New upstream version 2.4.36+dfsg (0a6ce561) · Commits · Debian Med / bedops

.travis.yml

+2 −2

Original line number	Diff line number	Diff line
		@@ -15,5 +15,5 @@ install:
		- if [[ "$CXX" == "g++" ]]; then if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then sudo apt-get install -qq g++-4.8; fi; fi
		- if [[ "$CXX" == "g++" ]]; then if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then sudo update-alternatives --install /usr/bin/g++ g++ /usr/bin/g++-4.8 50; fi; fi
		script:
		- if [[ "$CC" == "gcc" ]]; then if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then make all; fi; fi
		- if [[ "$CC" == "clang" ]]; then if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then make all; fi; fi
		No newline at end of file
		- if [[ "$CC" == "gcc" ]]; then if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then make all; make install_all; fi; fi
		- if [[ "$CC" == "clang" ]]; then if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then make all; make install_all; fi; fi

Makefile

+15 −3

Original line number	Diff line number	Diff line
		@@ -22,7 +22,7 @@ WRAPPERS = $(wildcard ${APPDIR}/conversion/src/wrappers/*)
		CWD := $(shell pwd)
		BINDIR = bin
		BINDIR_MODULE = modules

		export DESTBINDIR = .

		default:
		ifeq ($(KERNEL), Darwin)
		@@ -45,7 +45,7 @@ all:
		$(MAKE) megarow -f ${SELF}
		$(MAKE) float128 -f ${SELF}
		$(MAKE) install_all -f ${SELF}
		$(MAKE) symlink_typical -f ${SELF}
		$(MAKE) symlink_post_install_all -f ${SELF}

		module_all:
		$(MAKE) support -f ${SELF}
		@@ -64,6 +64,9 @@ megarow:
		typical:
		$(MAKE) BINARY_TYPE=$(TYPICAL) -f ${SELF}

		symlink_post_install_all:
		cd ${BINDIR} && ./switch-BEDOPS-binary-type --typical . && cd ${CWD}

		symlink_typical:
		$(eval SRCNAMES=`find $(BINDIR)/ -maxdepth 1 -mindepth 1 -type f -name '*$(TYPICAL)' -print0 \| xargs -L1 -0 -I{} sh -c 'basename {}'`)
		for SRCNAME in ${SRCNAMES}; do \
		@@ -242,7 +245,7 @@ install_starch_scripts_all: prep_c
		install_conversion_scripts: prep_c
		cp $(WRAPPERS) ${BINDIR}

		.PHONY: $(WRAPPERS)
		.PHONY: $(WRAPPERS) tests

		install_conversion_scripts_all: $(WRAPPERS)

		@@ -396,6 +399,9 @@ else
		find . -exec sed -i "s/"$$OLD_CPD"/"$$NEW_CPD"/g" {} \;
		endif

		#######################
		# packaging

		docker: packaging/docker/Dockerfile
		docker build -t bedops -f packaging/docker/Dockerfile .

		@@ -404,3 +410,9 @@ rpm: packaging/rpm/Dockerfile

		deb: packaging/deb/Dockerfile
		docker build -t bedops:deb -f packaging/deb/Dockerfile .

