[med-svn] [gmap] 01/04: New upstream version 2016-08-24
Alex Mestiashvili
malex-guest at moszumanska.debian.org
Sun Aug 28 07:32:52 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 11d1c6336bd40f10fef52dc91059380cc42d3dff
Author: Alexandre Mestiashvili <alex at biotec.tu-dresden.de>
Date: Sun Aug 28 09:13:04 2016 +0200
New upstream version 2016-08-24
---
ChangeLog | 4 ++
VERSION | 2 +-
configure | 24 +++++------
src/genome.c | 128 +++++++++++++++++++++++++++++++----------------------------
4 files changed, 84 insertions(+), 74 deletions(-)
diff --git a/ChangeLog b/ChangeLog
index e592956..da5ae31 100644
--- a/ChangeLog
+++ b/ChangeLog
@@ -1,3 +1,7 @@
+2016-08-24 twu
+
+ * genome.c: Not accessing beyond end of blocks when enddiscard is 0
+
2016-08-16 twu
* VERSION: Updated version number
diff --git a/VERSION b/VERSION
index 7e6fbae..f41d1f1 100644
--- a/VERSION
+++ b/VERSION
@@ -1 +1 @@
-2016-08-16
\ No newline at end of file
+2016-08-24
\ No newline at end of file
diff --git a/configure b/configure
index 5992757..304c0bc 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 2016-08-16.
+# Generated by GNU Autoconf 2.69 for gmap 2016-08-24.
#
# 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='2016-08-16'
-PACKAGE_STRING='gmap 2016-08-16'
+PACKAGE_VERSION='2016-08-24'
+PACKAGE_STRING='gmap 2016-08-24'
PACKAGE_BUGREPORT='Thomas Wu <twu at gene.com>'
PACKAGE_URL=''
@@ -1372,7 +1372,7 @@ 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 2016-08-16 to adapt to many kinds of systems.
+\`configure' configures gmap 2016-08-24 to adapt to many kinds of systems.
Usage: $0 [OPTION]... [VAR=VALUE]...
@@ -1443,7 +1443,7 @@ fi
if test -n "$ac_init_help"; then
case $ac_init_help in
- short | recursive ) echo "Configuration of gmap 2016-08-16:";;
+ short | recursive ) echo "Configuration of gmap 2016-08-24:";;
esac
cat <<\_ACEOF
@@ -1582,7 +1582,7 @@ fi
test -n "$ac_init_help" && exit $ac_status
if $ac_init_version; then
cat <<\_ACEOF
-gmap configure 2016-08-16
+gmap configure 2016-08-24
generated by GNU Autoconf 2.69
Copyright (C) 2012 Free Software Foundation, Inc.
@@ -2188,7 +2188,7 @@ 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 2016-08-16, which was
+It was created by gmap $as_me 2016-08-24, which was
generated by GNU Autoconf 2.69. Invocation command line was
$ $0 $@
@@ -2538,8 +2538,8 @@ ac_compiler_gnu=$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: 2016-08-16" >&5
-$as_echo "2016-08-16" >&6; }
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: 2016-08-24" >&5
+$as_echo "2016-08-24" >&6; }
### Read defaults
@@ -4404,7 +4404,7 @@ fi
# Define the identity of the package.
PACKAGE='gmap'
- VERSION='2016-08-16'
+ VERSION='2016-08-24'
cat >>confdefs.h <<_ACEOF
@@ -20109,7 +20109,7 @@ cat >>$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 2016-08-16, which was
+This file was extended by gmap $as_me 2016-08-24, which was
generated by GNU Autoconf 2.69. Invocation command line was
CONFIG_FILES = $CONFIG_FILES
@@ -20175,7 +20175,7 @@ _ACEOF
cat >>$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 2016-08-16
+gmap config.status 2016-08-24
configured by $0, generated by GNU Autoconf 2.69,
with options \\"\$ac_cs_config\\"
diff --git a/src/genome.c b/src/genome.c
index bf7cb5c..8695454 100644
--- a/src/genome.c
+++ b/src/genome.c
@@ -1,4 +1,4 @@
-static char rcsid[] = "$Id: genome.c 184156 2016-02-12 18:30:44Z twu $";
+static char rcsid[] = "$Id: genome.c 196872 2016-08-24 22:41:33Z twu $";
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
@@ -10098,24 +10098,26 @@ uncompress_mmap_nucleotides (unsigned char *gbuffer, Genomecomp_T *blocks, Univc
ptr += 3;
}
+ if (enddiscard > 0) {
#ifdef WORDS_BIGENDIAN
- high = Bigendian_convert_uint(blocks[ptr]);
