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Makefile
View file @ 337e9bc8
......@@ -330,7 +330,7 @@ install_osx_packaging_bins: prep_c all
-cp ${APPDIR}/conversion/src/wrappers/bam2starch_gnuParallel ${OSXPKGDIR}/bam2starch_gnuParallel
-cp ${OTHERDIR}/switch-BEDOPS-binary-type ${OSXPKGDIR}
-cd ${OSXPKGDIR}; \
./switch-BEDOPS-binary-type --typical
./switch-BEDOPS-binary-type --typical .
-cd ${CWD}; \
mkdir -p ${OSXLIBDIR}; \
......
README.md
View file @ 337e9bc8
## BEDOPS v2.4.32: high-performance genomic feature operations ##
## BEDOPS v2.4.35: high-performance genomic feature operations ##
[![Build Status](https://travis-ci.org/bedops/bedops.svg?branch=master)](https://travis-ci.org/bedops/bedops) [![GitHub stars](https://img.shields.io/github/stars/bedops/bedops.svg)](https://github.com/bedops/bedops/stargazers) [![Project license](https://img.shields.io/badge/license-GPLv2-blue.svg)](https://github.com/bedops/bedops/blob/master/LICENSE) [![Documentation Status](https://readthedocs.org/projects/bedops/badge/?version=latest)](https://readthedocs.org/projects/bedops/?badge=latest)
......@@ -6,9 +6,9 @@
### About ###
**BEDOPS v2.4.32** is a suite of tools to address common questions raised in genomic studies — mostly with regard to overlap and proximity relationships between data sets. It aims to be scalable and flexible, facilitating the efficient and accurate analysis and management of large-scale genomic data.
**BEDOPS v2.4.35** is a suite of tools to address common questions raised in genomic studies — mostly with regard to overlap and proximity relationships between data sets. It aims to be scalable and flexible, facilitating the efficient and accurate analysis and management of large-scale genomic data.
The <a href="https://bedops.readthedocs.io/en/latest/content/overview.html#overview">overview</a> section of the **BEDOPS v2.4.32** documentation summarizes the toolkit, functionality and performance enhancements. The <a href="https://bedops.readthedocs.io/en/latest/index.html#reference">reference</a> table offers documentation for all applications and scripts.
The <a href="https://bedops.readthedocs.io/en/latest/content/overview.html#overview">overview</a> section of the **BEDOPS v2.4.35** documentation summarizes the toolkit, functionality and performance enhancements. The <a href="https://bedops.readthedocs.io/en/latest/index.html#reference">reference</a> table offers documentation for all applications and scripts.
### Downloads ###
......@@ -28,20 +28,20 @@ The <a href="https://bedops.readthedocs.io/en/latest/content/overview.html#overv
<tr>
<td valign="top">
<ul style="list-style-type:square; font-size:smaller; margin-left:0; margin-right:0px; padding-right:0px; padding-left:20px;">
<li><a href="https://github.com/bedops/bedops/releases/download/v2.4.32/bedops_linux_x86_64-v2.4.32.tar.bz2">x86-64 (64-bit)</a> binaries</li>
<li><a href="https://github.com/bedops/bedops/releases/download/v2.4.35/bedops_linux_x86_64-v2.4.35.tar.bz2">x86-64 (64-bit)</a> binaries</li>
<li><a href="http://bedops.readthedocs.io/en/latest/content/installation.html#linux">Installation instructions</a> for Linux hosts</li>
</ul>
</td>
<td valign="top">
<ul style="list-style-type:square; font-size:smaller; margin-left:0; margin-right:0px; padding-right:0px; padding-left:20px;">
<li><a href="https://github.com/bedops/bedops/releases/download/v2.4.32/BEDOPS.2.4.32.pkg.zip">Intel (64-bit, 10.10-10.13)</a> installer package</li>
<li><a href="https://github.com/bedops/bedops/releases/download/v2.4.35/BEDOPS.2.4.35.pkg.zip">Intel (64-bit, 10.10-10.13)</a> installer package</li>
<li><a href="http://bedops.readthedocs.io/en/latest/content/installation.html#mac-os-x">Installation instructions</a> for Mac OS X hosts</li>
</ul>
</td>
<td valign="top">
<ul style="list-style-type:square; font-size:smaller; margin-left:0; margin-right:0px; padding-right:0px; padding-left:20px;">
