*/querylength - splice_pos,segmentj_nmismatches,probj);
-#endif
-
- /* if (sufficient1p && sufficient2p) { */
+ if (sufficient1p && sufficient2p) {
if (nmismatches < best_nmismatches ||
(nmismatches == best_nmismatches && probi + probj > best_prob)) {
/* Success */
@@ -368,7 +392,7 @@ Splice_resolve_sense (int *best_knowni_i, int *best_knowni_j,
*best_nmismatches_j = segmentj_nmismatches;
*best_nmismatches_i = segmenti_nmismatches;
}
- /* } */
+ }
}
i++;
j++;
@@ -376,6 +400,8 @@ Splice_resolve_sense (int *best_knowni_i, int *best_knowni_j,
}
}
+ debug1(printf("best_knowni_i is %d and best_knowni_j is %d\n",*best_knowni_i,*best_knowni_j));
+
if (*best_prob_i > 0.95 && *best_prob_j > 0.70) {
debug1(printf("Returning %d with probi %f and probj %f\n",best_splice_pos,*best_prob_i,*best_prob_j));
debug1(printf("nmismatches %d and %d\n",*best_nmismatches_i,*best_nmismatches_j));
@@ -417,6 +443,7 @@ Splice_resolve_antisense (int *best_knowni_i, int *best_knowni_j,
int best_nmismatches, nmismatches;
int segmenti_nmismatches, segmentj_nmismatches;
double best_prob, probi, probj;
+ bool sufficient1p, sufficient2p;
int donori_nsites, acceptorj_nsites, antiacceptori_nsites, antidonorj_nsites;
int *donori_positions, *acceptorj_positions, *antiacceptori_positions, *antidonorj_positions;
@@ -519,14 +546,18 @@ Splice_resolve_antisense (int *best_knowni_i, int *best_knowni_j,
} else if ((nmismatches = segmenti_nmismatches + segmentj_nmismatches) <= best_nmismatches) {
if (donori_knowni[i] >= 0) {
probi = 1.0; /* Needs to be 1.0 for output */
+ sufficient1p = true;
} else {
probi = Maxent_hr_donor_prob(segmenti_left + splice_pos,segmenti_chroffset);
+ sufficient1p = sufficient_splice_prob_local(/*support*/splice_pos,segmenti_nmismatches,probi);
}
if (acceptorj_knowni[j] >= 0) {
probj = 1.0; /* Needs to be 1.0 for output */
+ sufficient2p = true;
} else {
probj = Maxent_hr_acceptor_prob(segmentj_left + splice_pos,segmentj_chroffset);
+ sufficient2p = sufficient_splice_prob_local(/*support*/querylength - splice_pos,segmentj_nmismatches,probj);
}
debug1(
@@ -536,12 +567,7 @@ Splice_resolve_antisense (int *best_knowni_i, int *best_knowni_j,
printf("minus antisense splice_pos %d, i.donor %f, j.acceptor %f\n",splice_pos,probi,probj);
});
-#if 0
- sufficient1p = sufficient_splice_prob_local(/*support*/splice_pos,segmenti_nmismatches,probi);
- sufficient2p = sufficient_splice_prob_local(/*support*/querylength - splice_pos,segmentj_nmismatches,probj);
-#endif
-
- /* if (sufficient1p && sufficient2p) { */
+ if (sufficient1p && sufficient2p) {
if (nmismatches < best_nmismatches ||
(nmismatches == best_nmismatches && probi + probj > best_prob)) {
/* Success */
@@ -558,7 +584,7 @@ Splice_resolve_antisense (int *best_knowni_i, int *best_knowni_j,
*best_nmismatches_i = segmenti_nmismatches;
*best_nmismatches_j = segmentj_nmismatches;
}
- /* } */
+ }
}
i++;
j++;
@@ -636,14 +662,18 @@ Splice_resolve_antisense (int *best_knowni_i, int *best_knowni_j,
} else if ((nmismatches = segmenti_nmismatches + segmentj_nmismatches) <= best_nmismatches) {
if (antiacceptori_knowni[i] >= 0) {
probi = 1.0; /* Needs to be 1.0 for output */
+ sufficient1p = true;
} else {
