.gitignore

@@ -69,3 +69,5 @@ applications/bed/closestfeats/bin/
 applications/bed/conversion/bin/
 applications/bed/sort-bed/bin/
 applications/bed/starch/bin/
+
+.vscode
\ No newline at end of file

.readthedocs.yml

+# .readthedocs.yml
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+# Build documentation in the docs/ directory with Sphinx
+sphinx:
+  configuration: docs/conf.py
+
+# Build documentation with MkDocs
+#mkdocs:
+#  configuration: mkdocs.yml
+
+# Optionally build your docs in additional formats such as PDF and ePub
+formats: all
+
+# Optionally set the version of Python and requirements required to build your docs
+python:
+  version: 3.6
+  install:
+    - requirements: docs/requirements.txt
\ No newline at end of file

README.md

-## BEDOPS v2.4.36: high-performance genomic feature operations ##
+## BEDOPS v2.4.37: 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 v2.4.36** 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. 
+**BEDOPS v2.4.37** 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 v2.4.36** 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.
+The <a href="https://bedops.readthedocs.io/en/latest/content/overview.html#overview">overview</a> section of the **BEDOPS v2.4.37** 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 ###
@@ -16,32 +16,32 @@ The <a href="https://bedops.readthedocs.io/en/latest/content/overview.html#overv
 <table width="100%">
 <tr>
 <th width="33%" align="left">
-<img src="https://bedops.readthedocs.io/en/latest/_images/linux_v2.png" height="26px" style="height:26px !important; width: auto !important; margin-bottom:10px;">
+Linux
 </th>
 <th width="33%" align="left">
-<img src="https://bedops.readthedocs.io/en/latest/_images/macosx_v2.png" height="26px" style="height:26px !important; width: auto !important; margin-bottom:10px;">
+Mac OS X
 </th>
 <th width="34%" align="left">
-<img src="https://bedops.readthedocs.io/en/latest/_images/source_v2.png" height="26px" style="height:26px !important; width: auto !important; margin-bottom:10px;">
+Source code
 </th>
 </tr>
 <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/v2.4.36/bedops_linux_x86_64-v2.4.36.tar.bz2">x86-64 (64-bit)</a> binaries</li>
+<li><a href="https://github.com/bedops/bedops/releases/download/v2.4.37/bedops_linux_x86_64-v2.4.37.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/v2.4.36/BEDOPS.2.4.36.pkg.zip">Intel (64-bit, 10.10-10.13)</a> installer package</li>
+<li><a href="https://github.com/bedops/bedops/releases/download/v2.4.37/BEDOPS.2.4.37.pkg.zip">Intel (64-bit, 10.10-10.14)</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/v2.4.36.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="https://github.com/bedops/bedops/archive/v2.4.37.tar.gz">Source code</a> (tar.gz)</li>
+<li><a href="https://github.com/bedops/bedops/archive/v2.4.37.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 v2.4.36** tools is available at: <a href="https://bedops.readthedocs.io/en/latest/index.html">https://bedops.readthedocs.io/</a>
+Complete documentation for **BEDOPS v2.4.37** tools is available at: <a href="https://bedops.readthedocs.io/en/latest/index.html">https://bedops.readthedocs.io/</a>
 
 ### Citation ###
 
-If you use **BEDOPS v2.4.36** in your research, please cite the following manuscript:
+If you use **BEDOPS v2.4.37** 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/bedmap/src/Bedmap.cpp

@@ -187,6 +187,7 @@ int main(int argc, char **argv) {
     std::cout << "  citation: " << BedMap::citation << std::endl;
     std::cout << "  version:  " << BedMap::version << std::endl;
     std::cout << "  authors:  " << BedMap::authors << std::endl;
+    return EXIT_SUCCESS;
   } catch(const BedMap::NoInput& ni) { // show usage and exit failure
     std::cerr << BedMap::prognm << std::endl;
     std::cerr << "  citation: " << BedMap::citation << std::endl;

applications/bed/conversion/src/convert2bed.h

@@ -53,7 +53,7 @@
 
 #include "suite/BEDOPS.Constants.hpp"
 
