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bedops · Jan 25, 2017 · e7631c4 · e7631c4
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diff --git a/README.md b/README.md
@@ -1,14 +1,14 @@
-## BEDOPS v2.4.21: high-performance genomic feature operations ##
+## BEDOPS v2.4.22: 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)
 
 <!-- <img src="http://bedops.readthedocs.io/en/latest/_static/logo_with_label_v2.png" align="right" style="max-width:33%" /> -->
 
 ### About ###
 
-**BEDOPS v2.4.21** 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 v2.4.22** 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 v2.4.21** 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 v2.4.22** 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 ###
@@ -28,21 +28,21 @@ 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/v2.4.21/bedops_linux_x86_64-v2.4.21.tar.bz2">x86-64 (64-bit)</a> binaries</li>
-<li><a href="https://github.com/bedops/bedops/releases/download/v2.4.21/bedops_linux_i386-v2.4.21.tar.bz2">i386 (32-bit)</a> binaries</li>
+<li><a href="https://github.com/bedops/bedops/releases/download/v2.4.22/bedops_linux_x86_64-v2.4.22.tar.bz2">x86-64 (64-bit)</a> binaries</li>
+<li><a href="https://github.com/bedops/bedops/releases/download/v2.4.22/bedops_linux_i386-v2.4.22.tar.bz2">i386 (32-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/v2.4.21/BEDOPS.2.4.21.pkg.zip">Intel (32-/64-bit, 10.7-10.11)</a> installer package</li>
+<li><a href="https://github.com/bedops/bedops/releases/download/v2.4.22/BEDOPS.2.4.22.pkg.zip">Intel (32-/64-bit, 10.7-10.11)</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/v2.4.21.tar.gz">Source code</a> (tar.gz)</li>
-<li><a href="https://github.com/bedops/bedops/archive/v2.4.21.zip">Source code</a> (zip)</li>
+<li><a href="https://github.com/bedops/bedops/archive/v2.4.22.tar.gz">Source code</a> (tar.gz)</li>
+<li><a href="https://github.com/bedops/bedops/archive/v2.4.22.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>
@@ -51,11 +51,11 @@ The <a href="https://bedops.readthedocs.io/en/latest/content/overview.html#overv
 
 ### Documentation ###
 
-Complete documentation for **BEDOPS v2.4.21** tools is available at: <a href="https://bedops.readthedocs.io/en/latest/index.html">https://bedops.readthedocs.io/</a>
+Complete documentation for **BEDOPS v2.4.22** tools is available at: <a href="https://bedops.readthedocs.io/en/latest/index.html">https://bedops.readthedocs.io/</a>
 
 ### Citation ###
 
-If you use **BEDOPS v2.4.21** in your research, please cite the following manuscript:
+If you use **BEDOPS v2.4.22** in your research, please cite the following manuscript:
 
 > Shane Neph, M. Scott Kuehn, Alex P. Reynolds, et al.  
 > [**BEDOPS: high-performance genomic feature operations**  

diff --git a/applications/bed/conversion/src/convert2bed.h b/applications/bed/conversion/src/convert2bed.h
@@ -51,7 +51,7 @@
 #include <sys/param.h>
 #include <sys/wait.h>
 
-#define C2B_VERSION "2.4.21"
+#define C2B_VERSION "2.4.22"
 
 typedef int boolean;
 extern const boolean kTrue;

diff --git a/docs/conf.py b/docs/conf.py
@@ -52,7 +52,7 @@
 # The short X.Y version.
 version = '2.4'
 # The full version, including alpha/beta/rc tags.
-release = '2.4.21'
+release = '2.4.22'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

diff --git a/docs/content/reference/file-management/compression/starch.rst b/docs/content/reference/file-management/compression/starch.rst
@@ -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: 2.4.21 (creates archive version: 2.2.0)
+   binary version: 2.4.22 (creates archive version: 2.2.0)
    authors:  Alex Reynolds and Shane Neph
 
   USAGE: starch [ --note="foo bar..." ]

diff --git a/docs/content/reference/file-management/compression/starchcat.rst b/docs/content/reference/file-management/compression/starchcat.rst
@@ -57,7 +57,7 @@ Use the ``--help`` option to list all options:
 
   starchcat
    citation: http://bioinformatics.oxfordjournals.org/content/28/14/1919.abstract
-   version:  2.4.21
+   version:  2.4.22
    authors:  Alex Reynolds and Shane Neph
 