<li><a href="https://github.com/bedops/bedops/archive/v2.4.32.tar.gz">Source code</a> (tar.gz)</li>
<li><a href="https://github.com/bedops/bedops/archive/v2.4.32.zip">Source code</a> (zip)</li>
<li><a href="https://github.com/bedops/bedops/archive/v2.4.35.tar.gz">Source code</a> (tar.gz)</li>
<li><a href="https://github.com/bedops/bedops/archive/v2.4.35.zip">Source code</a> (zip)</li>
<li><a href="http://bedops.readthedocs.io/en/latest/content/installation.html#installation-via-source-code">Compilation instructions</a></li>
</ul>
</td>
......@@ -50,11 +50,11 @@ The <a href="https://bedops.readthedocs.io/en/latest/content/overview.html#overv
### Documentation ###
Complete documentation for **BEDOPS v2.4.32** tools is available at: <a href="https://bedops.readthedocs.io/en/latest/index.html">https://bedops.readthedocs.io/</a>
Complete documentation for **BEDOPS v2.4.35** tools is available at: <a href="https://bedops.readthedocs.io/en/latest/index.html">https://bedops.readthedocs.io/</a>
### Citation ###
If you use **BEDOPS v2.4.32** in your research, please cite the following manuscript:
If you use **BEDOPS v2.4.35** in your research, please cite the following manuscript:
> Shane Neph, M. Scott Kuehn, Alex P. Reynolds, et al.
> [**BEDOPS: high-performance genomic feature operations**
......
applications/bed/conversion/src/convert2bed.h
View file @ 337e9bc8
/*
convert2bed.h
-----------------------------------------------------------------------
Copyright (C) 2014-2017 Alex Reynolds
Copyright (C) 2014-2018 Alex Reynolds
wig2bed components, (C) 2011-2018 Scott Kuehn and Shane Neph
......@@ -53,7 +53,7 @@
#include "suite/BEDOPS.Constants.hpp"
#define C2B_VERSION "2.4.32"
#define C2B_VERSION "2.4.35"
typedef int boolean;
extern const boolean kTrue;
......@@ -82,7 +82,7 @@ const boolean kFalse = 0;
#define C2B_GTF_ELEMENT_FIELD_LENGTH_VALUE_INITIAL 32
#define C2B_RMSK_ELEMENT_FIELD_LENGTH_VALUE_INITIAL 32
#define C2B_PSL_ELEMENT_FIELD_LENGTH_VALUE_INITIAL 32
#define C2B_THREAD_IO_BUFFER_SIZE 5000000
#define C2B_THREAD_IO_BUFFER_SIZE TOKENS_MAX_LENGTH
extern const char* c2b_samtools;
extern const char* c2b_sort_bed;
......@@ -269,10 +269,14 @@ typedef struct sam {
char* modified_qname;
ssize_t modified_qname_capacity;
int flag;
char* flag_str;
ssize_t flag_str_capacity;
char* strand;
ssize_t strand_capacity;
char* rname;
ssize_t rname_capacity;
char* pos_str;
ssize_t pos_str_capacity;
uint64_t start;
uint64_t stop;
char* mapq;
......@@ -315,6 +319,8 @@ typedef struct sam {
*/
typedef struct gff {
char* header;
ssize_t header_capacity;
char* seqid;
ssize_t seqid_capacity;
char* source;
......@@ -322,7 +328,11 @@ typedef struct gff {
char* type;
ssize_t type_capacity;
uint64_t start;
char* start_str;
ssize_t start_str_capacity;
uint64_t end;
char* end_str;
ssize_t end_str_capacity;
char* score;
ssize_t score_capacity;
char* strand;
......@@ -333,6 +343,8 @@ typedef struct gff {
ssize_t attributes_capacity;
char* id;
ssize_t id_capacity;
char* non_int_prefix;
ssize_t non_int_prefix_capacity;
} c2b_gff_t;
/*
......@@ -364,7 +376,11 @@ typedef struct gtf {
char* feature;
ssize_t feature_capacity;
uint64_t start;
char* start_str;
ssize_t start_str_capacity;
uint64_t end;
char* end_str;
ssize_t end_str_capacity;
char* score;
ssize_t score_capacity;
char* strand;
......@@ -521,7 +537,11 @@ typedef struct rmsk {
char* query_seq;
ssize_t query_seq_capacity;
uint64_t query_start;
char* query_start_str;
ssize_t query_start_str_capacity;
uint64_t query_end;
char* query_end_str;
ssize_t query_end_str_capacity;
char* bases_past_match;
ssize_t bases_past_match_capacity;
char* strand;
......@@ -576,6 +596,8 @@ typedef struct vcf {
char* chrom;
ssize_t chrom_capacity;
uint64_t pos;
char* pos_str;
ssize_t pos_str_capacity;
uint64_t start;
uint64_t end;
char* id;
......