-#define C2B_VERSION "2.4.36"
+#define C2B_VERSION "2.4.37"
 
 typedef int boolean;
 extern const boolean kTrue;

applications/bed/sort-bed/src/update-sort-bed-migrate-candidates.py

@@ -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:  2.4.36"
+version = "  version:  2.4.37"
 usage = """  $ update-sort-bed-migrate-candidates [ --dry-run ] [ --debug ]
                                        [ --write-list |
                                          --resort-immediately |

applications/bed/sort-bed/src/update-sort-bed-slurm.py

@@ -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:  2.4.36"
+version = "  version:  2.4.37"
 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

@@ -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:  2.4.36"
+version = "  version:  2.4.37"
 usage = """  $ update-sort-bed-starch-slurm [ --slurm-memory <MB> ] 
                                  [ --slurm-partition <SLURM partition> ] 
                                  [ --slurm-workdir <working directory> ]

applications/bed/starch/src/Makefile.darwin

@@ -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               = v2.4.36
+BIN_VERSION               = v2.4.37
 TEST                      = ../test
 TEST_OSX_BINDIR           = ${TEST}/binaries/osx/${ARCH_VERSION}/bin
 

applications/bed/starch/src/starch-diff.py

@@ -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:  2.4.36"
+version = "  version:  2.4.37"
 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/starchcat.c

@@ -5107,7 +5107,9 @@ STARCHCAT_allocMetadataRecords(MetadataRecord **mdRecords, const unsigned int nu
         fprintf(stderr, "ERROR: Could not allocate space for metadata records.\n");
         return STARCHCAT_EXIT_FAILURE;
     }
+    
     for (recIdx = 0U; recIdx < numRecords; recIdx++) {
+        instance = *mdRecords + recIdx;
 #ifdef __cplusplus
         instance->metadata = nullptr;
         instance->filename = nullptr;
@@ -5119,7 +5121,6 @@ STARCHCAT_allocMetadataRecords(MetadataRecord **mdRecords, const unsigned int nu
         instance->fp = NULL;
         instance->av = NULL;
 #endif
-        instance = *mdRecords + recIdx;
         instance->type = STARCH_DEFAULT_COMPRESSION_TYPE;
         instance->hFlag = kStarchFalse;
     }

applications/bed/starch/src/starchcluster_gnuParallel.tcsh

@@ -2,7 +2,7 @@
 
 # author  : sjn and apr
 # date    : Feb 2012
-# version : v2.4.36
+# version : v2.4.37
 
 #
 #    BEDOPS

applications/bed/starch/src/starchcluster_sge.tcsh

@@ -2,7 +2,7 @@
 
 # author  : sjn and apr
 # date    : Feb 2012
-# version : v2.4.36
+# version : v2.4.37
 
 #
 #    BEDOPS

applications/bed/starch/src/starchcluster_slurm.tcsh

@@ -2,7 +2,7 @@
 
 # author  : sjn and apr
 # date    : 13 Sep 2016
-# version : v2.4.36
+# version : v2.4.37
 
 #
 #    BEDOPS

debian/changelog

+bedops (2.4.37+dfsg-1) UNRELEASED; urgency=medium
+
+  * Team upload.
+  * New upstream version - adjusted patches
+  * Improving cleanup after build
+
+ -- Steffen Moeller <moeller@debian.org>  Wed, 23 Oct 2019 16:44:58 +0200
+
 bedops (2.4.36+dfsg-2) unstable; urgency=medium
   
   * Team upload.