   USAGE: starchcat [ --note="..." ]

diff --git a/docs/content/reference/file-management/compression/unstarch.rst b/docs/content/reference/file-management/compression/unstarch.rst
@@ -43,7 +43,7 @@ Use the ``--help`` option to list all options:
 
   unstarch
    citation: http://bioinformatics.oxfordjournals.org/content/28/14/1919.abstract
-   binary version: 2.4.21 (extracts archive version: 2.2.0 or older)
+   binary version: 2.4.22 (extracts archive version: 2.2.0 or older)
    authors: Alex Reynolds and Shane Neph
 
   USAGE: unstarch [ <chromosome> ]  [ --elements | 

diff --git a/docs/content/reference/file-management/conversion/gtf2bed.rst b/docs/content/reference/file-management/conversion/gtf2bed.rst
@@ -41,18 +41,18 @@ To demonstrate these scripts, we use a sample GTF input called ``foo.gtf`` (see
 
 ::
 
-  chr20      protein_coding  exon    9874841 9874841 .       +       .       gene_id "ENSBTAG00000020601"; transcript_id "ENSBTAT0000002.4.21"; gene_name "ZNF366";
-  chr20      protein_coding  CDS     9873504 9874841 .       +       0       gene_id "ENSBTAG00000020601"; transcript_id "ENSBTAT0000002.4.21"; gene_name "ZNF366";
-  chr20      protein_coding  exon    9877488 9877679 .       +       .       gene_id "ENSBTAG00000020601"; transcript_id "ENSBTAT0000002.4.21";
+  chr20      protein_coding  exon    9874841 9874841 .       +       .       gene_id "ENSBTAG00000020601"; transcript_id "ENSBTAT0000002.4.22"; gene_name "ZNF366";
+  chr20      protein_coding  CDS     9873504 9874841 .       +       0       gene_id "ENSBTAG00000020601"; transcript_id "ENSBTAT0000002.4.22"; gene_name "ZNF366";
+  chr20      protein_coding  exon    9877488 9877679 .       +       .       gene_id "ENSBTAG00000020601"; transcript_id "ENSBTAT0000002.4.22";
 
 We can convert it to sorted BED data in the following manner:
 
 ::
 
   $ gtf2bed < foo.gtf
-  chr20   9874840 9874841 ZNF366  .       +       protein_coding  exon    .       gene_id "ENSBTAG00000020601"; transcript_id "ENSBTAT0000002.4.21"; gene_name "ZNF366"; zero_length_insertion "True";
-  chr20   9873503 9874841 ZNF366  .       +       protein_coding  CDS     0       gene_id "ENSBTAG00000020601"; transcript_id "ENSBTAT0000002.4.21"; gene_name "ZNF366";
-  chr20   9877487 9877679 ENSBTAG00000020601      .       +       protein_coding  exon    .       gene_id "ENSBTAG00000020601"; transcript_id "ENSBTAT0000002.4.21";
+  chr20   9874840 9874841 ZNF366  .       +       protein_coding  exon    .       gene_id "ENSBTAG00000020601"; transcript_id "ENSBTAT0000002.4.22"; gene_name "ZNF366"; zero_length_insertion "True";
+  chr20   9873503 9874841 ZNF366  .       +       protein_coding  CDS     0       gene_id "ENSBTAG00000020601"; transcript_id "ENSBTAT0000002.4.22"; gene_name "ZNF366";
+  chr20   9877487 9877679 ENSBTAG00000020601      .       +       protein_coding  exon    .       gene_id "ENSBTAG00000020601"; transcript_id "ENSBTAT0000002.4.22";
 
 .. tip:: After, say, performing set or statistical operations with :ref:`bedops`, :ref:`bedmap` etc., converting data back to GTF is accomplished through an ``awk`` statement that re-orders columns and shifts the coordinate index:
 

diff --git a/docs/content/reference/file-management/conversion/psl2bed.rst b/docs/content/reference/file-management/conversion/psl2bed.rst
@@ -57,7 +57,7 @@ To demonstrate these scripts, we use a sample PSL input called ``foo.psl`` (see
   30      0       0       0       0       0       0       0       +       foo     50      14      44      chr6    171115067       127685756       127685786       1       30,     14,     127685756,
   30      0       0       0       0       0       0       0       +       foo     50      14      44      chr6    171115067       93161871        93161901        1       30,     14,     93161871,
   31      0       0       0       0       0       0       0       +       foo     50      13      44      chr5    180915260       119897315       119897346       1       31,     13,     119897315,
-  30      0       0       0       0       0       0       0       +       foo     50      14      44      chr5    180915260       123254725       1232.4.215       1       30,     14,     123254725,
+  30      0       0       0       0       0       0       0       +       foo     50      14      44      chr5    180915260       123254725       1232.4.225       1       30,     14,     123254725,
   ...
 