probi = Maxent_hr_antiacceptor_prob(segmenti_left + splice_pos,segmenti_chroffset);
+ sufficient1p = sufficient_splice_prob_local(/*support*/splice_pos,segmenti_nmismatches,probi);
}
if (antidonorj_knowni[j] >= 0) {
probj = 1.0; /* Needs to be 1.0 for output */
+ sufficient2p = true;
} else {
probj = Maxent_hr_antidonor_prob(segmentj_left + splice_pos,segmentj_chroffset);
+ sufficient2p = sufficient_splice_prob_local(/*support*/querylength - splice_pos,segmentj_nmismatches,probj);
}
debug1(
@@ -653,12 +683,7 @@ Splice_resolve_antisense (int *best_knowni_i, int *best_knowni_j,
printf("minus sense splice_pos %d, j.donor %f, i.acceptor %f\n",splice_pos,probj,probi);
});
-#if 0
- sufficient1p = sufficient_splice_prob_local(/*support*/splice_pos,segmenti_nmismatches,probi);
- sufficient2p = sufficient_splice_prob_local(/*support*/querylength - splice_pos,segmentj_nmismatches,probj);
-#endif
-
- /* if (sufficient1p && sufficient2p) { */
+ if (sufficient1p && sufficient2p) {
if (nmismatches < best_nmismatches ||
(nmismatches == best_nmismatches && probi + probj > best_prob)) {
/* Success */
@@ -675,7 +700,7 @@ Splice_resolve_antisense (int *best_knowni_i, int *best_knowni_j,
*best_nmismatches_j = segmentj_nmismatches;
*best_nmismatches_i = segmenti_nmismatches;
}
- /* } */
+ }
}
i++;
j++;
@@ -683,6 +708,8 @@ Splice_resolve_antisense (int *best_knowni_i, int *best_knowni_j,
}
}
+ debug1(printf("best_knowni_i is %d and best_knowni_j is %d\n",*best_knowni_i,*best_knowni_j));
+
if (*best_prob_i > 0.95 && *best_prob_j > 0.70) {
debug1(printf("Returning %d with probi %f and probj %f\n",best_splice_pos,*best_prob_i,*best_prob_j));
debug1(printf("nmismatches %d and %d\n",*best_nmismatches_i,*best_nmismatches_j));
diff --git a/src/splicetrie.c b/src/splicetrie.c
index d06520b..8e24f16 100644
--- a/src/splicetrie.c
+++ b/src/splicetrie.c
@@ -1,4 +1,4 @@
-static char rcsid[] = "$Id: splicetrie.c 184475 2016-02-18 00:13:10Z twu $";
+static char rcsid[] = "$Id: splicetrie.c 191634 2016-06-09 22:03:50Z twu $";
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
@@ -200,7 +200,7 @@ Splicetrie_splicesite_p (Univcoord_T left, int pos5, int pos3) {
/* 1/n: Go second to start block */
splicesitep = splicecomp[startblocki];
splicesitep = clear_start(splicesitep,startdiscard);
- debug4(printf("adding start mask %08X\n",clear_start_mask(startdiscard)));
+ /* debug4(printf("adding start mask %08X\n",clear_start_mask(startdiscard))); */
return (splicesitep ? true : false);
diff --git a/src/stage3.c b/src/stage3.c
index ffa2bdb..23ec75c 100644
--- a/src/stage3.c
+++ b/src/stage3.c
@@ -1,4 +1,4 @@
-static char rcsid[] = "$Id: stage3.c 190429 2016-05-24 21:28:28Z twu $";
+static char rcsid[] = "$Id: stage3.c 191630 2016-06-09 22:00:21Z twu $";
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
@@ -3500,7 +3500,7 @@ canonicalp (bool knowngapp, char comp, double donor_prob, double acceptor_prob,
}
-/* Copied from stage1hr.c */
+/* Copied from stage1hr.c. A slightly different version is used in splice.c */
static int
sufficient_splice_prob_local (int support, int nmatches, int nmismatches, double distal_spliceprob,
double medial_spliceprob) {
--
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