debian/control

@@ -11,7 +11,7 @@ Build-Depends: debhelper-compat (= 12),
                python3-distutils,
                python3-sphinx,
                zlib1g-dev
-Standards-Version: 4.4.0
+Standards-Version: 4.4.1
 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

debian/patches/2to3.patch

@@ -6,8 +6,8 @@ Last-Update: 2019-09-13
 
 Index: bedops/applications/bed/sort-bed/src/update-sort-bed-migrate-candidates.py
 ===================================================================
---- bedops.orig/applications/bed/sort-bed/src/update-sort-bed-migrate-candidates.py	2019-09-13 15:06:08.879696791 +0100
-+++ bedops/applications/bed/sort-bed/src/update-sort-bed-migrate-candidates.py	2019-09-13 15:06:08.871696823 +0100
+--- bedops.orig/applications/bed/sort-bed/src/update-sort-bed-migrate-candidates.py
++++ bedops/applications/bed/sort-bed/src/update-sort-bed-migrate-candidates.py
 @@ -19,7 +19,7 @@
  #    51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
  #
@@ -19,8 +19,8 @@ Index: bedops/applications/bed/sort-bed/src/update-sort-bed-migrate-candidates.p
  import os
 Index: bedops/applications/bed/sort-bed/src/update-sort-bed-slurm.py
 ===================================================================
---- bedops.orig/applications/bed/sort-bed/src/update-sort-bed-slurm.py	2019-09-13 15:06:08.879696791 +0100
-+++ bedops/applications/bed/sort-bed/src/update-sort-bed-slurm.py	2019-09-13 15:06:08.871696823 +0100
+--- bedops.orig/applications/bed/sort-bed/src/update-sort-bed-slurm.py
++++ bedops/applications/bed/sort-bed/src/update-sort-bed-slurm.py
 @@ -19,7 +19,7 @@
  #    51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
  #
@@ -32,8 +32,8 @@ Index: bedops/applications/bed/sort-bed/src/update-sort-bed-slurm.py
  import os
 Index: bedops/applications/bed/sort-bed/src/update-sort-bed-starch-slurm.py
 ===================================================================
---- bedops.orig/applications/bed/sort-bed/src/update-sort-bed-starch-slurm.py	2019-09-13 15:06:08.879696791 +0100
-+++ bedops/applications/bed/sort-bed/src/update-sort-bed-starch-slurm.py	2019-09-13 15:06:08.871696823 +0100
+--- bedops.orig/applications/bed/sort-bed/src/update-sort-bed-starch-slurm.py
++++ bedops/applications/bed/sort-bed/src/update-sort-bed-starch-slurm.py
 @@ -19,7 +19,7 @@
  #    51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
  #
@@ -45,8 +45,8 @@ Index: bedops/applications/bed/sort-bed/src/update-sort-bed-starch-slurm.py
  import os
 Index: bedops/applications/bed/starch/src/starch-diff.py
 ===================================================================
---- bedops.orig/applications/bed/starch/src/starch-diff.py	2019-09-13 15:06:08.879696791 +0100
-+++ bedops/applications/bed/starch/src/starch-diff.py	2019-09-13 15:06:08.871696823 +0100
+--- bedops.orig/applications/bed/starch/src/starch-diff.py
++++ bedops/applications/bed/starch/src/starch-diff.py
 @@ -19,7 +19,7 @@
  #    51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
  #
@@ -56,7 +56,7 @@ Index: bedops/applications/bed/starch/src/starch-diff.py
  
  import sys
  import os
-@@ -77,7 +77,7 @@
+@@ -77,7 +77,7 @@ def main():
  
      all_tests_pass = True
  
@@ -65,7 +65,7 @@ Index: bedops/applications/bed/starch/src/starch-diff.py
      if args.debug: logger.info('Selected chromosome [%s]' % (selected_chromosome))
  
      archive_paths = list()
-@@ -132,11 +132,11 @@
+@@ -132,11 +132,11 @@ def main():
                      all_chromosomes[chromosome] = 0
                  all_chromosomes[chromosome] += 1
  
