From 243f7a5be29afba188fbd03c7651c6e3cecf02ab Mon Sep 17 00:00:00 2001
From: Mark Iskander <motiontracker@gmail.com>
Date: Fri, 20 Nov 2015 09:54:24 -0600
Subject: [PATCH 1/3] Added bcf_bgzip to bcf converter

---
 .../converters/bcfgz_to_bcf_converter.py      | 22 +++++++++++++++++++
 .../converters/bcfgz_to_bcf_converter.xml     | 14 ++++++++++++
 2 files changed, 36 insertions(+)
 create mode 100644 lib/galaxy/datatypes/converters/bcfgz_to_bcf_converter.py
 create mode 100644 lib/galaxy/datatypes/converters/bcfgz_to_bcf_converter.xml

diff --git a/lib/galaxy/datatypes/converters/bcfgz_to_bcf_converter.py b/lib/galaxy/datatypes/converters/bcfgz_to_bcf_converter.py
new file mode 100644
index 00000000000..35dd32a711e
--- /dev/null
+++ b/lib/galaxy/datatypes/converters/bcfgz_to_bcf_converter.py
@@ -0,0 +1,22 @@
+#!/usr/bin/env python
+
+"""
+Uses bcftools to extract a bcf from a bcf.gz
+
+usage: %prog in_file out_file
+"""
+import optparse
+import subprocess
+
+
+def main():
+    # Read options, args.
+    parser = optparse.OptionParser()
+    (options, args) = parser.parse_args()
+    input_fname, output_fname = args
+
+    subprocess.call(["bcftools", "view", input_fname, "-o", output_fname, "-O", "u"])
+
+
+if __name__ == "__main__":
+    main()
diff --git a/lib/galaxy/datatypes/converters/bcfgz_to_bcf_converter.xml b/lib/galaxy/datatypes/converters/bcfgz_to_bcf_converter.xml
new file mode 100644
index 00000000000..55044300bba
--- /dev/null
+++ b/lib/galaxy/datatypes/converters/bcfgz_to_bcf_converter.xml
@@ -0,0 +1,14 @@
+<tool id="CONVERTER_bcf_bgzip_to_bcf" name="Convert BCF_BGZIP to BCF" version="0.0.1" hidden="false">
+<!--  <description>__NOT_USED_CURRENTLY_FOR_CONVERTERS__</description> -->
+  <command interpreter="python">bcfgz_to_bcf_converter.py '$input1' '$output1'</command>
+  <inputs>
+    <page>
+        <param format="bcf_bgzip" name="input1" type="data" label="Choose bcf_bgzip file"/>
+    </page>
+   </inputs>
+  <outputs>
+    <data format="bcf" name="output1"/>
+  </outputs>
+  <help>
+  </help>
+</tool>

From 6cd550e0c7844cf89289f8ff25b9e3995b2d0bac Mon Sep 17 00:00:00 2001
From: Mark Iskander <motiontracker@gmail.com>
Date: Fri, 20 Nov 2015 12:25:00 -0600
Subject: [PATCH 2/3] Added the bcf_bgzip_to_bcf converter to
 datatype.converters.rst, renamed files to follow standard naming scheme

---
 doc/source/lib/galaxy.datatypes.converters.rst         | 10 ++++++++--
 .../{bcfgz_to_bcf_converter.py => bcf_bgzip_to_bcf.py} |  0
 ...bcfgz_to_bcf_converter.xml => bcf_bgzip_to_bcf.xml} |  0
 3 files changed, 8 insertions(+), 2 deletions(-)
 rename lib/galaxy/datatypes/converters/{bcfgz_to_bcf_converter.py => bcf_bgzip_to_bcf.py} (100%)
 rename lib/galaxy/datatypes/converters/{bcfgz_to_bcf_converter.xml => bcf_bgzip_to_bcf.xml} (100%)

diff --git a/doc/source/lib/galaxy.datatypes.converters.rst b/doc/source/lib/galaxy.datatypes.converters.rst
index 7435e980ab5..f0f735a2d98 100644
--- a/doc/source/lib/galaxy.datatypes.converters.rst
+++ b/doc/source/lib/galaxy.datatypes.converters.rst
@@ -225,6 +225,14 @@ galaxy.datatypes.converters.vcf_to_vcf_bgzip module
     :undoc-members:
     :show-inheritance:
 
+galaxy.datatypes.converters.bcf_bgzip_to_bcf module
+---------------------------------------------------
+
+.. automodule:: galaxy.datatypes.converters.bcf_bgzip_to_bcf
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
 galaxy.datatypes.converters.wiggle_to_array_tree_converter module
 -----------------------------------------------------------------
 
@@ -240,5 +248,3 @@ galaxy.datatypes.converters.wiggle_to_simple_converter module
     :members:
     :undoc-members:
     :show-inheritance:
-
-
diff --git a/lib/galaxy/datatypes/converters/bcfgz_to_bcf_converter.py b/lib/galaxy/datatypes/converters/bcf_bgzip_to_bcf.py
similarity index 100%
rename from lib/galaxy/datatypes/converters/bcfgz_to_bcf_converter.py
rename to lib/galaxy/datatypes/converters/bcf_bgzip_to_bcf.py
diff --git a/lib/galaxy/datatypes/converters/bcfgz_to_bcf_converter.xml b/lib/galaxy/datatypes/converters/bcf_bgzip_to_bcf.xml
similarity index 100%
rename from lib/galaxy/datatypes/converters/bcfgz_to_bcf_converter.xml
rename to lib/galaxy/datatypes/converters/bcf_bgzip_to_bcf.xml