 We can convert it to sorted BED data in the following manner:

diff --git a/docs/content/reference/file-management/conversion/vcf2bed.rst b/docs/content/reference/file-management/conversion/vcf2bed.rst
@@ -54,7 +54,7 @@ In addition, using any of these three custom options automatically results in pr
 ::
 
   #CHROM POS     ID        REF    ALT     QUAL FILTER INFO                              FORMAT      NA00001        NA00002        NA00003
-  20     12.4.217 microsat1 GTC    G,GTCT  50   PASS   NS=3;DP=9;AA=G                    GT:GQ:DP    0/1:35:4       0/2:17:2       1/1:40:3
+  20     12.4.227 microsat1 GTC    G,GTCT  50   PASS   NS=3;DP=9;AA=G                    GT:GQ:DP    0/1:35:4       0/2:17:2       1/1:40:3
 
 When using ``--snvs``, ``--insertions`` or ``--deletions``, this record is split into two distinct BED records and filtered depending on which custom option was chosen. The ``--insertions`` option would only export the single-base position of the insertion in this mixed variant, while ``--deletions`` would show the deletion.
 

diff --git a/docs/content/reference/file-management/sorting/sort-bed.rst b/docs/content/reference/file-management/sorting/sort-bed.rst
@@ -35,7 +35,7 @@ The ``--help`` option is fairly basic, but describes the usage:
 
   sort-bed
     citation: http://bioinformatics.oxfordjournals.org/content/28/14/1919.abstract
-    version:  2.4.21
+    version:  2.4.22
     authors:  Scott Kuehn
 
   USAGE: sort-bed [--help] [--version] [--check-sort] [--max-mem <val>] [--tmpdir <path>] <file1.bed> <file2.bed> <...>

diff --git a/docs/content/reference/set-operations/bedops.rst b/docs/content/reference/set-operations/bedops.rst
@@ -53,7 +53,7 @@ The ``--help`` option describes the set operation and other options available to
 
   bedops
     citation: http://bioinformatics.oxfordjournals.org/content/28/14/1919.abstract
-    version:  2.4.21
+    version:  2.4.22
     authors:  Shane Neph & Scott Kuehn
 
         USAGE: bedops [process-flags] <operation> <File(s)>*

diff --git a/docs/content/reference/set-operations/closest-features.rst b/docs/content/reference/set-operations/closest-features.rst
@@ -45,7 +45,7 @@ The ``--help`` option describes the various operations and options available to
 
   closest-features
     citation: http://bioinformatics.oxfordjournals.org/content/28/14/1919.abstract
-    version:  2.4.21
+    version:  2.4.22
     authors:  Shane Neph & Scott Kuehn
 
   USAGE: closest-features [Process-Flags] <input-file> <query-file>

diff --git a/docs/content/reference/statistics/bedmap.rst b/docs/content/reference/statistics/bedmap.rst
@@ -48,7 +48,7 @@ The ``--help`` option describes the various mapping and analytical operations an
 
   bedmap
     citation: http://bioinformatics.oxfordjournals.org/content/28/14/1919.abstract
-    version:  2.4.21
+    version:  2.4.22
     authors:  Shane Neph & Scott Kuehn
 
    USAGE: bedmap [process-flags] [overlap-option] <operation(s)...> <ref-file> [map-file]
@@ -420,9 +420,9 @@ As an example of using the ``--echo-map-id`` operator in a biological context, w
 ::
 
   chr1    4534161 4534177 -V_GRE_C        4.20586e-06     -       CGTACACACAGTTCTT
-  chr1    4534192.4.214205 -V_STAT_Q6      2.21622e-06     -       AGCACTTCTGGGA
+  chr1    4534192.4.224205 -V_STAT_Q6      2.21622e-06     -       AGCACTTCTGGGA
   chr1    4534209 4534223 +V_HNF4_Q6_01   6.93604e-06     +       GGACCAGAGTCCAC
-  chr1    4962522.4.212540 -V_GCNF_01      9.4497e-06      -       CCCAAGGTCAAGATAAAG
+  chr1    4962522.4.222540 -V_GCNF_01      9.4497e-06      -       CCCAAGGTCAAGATAAAG
   chr1    4962529 4962539 +V_NUR77_Q5     8.43564e-06     +       TTGACCTTGG
   ...
 
