[med-svn] [vsearch] 01/03: Imported Upstream version 2.0.2
Andreas Tille
tille at debian.org
Thu Jul 14 15:10:00 UTC 2016
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository vsearch.
commit ff7f4d00754dde4989de492674026493905c6eb9
Author: Andreas Tille <tille at debian.org>
Date: Thu Jul 14 17:09:23 2016 +0200
Imported Upstream version 2.0.2
---
configure.ac | 2 +-
man/vsearch.1 | 8 +++++++-
src/fasta.cc | 4 ++--
src/fasta.h | 2 +-
src/fastq.cc | 4 ++--
src/fastq.h | 2 +-
src/fastx.cc | 2 +-
src/fastx.h | 2 +-
src/maps.cc | 10 +++++-----
src/maps.h | 10 +++++-----
src/mask.cc | 4 +++-
11 files changed, 29 insertions(+), 21 deletions(-)
diff --git a/configure.ac b/configure.ac
index 6260dd7..0db8795 100644
--- a/configure.ac
+++ b/configure.ac
@@ -2,7 +2,7 @@
# Process this file with autoconf to produce a configure script.
AC_PREREQ([2.63])
-AC_INIT([vsearch], [2.0.0], [torognes at ifi.uio.no])
+AC_INIT([vsearch], [2.0.2], [torognes at ifi.uio.no])
AM_INIT_AUTOMAKE([subdir-objects])
AC_LANG([C++])
AC_CONFIG_SRCDIR([src/vsearch.cc])
diff --git a/man/vsearch.1 b/man/vsearch.1
index 672d911..f170074 100644
--- a/man/vsearch.1
+++ b/man/vsearch.1
@@ -1,5 +1,5 @@
.\" ============================================================================
-.TH vsearch 1 "June 24, 2016" "version 2.0.0" "USER COMMANDS"
+.TH vsearch 1 "July 5, 2016" "version 2.0.2" "USER COMMANDS"
.\" ============================================================================
.SH NAME
vsearch \(em chimera detection, clustering, dereplication and
@@ -2495,6 +2495,12 @@ enables piping of results for further processing. The file name '\-'
now represent standard input (/dev/stdin) or standard outout
(/dev/stdout) when reading or writing files, respectively. Code for
reading FASTA and FASTQ files have been refactored.
+.TP
+.BR v2.0.1\~ "released June 30, 2016"
+Avoid segmentation fault when masking very long sequences.
+.TP
+.BR v2.0.2\~ "released July 5, 2016"
+Avoid warnings when compiling with GCC 6.
.RE
.LP
.\" ============================================================================
diff --git a/src/fasta.cc b/src/fasta.cc
index d788c4b..d618135 100644
--- a/src/fasta.cc
+++ b/src/fasta.cc
@@ -91,7 +91,7 @@ void fasta_truncate_header(fastx_handle h, bool truncateatspace)
void fasta_filter_sequence(fastx_handle h,
unsigned int * char_action,
- char * char_mapping)
+ const unsigned char * char_mapping)
{
/* Strip unwanted characters from the sequence and raise warnings or
errors on certain characters. */
@@ -153,7 +153,7 @@ void fasta_filter_sequence(fastx_handle h,
bool fasta_next(fastx_handle h,
bool truncateatspace,
- char * char_mapping)
+ const unsigned char * char_mapping)
{
h->lineno_start = h->lineno;
diff --git a/src/fasta.h b/src/fasta.h
index 38f5f4d..0369d0b 100644
--- a/src/fasta.h
+++ b/src/fasta.h
@@ -66,7 +66,7 @@ fastx_handle fasta_open(const char * filename);
void fasta_close(fastx_handle h);
bool fasta_next(fastx_handle h,
bool truncateatspace,
- char * char_mapping);
+ const unsigned char * char_mapping);
unsigned long fasta_get_position(fastx_handle h);
unsigned long fasta_get_size(fastx_handle h);
unsigned long fasta_get_lineno(fastx_handle h);
diff --git a/src/fastq.cc b/src/fastq.cc
index b45cedc..43bd488 100644
--- a/src/fastq.cc
+++ b/src/fastq.cc
@@ -83,7 +83,7 @@ void buffer_filter_extend(fastx_handle h,
char * source_buf,
unsigned long len,
unsigned int * char_action,
- char * char_mapping,
+ const unsigned char * char_mapping,
unsigned long lineno_start)
{
buffer_makespace(dest_buffer, len+1);
@@ -164,7 +164,7 @@ void fastq_close(fastx_handle h)
bool fastq_next(fastx_handle h,
bool truncateatspace,