@@ -81,9 +81,9 @@ Index: bedops/applications/bed/starch/src/starch-diff.py
  
 Index: bedops/applications/bed/starch/test/nested_and_duplicate_elements/src/hasDuplicateElements.py
 ===================================================================
---- bedops.orig/applications/bed/starch/test/nested_and_duplicate_elements/src/hasDuplicateElements.py	2019-09-13 15:06:08.879696791 +0100
-+++ bedops/applications/bed/starch/test/nested_and_duplicate_elements/src/hasDuplicateElements.py	2019-09-13 15:06:08.871696823 +0100
-@@ -10,35 +10,35 @@
+--- bedops.orig/applications/bed/starch/test/nested_and_duplicate_elements/src/hasDuplicateElements.py
++++ bedops/applications/bed/starch/test/nested_and_duplicate_elements/src/hasDuplicateElements.py
+@@ -10,35 +10,35 @@ chr1_proc = subprocess.Popen([unstarch,
  chr1_proc_out, chr1_proc_err = chr1_proc.communicate()
  chr1_proc_out.strip('\n')
  if int(chr1_proc_out) == 0:
@@ -126,9 +126,9 @@ Index: bedops/applications/bed/starch/test/nested_and_duplicate_elements/src/has
  sys.exit(os.EX_OK)
 Index: bedops/applications/bed/starch/test/nested_and_duplicate_elements/src/hasNestedElements.py
 ===================================================================
---- bedops.orig/applications/bed/starch/test/nested_and_duplicate_elements/src/hasNestedElements.py	2019-09-13 15:06:08.879696791 +0100
-+++ bedops/applications/bed/starch/test/nested_and_duplicate_elements/src/hasNestedElements.py	2019-09-13 15:06:08.871696823 +0100
-@@ -10,35 +10,35 @@
+--- bedops.orig/applications/bed/starch/test/nested_and_duplicate_elements/src/hasNestedElements.py
++++ bedops/applications/bed/starch/test/nested_and_duplicate_elements/src/hasNestedElements.py
+@@ -10,35 +10,35 @@ chr1_proc = subprocess.Popen([unstarch,
  chr1_proc_out, chr1_proc_err = chr1_proc.communicate()
  chr1_proc_out.strip('\n')
  if int(chr1_proc_out) == 1:
@@ -171,9 +171,9 @@ Index: bedops/applications/bed/starch/test/nested_and_duplicate_elements/src/has
  sys.exit(os.EX_OK)
 Index: bedops/docs/conf.py
 ===================================================================
---- bedops.orig/docs/conf.py	2019-09-13 15:06:08.879696791 +0100
-+++ bedops/docs/conf.py	2019-09-13 15:06:08.875696807 +0100
-@@ -42,8 +42,8 @@
+--- bedops.orig/docs/conf.py
++++ bedops/docs/conf.py
+@@ -42,8 +42,8 @@ source_suffix = '.rst'
  master_doc = 'index'
  
  # General information about the project.
@@ -184,7 +184,7 @@ Index: bedops/docs/conf.py
  
  # The version info for the project you're documenting, acts as replacement for
  # |version| and |release|, also used in various other places throughout the
-@@ -200,8 +200,8 @@
+@@ -200,8 +200,8 @@ latex_elements = {
  # Grouping the document tree into LaTeX files. List of tuples
  # (source start file, target name, title, author, documentclass [howto/manual]).
  latex_documents = [
@@ -195,7 +195,7 @@ Index: bedops/docs/conf.py
  ]
  
  # The name of an image file (relative to this directory) to place at the top of
-@@ -230,8 +230,8 @@
+@@ -230,8 +230,8 @@ latex_documents = [
  # One entry per manual page. List of tuples
  # (source start file, name, description, authors, manual section).
  man_pages = [
@@ -206,7 +206,7 @@ Index: bedops/docs/conf.py
  ]
  
  # If true, show URL addresses after external links.
-@@ -244,8 +244,8 @@
+@@ -244,8 +244,8 @@ man_pages = [
  # (source start file, target name, title, author,
  #  dir menu entry, description, category)
  texinfo_documents = [
@@ -217,7 +217,7 @@ Index: bedops/docs/conf.py
     'Miscellaneous'),
  ]
  