@@ -674,9 +674,9 @@ To demonstrate their use, we revisit the ``Motifs`` dataset, which includes *p*-
 ::
 
   chr1    4534161 4534177 -V_GRE_C        4.20586e-06     -       CGTACACACAGTTCTT
-  chr1    4534192.4.214205 -V_STAT_Q6      2.21622e-06     -       AGCACTTCTGGGA
+  chr1    4534192.4.224205 -V_STAT_Q6      2.21622e-06     -       AGCACTTCTGGGA
   chr1    4534209 4534223 +V_HNF4_Q6_01   6.93604e-06     +       GGACCAGAGTCCAC
-  chr1    4962522.4.212540 -V_GCNF_01      9.4497e-06      -       CCCAAGGTCAAGATAAAG
+  chr1    4962522.4.222540 -V_GCNF_01      9.4497e-06      -       CCCAAGGTCAAGATAAAG
   chr1    4962529 4962539 +V_NUR77_Q5     8.43564e-06     +       TTGACCTTGG
   ...
 

diff --git a/docs/content/release.rst b/docs/content/release.rst
@@ -15,7 +15,7 @@ Preparing a major, minor or maintenance release of BEDOPS from a development bra
 
    a. Close out open documentation or feature issues, making necessary pushes to the current development branch.
 
-   b. If any issues can't be closed out, rename the assigned version tag to the next anticipated release version (*e.g.*, *v2.4.21* to *v2p5p0*, etc.)
+   b. If any issues can't be closed out, rename the assigned version tag to the next anticipated release version (*e.g.*, *v2.4.22* to *v2p5p0*, etc.)
 
 2. Pull the most recent commit for the development branch to a local folder on build hosts (Linux with sufficiently old kernel, current OS X, etc.).
 
@@ -44,7 +44,7 @@ Preparing a major, minor or maintenance release of BEDOPS from a development bra
 
      BEDOPS.X.Y.Z.pkg.zip
 
-   The *X.Y.Z* scheme should follow the development branch name, *e.g.* 2.4.21, etc.
+   The *X.Y.Z* scheme should follow the development branch name, *e.g.* 2.4.22, etc.
 
 3. Collect tarballs and zipped Installer in one location for later addition with web browser, via BEDOPS Github web site.
 
@@ -63,7 +63,7 @@ Release
 
    Ideally, whatever steps are used to merge the development branch into the master branch should preserve the overall commit history.
 
-   As before, the *X.Y.Z* scheme should follow the development branch name, *e.g.* 2.4.21, etc.
+   As before, the *X.Y.Z* scheme should follow the development branch name, *e.g.* 2.4.22, etc.
 
 2. Add a `new release <https://github.com/bedops/bedops/releases/new>`_ via the Github site. Or click on the `Draft a new release <https://github.com/bedops/bedops/releases>`_ button from the Github Releases page.
 

diff --git a/docs/content/revision-history.rst b/docs/content/revision-history.rst
@@ -11,6 +11,20 @@ This page summarizes some of the more important changes between releases.
 Current version
 ===============
 
+-------
+v2.4.22
+-------
+
+Released: **January 25, 2017**
+
+* :ref:`convert2bed <convert2bed>`
+
+  * Fixed heap corruption in GFF conversion. Thanks to J. Miguel Mendez (ObjectiveTruth) for the bug report.
+
+=================
+Previous versions
+=================
+
 -------
 v2.4.21
 -------
@@ -119,10 +133,6 @@ Released: **January 23, 2017**
 
   * Our use of Travis CI to automate testing of builds now includes Clang on `their OS X environment <https://docs.travis-ci.com/user/osx-ci-environment/>`_.
 
-=================
-Previous versions
-=================
-
 -------
 v2.4.20
 -------