		#######################
		# tests

		tests:
		$(MAKE) all -f tests/Makefile

README.md

+10 −10

Original line number	Diff line number	Diff line
		## BEDOPS v2.4.35: high-performance genomic feature operations ##
		## BEDOPS v2.4.36: 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 v2.4.35 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.
		BEDOPS v2.4.36 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 v2.4.35 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.
		The <a href="https://bedops.readthedocs.io/en/latest/content/overview.html#overview">overview</a> section of the BEDOPS v2.4.36 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/v2.4.35/bedops_linux_x86_64-v2.4.35.tar.bz2">x86-64 (64-bit)</a> binaries</li>
		<li><a href="https://github.com/bedops/bedops/releases/download/v2.4.36/bedops_linux_x86_64-v2.4.36.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/v2.4.35/BEDOPS.2.4.35.pkg.zip">Intel (64-bit, 10.10-10.13)</a> installer package</li>
		<li><a href="https://github.com/bedops/bedops/releases/download/v2.4.36/BEDOPS.2.4.36.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/v2.4.35.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="https://github.com/bedops/bedops/archive/v2.4.36.tar.gz">Source code</a> (tar.gz)</li>
		<li><a href="https://github.com/bedops/bedops/archive/v2.4.36.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 v2.4.35 tools is available at: <a href="https://bedops.readthedocs.io/en/latest/index.html">https://bedops.readthedocs.io/</a>
		Complete documentation for BEDOPS v2.4.36 tools is available at: <a href="https://bedops.readthedocs.io/en/latest/index.html">https://bedops.readthedocs.io/</a>

		### Citation ###

		If you use BEDOPS v2.4.35 in your research, please cite the following manuscript:
		If you use BEDOPS v2.4.36 in your research, please cite the following manuscript:

		> Shane Neph, M. Scott Kuehn, Alex P. Reynolds, et al.
		> [BEDOPS: high-performance genomic feature operations
		@@ -62,7 +62,7 @@ If you use BEDOPS v2.4.35 in your research, please cite the following manusc

		### Copyright ###

		> Copyright (C) 2011-2018 Shane J. Neph, M. Scott Kuehn and Alex P. Reynolds
		> Copyright (C) 2011-2019 Shane J. Neph, M. Scott Kuehn and Alex P. Reynolds
		>
		> Source code, documentation and media assets released under <a href="https://github.com/bedops/bedops/blob/master/LICENSE">GNU Public License Version 2</a> (GPL v2).

applications/bed/bedmap/src/Bedmap.cpp

+69 −43

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applications/bed/bedmap/src/Input.hpp

+10 −1

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		@@ -79,7 +79,7 @@ namespace BedMap {
		precision_(6), useScientific_(false), useMinMemory_(false), setPrec_(false), numFiles_(0),
		minRefFields_(0), minMapFields_(0), errorCheck_(false), sweepAll_(false),
		outDelim_("\|"), multiDelim_(";"), fastMode_(false), rangeAlias_(false),
		chrom_("all"), skipUnmappedRows_(false) {
		chrom_("all"), skipUnmappedRows_(false), unmappedVal_("") {

		// Process user's operation options
		if ( argc <= 1 )
		@@ -108,6 +108,12 @@ namespace BedMap {
		fastMode_ = true;
		} else if ( next == "sweep-all" ) { // --> sweep through all of second file
		sweepAll_ = true;
		} else if ( next == "unmapped-val" ) {
		Ext::Assert<ArgError>(unmappedVal_.empty(), "--unmapped-val specified multiple times");
		Ext::Assert<ArgError>(argcntr < argc, "No value given for --unmapped-val");
		unmappedVal_ = argv[argcntr++];
		Ext::Assert<ArgError>(unmappedVal_.find("--") != 0,
		"Apparent option: " + std::string(argv[argcntr]) + " where <val> expected for --unmapped-val.");
		} else if ( next == "delim" ) {
		Ext::Assert<ArgError>(outDelim_ == "\|", "--delim specified multiple times");
		Ext::Assert<ArgError>(argcntr < argc, "No output delimiter given");
		@@ -399,6 +405,7 @@ namespace BedMap {
		bool rangeAlias_;
		std::string chrom_;
		bool skipUnmappedRows_;
		std::string unmappedVal_;

		private:
		struct MapFields {
		@@ -480,6 +487,8 @@ namespace BedMap {
		usage << " --sci Use scientific notation for score outputs. \n";
		usage << " --skip-unmapped Print no output for a row with no mapped elements. \n";
		usage << " --sweep-all Ensure <map-file> is read completely (helps to prevent broken pipes). \n";
		usage << " --unmapped-val <val> Print <val> on unmapped --echo-map* and --min/max-element* operations. \n";
		usage << " The default is to print nothing. \n";
		usage << " --version Print program information. \n";
		usage << " \n";
		usage << " \n";