-@@ -265,10 +265,10 @@
+@@ -265,10 +265,10 @@ texinfo_documents = [
  # -- Options for Epub output ---------------------------------------------------
  
  # Bibliographic Dublin Core info.

debian/patches/tests_use_installed_binaries.patch

@@ -4,9 +4,9 @@ Description: use the installed binaries instead of the locally generated ones
 
 Index: bedops/tests/starch/Makefile
 ===================================================================
---- bedops.orig/tests/starch/Makefile	2019-09-13 19:28:55.216495617 +0100
-+++ bedops/tests/starch/Makefile	2019-09-13 19:55:44.350045227 +0100
-@@ -1,14 +1,14 @@
+--- bedops.orig/tests/starch/Makefile
++++ bedops/tests/starch/Makefile
+@@ -1,15 +1,15 @@
  APPGROUP = starch
  CWD := $(abspath $(patsubst %/,%,$(dir $(abspath $(lastword $(MAKEFILE_LIST))))))
 -STARCH = $(CWD)/../../bin/starch
@@ -22,11 +22,13 @@ Index: bedops/tests/starch/Makefile
 +STARCHSTRIP = starchstrip
  STARCHSTRIPBIN = starchstrip
 -SORTBED = $(CWD)/../../bin/sort-bed
+-BEDMAP = $(CWD)/../../bin/bedmap
 +SORTBED = sort-bed
++BEDMAP = bedmap
  TMP := $(shell mktemp -d)
  DATA = $(CWD)/data
  SHELL := /bin/bash
-@@ -84,4 +84,4 @@
+@@ -108,4 +108,4 @@ starchstrip: starchstrip_prep
  starchstrip_prep:
  	@[ -f $(STARCHSTRIP) ] || echo "Missing binary [$(STARCHSTRIP)] for build type [$(BUILDTYPE)]"
  	@echo "Writing to [$(TMP)]"
@@ -35,8 +37,8 @@ Index: bedops/tests/starch/Makefile
 +	$(STARCHSTRIP) --version
 Index: bedops/tests/bedops/Makefile
 ===================================================================
---- bedops.orig/tests/bedops/Makefile	2019-09-13 19:28:55.208495649 +0100
-+++ bedops/tests/bedops/Makefile	2019-09-13 19:57:07.897710316 +0100
+--- bedops.orig/tests/bedops/Makefile
++++ bedops/tests/bedops/Makefile
 @@ -1,6 +1,6 @@
  APP = bedops
  CWD := $(abspath $(patsubst %/,%,$(dir $(abspath $(lastword $(MAKEFILE_LIST))))))

debian/patches/use_debian_libs

@@ -3,8 +3,10 @@ Description: upstream makes use of embedded libs, use debian ones.
 Author: Olivier Sallou <osallou@debian.org>
 Last-Update: 2017-01-13
 Forwarded: no
---- a/interfaces/src/data/starch/starchFileHelpers.c
-+++ b/interfaces/src/data/starch/starchFileHelpers.c
+Index: bedops/interfaces/src/data/starch/starchFileHelpers.c
+===================================================================
+--- bedops.orig/interfaces/src/data/starch/starchFileHelpers.c
++++ bedops/interfaces/src/data/starch/starchFileHelpers.c
 @@ -194,7 +194,7 @@ STARCH_gzip_deflate(FILE *source, FILE *
      /* deflateInit2 allows creation of archive with gzip header, i.e. a gzip file */
      /* cf. http://www.zlib.net/manual.html */
@@ -14,8 +16,10 @@ Forwarded: no
  #else
      ret = deflateInit2(&strm, level, Z_DEFLATED, (15+16), 8, Z_DEFAULT_STRATEGY);
  #endif
---- a/system.mk/Makefile.linux
-+++ b/system.mk/Makefile.linux
+Index: bedops/system.mk/Makefile.linux
+===================================================================
+--- bedops.orig/system.mk/Makefile.linux
++++ bedops/system.mk/Makefile.linux
 @@ -60,14 +60,14 @@ LIBS = $(addprefix $(PARTY3)/, jansson/l
  