- char * char_mapping)
+ const unsigned char * char_mapping)
{
h->header_buffer.length = 0;
h->header_buffer.data[0] = 0;
diff --git a/src/fastq.h b/src/fastq.h
index daad7c7..9fcfb58 100644
--- a/src/fastq.h
+++ b/src/fastq.h
@@ -63,7 +63,7 @@ fastx_handle fastq_open(const char * filename);
void fastq_close(fastx_handle h);
bool fastq_next(fastx_handle h,
bool truncateatspace,
- char * char_mapping);
+ const unsigned char * char_mapping);
unsigned long fastq_get_position(fastx_handle h);
unsigned long fastq_get_size(fastx_handle h);
unsigned long fastq_get_lineno(fastx_handle h);
diff --git a/src/fastx.cc b/src/fastx.cc
index 0d5344a..c64658b 100644
--- a/src/fastx.cc
+++ b/src/fastx.cc
@@ -496,7 +496,7 @@ unsigned long fastx_file_fill_buffer(fastx_handle h)
bool fastx_next(fastx_handle h,
bool truncateatspace,
- char * char_mapping)
+ const unsigned char * char_mapping)
{
if (h->is_fastq)
return fastq_next(h, truncateatspace, char_mapping);
diff --git a/src/fastx.h b/src/fastx.h
index d3b396f..ff5815d 100644
--- a/src/fastx.h
+++ b/src/fastx.h
@@ -118,7 +118,7 @@ fastx_handle fastx_open(const char * filename);
void fastx_close(fastx_handle h);
bool fastx_next(fastx_handle h,
bool truncateatspace,
- char * char_mapping);
+ const unsigned char * char_mapping);
unsigned long fastx_get_position(fastx_handle h);
unsigned long fastx_get_size(fastx_handle h);
unsigned long fastx_get_lineno(fastx_handle h);
diff --git a/src/maps.cc b/src/maps.cc
index 7ad4351..4b0ca89 100644
--- a/src/maps.cc
+++ b/src/maps.cc
@@ -305,7 +305,7 @@ unsigned int chrmap_mask_ambig[256] =
};
-char chrmap_complement[256] =
+const unsigned char chrmap_complement[256] =
{
/*
@@ -336,7 +336,7 @@ char chrmap_complement[256] =
'N','N','N','N','N','N','N','N','N','N','N','N','N','N','N','N'
};
-char chrmap_normalize[256] =
+const unsigned char chrmap_normalize[256] =
{
/*
@@ -368,7 +368,7 @@ char chrmap_normalize[256] =
'N','N','N','N','N','N','N','N','N','N','N','N','N','N','N','N'
};
-char chrmap_upcase[256] =
+const unsigned char chrmap_upcase[256] =
{
/*
@@ -400,7 +400,7 @@ char chrmap_upcase[256] =
'N','N','N','N','N','N','N','N','N','N','N','N','N','N','N','N'
};
-char chrmap_no_change[256] =
+const unsigned char chrmap_no_change[256] =
{
/*
@@ -431,7 +431,7 @@ char chrmap_no_change[256] =
'N','N','N','N','N','N','N','N','N','N','N','N','N','N','N','N'
};
-char chrmap_identity[256] =
+const unsigned char chrmap_identity[256] =
{
/* identity map */
diff --git a/src/maps.h b/src/maps.h
index 10bf8ce..d011626 100644
--- a/src/maps.h
+++ b/src/maps.h
@@ -68,8 +68,8 @@ extern unsigned int chrmap_2bit[256];
extern unsigned int chrmap_4bit[256];
extern unsigned int chrmap_mask_ambig[256];
extern unsigned int chrmap_mask_lower[256];
-extern char chrmap_complement[256];
-extern char chrmap_normalize[256];
-extern char chrmap_upcase[256];
-extern char chrmap_no_change[256];
-extern char chrmap_identity[256];
+extern const unsigned char chrmap_complement[256];
+extern const unsigned char chrmap_normalize[256];
+extern const unsigned char chrmap_upcase[256];
+extern const unsigned char chrmap_no_change[256];
+extern const unsigned char chrmap_identity[256];
diff --git a/src/mask.cc b/src/mask.cc
index c6cdc3a..4d38f81 100644
--- a/src/mask.cc
+++ b/src/mask.cc
@@ -124,7 +124,7 @@ void dust(char * m, int len)
int a, b;
/* make a local copy of the original sequence */
- char * s = (char*) alloca(len+1);
+ char * s = (char*) xmalloc(len+1);
strcpy(s, m);
if (! opt_hardmask)
@@ -153,6 +153,8 @@ void dust(char * m, int len)
i += dust_window2 - b;
}
}
+
+ free(s);
}
static pthread_t * pthread;
--
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