- low = Bigendian_convert_uint(blocks[ptr+1]);
+ high = Bigendian_convert_uint(blocks[ptr]);
+ low = Bigendian_convert_uint(blocks[ptr+1]);
#else
- high = blocks[ptr]; low = blocks[ptr+1];
+ high = blocks[ptr]; low = blocks[ptr+1];
#endif
- i = 0;
- while (i < enddiscard && i < 16) {
- *gbuffer++ = (unsigned char) (low & 0x03);
- low >>= 2;
- i++;
- }
- while (i < enddiscard) {
- *gbuffer++ = (unsigned char) (high & 0x03);
- high >>= 2;
- i++;
+ i = 0;
+ while (i < enddiscard && i < 16) {
+ *gbuffer++ = (unsigned char) (low & 0x03);
+ low >>= 2;
+ i++;
+ }
+ while (i < enddiscard) {
+ *gbuffer++ = (unsigned char) (high & 0x03);
+ high >>= 2;
+ i++;
+ }
+ /* printf("Block %d assigned up to %d\n",ptr,k); */
}
- /* printf("Block %d assigned up to %d\n",ptr,k); */
}
#if 0
@@ -10265,35 +10267,37 @@ uncompress_mmap_int_string (unsigned char *gbuffer, Genomecomp_T *blocks, Univco
ptr += 3;
}
+ if (enddiscard > 0) {
#ifdef WORDS_BIGENDIAN
- high = Bigendian_convert_uint(blocks[ptr]);
- low = Bigendian_convert_uint(blocks[ptr+1]);
- flags = Bigendian_convert_uint(blocks[ptr+2]);
+ high = Bigendian_convert_uint(blocks[ptr]);
+ low = Bigendian_convert_uint(blocks[ptr+1]);
+ flags = Bigendian_convert_uint(blocks[ptr+2]);
#else
- high = blocks[ptr]; low = blocks[ptr+1]; flags = blocks[ptr+2];
+ high = blocks[ptr]; low = blocks[ptr+1]; flags = blocks[ptr+2];
#endif
- i = 0;
- while (i < enddiscard && i < 16) {
- if (flags & 0x01) {
- *gbuffer++ = (unsigned char) 4;
- } else {
- *gbuffer++ = (unsigned char) (low & 0x03);
+ i = 0;
+ while (i < enddiscard && i < 16) {
+ if (flags & 0x01) {
+ *gbuffer++ = (unsigned char) 4;
+ } else {
+ *gbuffer++ = (unsigned char) (low & 0x03);
+ }
+ low >>= 2;
+ flags >>= 1;
+ i++;
}
- low >>= 2;
- flags >>= 1;
- i++;
- }
- while (i < enddiscard) {
- if (flags & 0x01) {
- *gbuffer++ = (unsigned char) 4;
- } else {
- *gbuffer++ = (unsigned char) (high & 0x03);
+ while (i < enddiscard) {
+ if (flags & 0x01) {
+ *gbuffer++ = (unsigned char) 4;
+ } else {
+ *gbuffer++ = (unsigned char) (high & 0x03);
+ }
+ high >>= 2;
+ flags >>= 1;
+ i++;
}
- high >>= 2;
- flags >>= 1;
- i++;
+ /* printf("Block %d assigned up to %d\n",ptr,k); */
}
- /* printf("Block %d assigned up to %d\n",ptr,k); */
}
#if 0
@@ -10442,35 +10446,37 @@ uncompress_mmap_int_string_convert (unsigned char *gbuffer, Genomecomp_T *blocks
ptr += 3;
}
+ if (enddiscard > 0) {
#ifdef WORDS_BIGENDIAN
- high = Bigendian_convert_uint(blocks[ptr]);
- low = Bigendian_convert_uint(blocks[ptr+1]);
- flags = Bigendian_convert_uint(blocks[ptr+2]);
+ high = Bigendian_convert_uint(blocks[ptr]);
+ low = Bigendian_convert_uint(blocks[ptr+1]);
+ flags = Bigendian_convert_uint(blocks[ptr+2]);
#else
- high = blocks[ptr]; low = blocks[ptr+1]; flags = blocks[ptr+2];
+ high = blocks[ptr]; low = blocks[ptr+1]; flags = blocks[ptr+2];
#endif
- i = 0;
- while (i < enddiscard && i < 16) {
- if (flags & 0x01) {
- *gbuffer++ = (unsigned char) 4;
- } else {
- *gbuffer++ = conversion[(int) (low & 0x03)];
+ i = 0;
+ while (i < enddiscard && i < 16) {
+ if (flags & 0x01) {
+ *gbuffer++ = (unsigned char) 4;
+ } else {
+ *gbuffer++ = conversion[(int) (low & 0x03)];
+ }
+ low >>= 2;
+ flags >>= 1;
+ i++;
}
- low >>= 2;
- flags >>= 1;
- i++;
- }
- while (i < enddiscard) {
- if (flags & 0x01) {
- *gbuffer++ = (unsigned char) 4;
- } else {
- *gbuffer++ = conversion[(int) (high & 0x03)];
+ while (i < enddiscard) {
+ if (flags & 0x01) {
+ *gbuffer++ = (unsigned char) 4;
+ } else {
+ *gbuffer++ = conversion[(int) (high & 0x03)];
+ }
+ high >>= 2;
+ flags >>= 1;
+ i++;
}
- high >>= 2;
- flags >>= 1;
- i++;
+ /* printf("Block %d assigned up to %d\n",ptr,k); */
}
- /* printf("Block %d assigned up to %d\n",ptr,k); */
}
#if 0
--
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