applications/bed/sort-bed/src/update-sort-bed-migrate-candidates.py
View file @ 337e9bc8
......@@ -32,7 +32,7 @@ import logging
name = "update-sort-bed-migrate-candidates"
citation = " citation: http://bioinformatics.oxfordjournals.org/content/28/14/1919.abstract"
authors = " authors: Alex Reynolds and Shane Neph"
version = " version: 2.4.32"
version = " version: 2.4.35"
usage = """ $ update-sort-bed-migrate-candidates [ --dry-run ] [ --debug ]
[ --write-list |
--resort-immediately |
......
applications/bed/sort-bed/src/update-sort-bed-slurm.py
View file @ 337e9bc8
......@@ -33,7 +33,7 @@ import logging
name = "update-sort-bed-slurm"
citation = " citation: http://bioinformatics.oxfordjournals.org/content/28/14/1919.abstract"
authors = " authors: Alex Reynolds and Shane Neph"
version = " version: 2.4.32"
version = " version: 2.4.35"
usage = """ $ update-sort-bed-slurm [ --slurm-memory <MB> ]
[ --slurm-partition <SLURM partition> ]
[ --slurm-workdir <working directory> ]
......
applications/bed/sort-bed/src/update-sort-bed-starch-slurm.py
View file @ 337e9bc8
......@@ -33,7 +33,7 @@ import logging
name = "update-sort-bed-starch-slurm"
citation = " citation: http://bioinformatics.oxfordjournals.org/content/28/14/1919.abstract"
authors = " authors: Alex Reynolds and Shane Neph"
version = " version: 2.4.32"
version = " version: 2.4.35"
usage = """ $ update-sort-bed-starch-slurm [ --slurm-memory <MB> ]
[ --slurm-partition <SLURM partition> ]
[ --slurm-workdir <working directory> ]
......
applications/bed/starch/src/Makefile.darwin
View file @ 337e9bc8
......@@ -31,7 +31,7 @@ LIBRARIES = ${LOCALJANSSONLIB} ${LOCALBZIP2LIB} ${LOCALZLIBLIB}
BINDIR = ../bin
WARNINGS = -Weverything -Wno-c++98-compat-pedantic -Wno-padded
ARCH_VERSION = v2.2
BIN_VERSION = v2.4.32
BIN_VERSION = v2.4.35
TEST = ../test
TEST_OSX_BINDIR = ${TEST}/binaries/osx/${ARCH_VERSION}/bin
......
applications/bed/starch/src/starch-diff.py
View file @ 337e9bc8
......@@ -32,7 +32,7 @@ import logging
name = "starch-diff"
citation = " citation: http://bioinformatics.oxfordjournals.org/content/28/14/1919.abstract"
authors = " authors: Alex Reynolds and Shane Neph"
version = " version: 2.4.32"
version = " version: 2.4.35"
usage = " $ starch-diff [ --chr <chr> ] starch-file-1 starch-file-2 [ starch-file-3 ... ]"
help = """
The 'starch-diff' utility compares the signatures of two or more specified
......
applications/bed/starch/src/starchcluster_gnuParallel.tcsh
View file @ 337e9bc8
......@@ -2,7 +2,7 @@
# author : sjn and apr
# date : Feb 2012
# version : v2.4.32
# version : v2.4.35
#
# BEDOPS
......
applications/bed/starch/src/starchcluster_sge.tcsh
View file @ 337e9bc8
......@@ -2,7 +2,7 @@
# author : sjn and apr
# date : Feb 2012
# version : v2.4.32
# version : v2.4.35
#
# BEDOPS
......
applications/bed/starch/src/starchcluster_slurm.tcsh
View file @ 337e9bc8
......@@ -2,7 +2,7 @@
# author : sjn and apr
# date : 13 Sep 2016
# version : v2.4.32
# version : v2.4.35
#
# BEDOPS
......