  support: $(LIBS)
@@ -40,8 +44,10 @@ Forwarded: no
 +${PARTY3}/zlib/libz.a:
 +	#bzcat $^ | tar -x -C ${PARTY3}
 +	#cd ${PARTY3}/${ZLIBVERSION} && ./configure --static && $(MAKE) && cd ${WDIR} && rm -f zlib && ln -sf ${ZLIBVERSION} ${PARTY3}/zlib
---- a/applications/bed/conversion/src/Makefile
-+++ b/applications/bed/conversion/src/Makefile
+Index: bedops/applications/bed/conversion/src/Makefile
+===================================================================
+--- bedops.orig/applications/bed/conversion/src/Makefile
++++ bedops/applications/bed/conversion/src/Makefile
 @@ -13,7 +13,7 @@ OBJDIR                    = objects${POS
  WRAPPERDIR                = wrappers
  PROG                      = convert2bed
@@ -51,8 +57,10 @@ Forwarded: no
  
  all: build
  
---- a/applications/bed/sort-bed/src/Makefile
-+++ b/applications/bed/sort-bed/src/Makefile
+Index: bedops/applications/bed/sort-bed/src/Makefile
+===================================================================
+--- bedops.orig/applications/bed/sort-bed/src/Makefile
++++ bedops/applications/bed/sort-bed/src/Makefile
 @@ -4,7 +4,7 @@ LIB1                = $(MAIN)/interfaces
  LIB2                = $(MAIN)/interfaces/src/utility
  LIB3                = $(MAIN)/interfaces/src/data/starch
@@ -81,8 +89,10 @@ Forwarded: no
  
  dependency_names    = starchConstants starchFileHelpers starchHelpers starchMetadataHelpers unstarchHelpers starchSha1Digest starchBase64Coding SortDetails Sort CheckSort
  dependencies        = $(addprefix $(OBJDIR)/, $(addsuffix .o, $(dependency_names)))
---- a/applications/bed/starch/src/Makefile
-+++ b/applications/bed/starch/src/Makefile
+Index: bedops/applications/bed/starch/src/Makefile
+===================================================================
+--- bedops.orig/applications/bed/starch/src/Makefile
++++ bedops/applications/bed/starch/src/Makefile
 @@ -29,15 +29,15 @@ LOCALZLIBLIB              = ${LOCALZLIBL
  LOCALZLIBINCDIR           = ${LOCALZLIBDIR}
  OBJDIR                    = ${INTERFACES}/src/data/starch
@@ -120,9 +130,11 @@ Forwarded: no
  	mkdir -p $(LOCALOBJDIR)
  	${CXX} ${CXXFLAGS} ${MEGAFLAGS} -c $< -o $@ ${INCLUDES}
  
---- a/applications/bed/starch/src/starchcat.c
-+++ b/applications/bed/starch/src/starchcat.c
-@@ -6177,7 +6177,7 @@ STARCHCAT2_setupGzipOutputStream(z_strea
+Index: bedops/applications/bed/starch/src/starchcat.c
+===================================================================
+--- bedops.orig/applications/bed/starch/src/starchcat.c
++++ bedops/applications/bed/starch/src/starchcat.c
+@@ -6178,7 +6178,7 @@ STARCHCAT2_setupGzipOutputStream(z_strea
  
      /* cf. http://www.zlib.net/manual.html for level information */
  #ifdef __cplusplus
@@ -131,8 +143,10 @@ Forwarded: no
  #else
      zError = deflateInit2(zStreamPtr, STARCH_Z_COMPRESSION_LEVEL, Z_DEFLATED, STARCH_Z_WINDOW_BITS, STARCH_Z_MEMORY_LEVEL, Z_DEFAULT_STRATEGY);
  #endif
---- a/docs/conf.py
-+++ b/docs/conf.py
+Index: bedops/docs/conf.py
+===================================================================
+--- bedops.orig/docs/conf.py
++++ bedops/docs/conf.py
 @@ -12,7 +12,6 @@
  # serve to show the default.
  
