Commit d6455ca8 authored by Andreas Tille's avatar Andreas Tille
Browse files

New upstream version 2.4.35+dfsg

parent fe8d9e15

Makefile

+1 −1
Original line number Diff line number Diff line
@@ -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

+9 −9
Original line number Diff line number Diff line 
## 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.c

+327 −82

File changed.

Preview size limit exceeded, changes collapsed.

applications/bed/conversion/src/convert2bed.h

+25 −3
Original line number Diff line number Diff line 
/* 

   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

+1 −1
Original line number Diff line number Diff line
@@ -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 |