applications/bed/starch/src/starchstrip.c
View file @ 337e9bc8
......@@ -654,7 +654,11 @@ static int
STARCHSTRIP_compare_chromosome_names(const void* a, const void* b)
{
#ifdef __cplusplus
return strcmp((static_cast<const char*>(a)), (static_cast<const char*>(b)));
auto a_recast = const_cast<void *>(a);
auto b_recast = const_cast<void *>(b);
auto a_rerecast = const_cast<const char **>(reinterpret_cast<char **>(a_recast));
auto b_rerecast = const_cast<const char **>(reinterpret_cast<char **>(b_recast));
return strcmp(*a_rerecast, *b_rerecast);
#else
return strcmp(*(const char**) a, *(const char**) b);
#endif
......
applications/other/switch-BEDOPS-binary-type
View file @ 337e9bc8
......@@ -3,13 +3,14 @@
# date : July.2017
BINDIR=$(dirname `which bedops`)
[ -n "${2}" ] && BINDIR=${2}
CMD="switch-BEDOPS-binary-type"
help()
{
echo "Switch the BEDOPS binary build to typical, megarow, or float128"
echo "Usage: ${CMD} [ --help ] [ --typical | --megarow | --float128 ]" >&2
echo "Usage: ${CMD} [ --help ] [ --typical | --megarow | --float128 ] [ <binary-directory> (optional) ]" >&2
exit $1
}
......
debian/changelog
View file @ 337e9bc8
bedops (2.4.35+dfsg-1) unstable; urgency=medium
* Team upload.
* New upstream version
* Point Vcs fields to salsa.debian.org
* Standards-Version: 4.1.4
-- Andreas Tille <tille@debian.org> Wed, 23 May 2018 17:43:00 +0200
bedops (2.4.32+dfsg-2) unstable; urgency=medium
* Team upload.
......
debian/control
View file @ 337e9bc8
......@@ -11,9 +11,9 @@ Build-Depends: debhelper (>= 11~),
python3-distutils,
python3-sphinx,
zlib1g-dev
Standards-Version: 4.1.3
Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/bedops.git
Vcs-Git: https://anonscm.debian.org/debian-med/bedops.git
Standards-Version: 4.1.4
Vcs-Browser: https://salsa.debian.org/med-team/bedops
Vcs-Git: https://salsa.debian.org/med-team/bedops.git
Homepage: https://github.com/bedops/bedops
Package: bedops
......@@ -35,7 +35,6 @@ Section: doc
Depends: ${misc:Depends},
libjs-sphinxdoc,
libjs-mathjax
Breaks: bedops (<= 2.4.32)
Description: high-performance genomic feature operations (documentation)
BEDOPS is a suite of tools to address common questions raised in genomic
studies, mostly with regard to overlap and proximity relationships between
......
docs/conf.py
View file @ 337e9bc8
......@@ -52,7 +52,7 @@ copyright = u'2011-2018, Shane Neph, Alex Reynolds'
# The short X.Y version.
version = '2.4'
# The full version, including alpha/beta/rc tags.
release = '2.4.32'
release = '2.4.35'
# The language for content autogenerated by Sphinx. Refer to documentation
# for a list of supported languages.
......
docs/content/reference/file-management/compression/starch-diff.rst
View file @ 337e9bc8
......@@ -39,7 +39,7 @@ Use the ``--help`` option to list all options:
starch-diff
citation: http://bioinformatics.oxfordjournals.org/content/28/14/1919.abstract
version: 2.4.32
version: 2.4.35
authors: Alex Reynolds and Shane Neph
$ starch-diff [ --chr <chr> ] starch-file-1 starch-file-2 [ starch-file-3 ... ]
......
docs/content/reference/file-management/compression/starch.rst
View file @ 337e9bc8
......@@ -49,7 +49,7 @@ Use the ``--help`` option to list all options:
starch
citation: http://bioinformatics.oxfordjournals.org/content/28/14/1919.abstract
binary version: 2.4.32 (typical) (creates archive version: 2.2.0)
binary version: 2.4.35 (typical) (creates archive version: 2.2.0)
authors: Alex Reynolds and Shane Neph
USAGE: starch [ --note="foo bar..." ]
......
docs/content/reference/file-management/compression/starchcat.rst
View file @ 337e9bc8
......@@ -57,7 +57,7 @@ Use the ``--help`` option to list all options:
starchcat
citation: http://bioinformatics.oxfordjournals.org/content/28/14/1919.abstract
version: 2.4.32 (typical)
version: 2.4.35 (typical)
authors: Alex Reynolds and Shane Neph
USAGE: starchcat [ --note="..." ]
......