@@ -163,8 +177,10 @@ Forwarded: no
  
  # The name for this set of Sphinx documents.  If None, it defaults to
  # "<project> v<release> documentation".
---- a/applications/bed/bedops/src/Makefile
-+++ b/applications/bed/bedops/src/Makefile
+Index: bedops/applications/bed/bedops/src/Makefile
+===================================================================
+--- bedops.orig/applications/bed/bedops/src/Makefile
++++ bedops/applications/bed/bedops/src/Makefile
 @@ -22,11 +22,11 @@ LOCALZLIBDIR        = ${PARTY3}/zlib
  LOCALZLIBLIB        = ${LOCALZLIBDIR}/${LIBZLIB}
  LOCALZLIBINCDIR     = ${LOCALZLIBDIR}
@@ -181,8 +197,10 @@ Forwarded: no
  
  dependency_names    = NaN starchConstants starchFileHelpers starchHelpers starchMetadataHelpers unstarchHelpers starchSha1Digest starchBase64Coding
  dependencies        = $(addprefix $(OBJDIR)/, $(addsuffix .o, $(dependency_names)))
---- a/applications/bed/bedextract/src/Makefile
-+++ b/applications/bed/bedextract/src/Makefile
+Index: bedops/applications/bed/bedextract/src/Makefile
+===================================================================
+--- bedops.orig/applications/bed/bedextract/src/Makefile
++++ bedops/applications/bed/bedextract/src/Makefile
 @@ -21,11 +21,11 @@ LOCALBZIP2INCDIR        = ${LOCALBZIP2DI
  LOCALZLIBDIR            = ${PARTY3}/zlib
  LOCALZLIBLIB            = ${LOCALZLIBDIR}/${LIBZLIB}
@@ -199,8 +217,10 @@ Forwarded: no
  
  dependency_names        = NaN starchConstants starchFileHelpers starchHelpers starchMetadataHelpers unstarchHelpers starchSha1Digest starchBase64Coding
  dependencies            = $(addprefix $(OBJDIR)/, $(addsuffix .o, $(dependency_names)))
---- a/applications/bed/bedmap/src/Makefile
-+++ b/applications/bed/bedmap/src/Makefile
+Index: bedops/applications/bed/bedmap/src/Makefile
+===================================================================
+--- bedops.orig/applications/bed/bedmap/src/Makefile
++++ bedops/applications/bed/bedmap/src/Makefile
 @@ -20,11 +20,11 @@ LOCALZLIBDIR        = ${PARTY3}/zlib
  LOCALZLIBLIB        = ${LOCALZLIBDIR}/${LIBZLIB}
  LOCALZLIBINCDIR     = ${LOCALZLIBDIR}
@@ -217,8 +237,10 @@ Forwarded: no
  
  dependency_names    = NaN starchConstants starchFileHelpers starchHelpers starchMetadataHelpers unstarchHelpers starchSha1Digest starchBase64Coding
  dependencies        = $(addprefix $(OBJDIR)/, $(addsuffix .o, $(dependency_names)))
---- a/applications/bed/closestfeats/src/Makefile
-+++ b/applications/bed/closestfeats/src/Makefile
+Index: bedops/applications/bed/closestfeats/src/Makefile
+===================================================================
+--- bedops.orig/applications/bed/closestfeats/src/Makefile
++++ bedops/applications/bed/closestfeats/src/Makefile
 @@ -20,11 +20,11 @@ LOCALZLIBDIR        = ${PARTY3}/zlib
  LOCALZLIBLIB        = ${LOCALZLIBDIR}/${LIBZLIB}
  LOCALZLIBINCDIR     = ${LOCALZLIBDIR}

debian/rules

@@ -48,3 +48,7 @@ override_dh_installman-arch:
 override_dh_dwz:
 	# Work around: dwz: Too few files for multifile optimization
 	echo "Do not run dh_dwz"
+
+override_dh_auto_clean:
+	dh_auto_clean
+	rm -rf docs/_build/