From 825a20ef8138d04b25ebb5bea907abe23abc889d Mon Sep 17 00:00:00 2001
From: Mark Iskander <motiontracker@gmail.com>
Date: Fri, 20 Nov 2015 13:49:04 -0600
Subject: [PATCH 3/3] Modified more names, added bcf_bgzip to datatypes, added
 converters going both ways

---
 config/datatypes_conf.xml.sample              |  7 +++++-
 .../lib/galaxy.datatypes.converters.rst       |  8 +++++++
 ...o_bcf.py => bcf_bgzip_to_bcf_converter.py} |  0
 ...bcf.xml => bcf_bgzip_to_bcf_converter.xml} |  2 +-
 .../converters/bcf_to_bcf_bgzip_converter.py  | 22 +++++++++++++++++++
 .../converters/bcf_to_bcf_bgzip_converter.xml | 14 ++++++++++++
 6 files changed, 51 insertions(+), 2 deletions(-)
 rename lib/galaxy/datatypes/converters/{bcf_bgzip_to_bcf.py => bcf_bgzip_to_bcf_converter.py} (100%)
 rename lib/galaxy/datatypes/converters/{bcf_bgzip_to_bcf.xml => bcf_bgzip_to_bcf_converter.xml} (81%)
 create mode 100644 lib/galaxy/datatypes/converters/bcf_to_bcf_bgzip_converter.py
 create mode 100644 lib/galaxy/datatypes/converters/bcf_to_bcf_bgzip_converter.xml

diff --git a/config/datatypes_conf.xml.sample b/config/datatypes_conf.xml.sample
index d3505088219..eb6e3193a28 100644
--- a/config/datatypes_conf.xml.sample
+++ b/config/datatypes_conf.xml.sample
@@ -247,7 +247,12 @@
       <display file="igv/vcf.xml" />
       <display file="rviewer/vcf.xml" inherit="True"/>
     </datatype>
-    <datatype extension="bcf" type="galaxy.datatypes.binary:Bcf" mimetype="application/octet-stream" display_in_upload="True"/>
+    <datatype extension="bcf" type="galaxy.datatypes.binary:Bcf" mimetype="application/octet-stream" display_in_upload="True">
+      <converter file="bcf_to_bcf_bgzip_converter.xml" target_datatype="bcf_bgzip"/>
+    </datatype>
+    <datatype extension="bcf_bgzip" type="galaxy.datatypes.binary:Binary" mimetype="application/octet-stream" subclass="True">
+      <converter file="bcf_bgzip_to_bcf_converter.xml" target_datatype="bcf"/>
+    </datatype>
     <datatype extension="velvet" type="galaxy.datatypes.assembly:Velvet" display_in_upload="false"/>
     <datatype extension="wig" type="galaxy.datatypes.interval:Wiggle" display_in_upload="true" description="The wiggle format is line-oriented.  Wiggle data is preceded by a track definition line, which adds a number of options for controlling the default display of this track." description_url="https://wiki.galaxyproject.org/Learn/Datatypes#Wig">
       <converter file="wig_to_bigwig_converter.xml" target_datatype="bigwig"/>
diff --git a/doc/source/lib/galaxy.datatypes.converters.rst b/doc/source/lib/galaxy.datatypes.converters.rst
index f0f735a2d98..dacdc91828d 100644
--- a/doc/source/lib/galaxy.datatypes.converters.rst
+++ b/doc/source/lib/galaxy.datatypes.converters.rst
@@ -233,6 +233,14 @@ galaxy.datatypes.converters.bcf_bgzip_to_bcf module
     :undoc-members:
     :show-inheritance:
 
+galaxy.datatypes.converters.bcf_to_bcf_bgzip module
+---------------------------------------------------
+
+.. automodule:: galaxy.datatypes.converters.bcf_to_bcf_bgzip
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
 galaxy.datatypes.converters.wiggle_to_array_tree_converter module
 -----------------------------------------------------------------
 
diff --git a/lib/galaxy/datatypes/converters/bcf_bgzip_to_bcf.py b/lib/galaxy/datatypes/converters/bcf_bgzip_to_bcf_converter.py
similarity index 100%
rename from lib/galaxy/datatypes/converters/bcf_bgzip_to_bcf.py
rename to lib/galaxy/datatypes/converters/bcf_bgzip_to_bcf_converter.py
diff --git a/lib/galaxy/datatypes/converters/bcf_bgzip_to_bcf.xml b/lib/galaxy/datatypes/converters/bcf_bgzip_to_bcf_converter.xml
similarity index 81%
rename from lib/galaxy/datatypes/converters/bcf_bgzip_to_bcf.xml
rename to lib/galaxy/datatypes/converters/bcf_bgzip_to_bcf_converter.xml
index 55044300bba..90b67ca1db6 100644
--- a/lib/galaxy/datatypes/converters/bcf_bgzip_to_bcf.xml
+++ b/lib/galaxy/datatypes/converters/bcf_bgzip_to_bcf_converter.xml
@@ -1,6 +1,6 @@
 <tool id="CONVERTER_bcf_bgzip_to_bcf" name="Convert BCF_BGZIP to BCF" version="0.0.1" hidden="false">
 <!--  <description>__NOT_USED_CURRENTLY_FOR_CONVERTERS__</description> -->
-  <command interpreter="python">bcfgz_to_bcf_converter.py '$input1' '$output1'</command>
+  <command interpreter="python">bcf_bgzip_to_bcf_converter.py '$input1' '$output1'</command>
   <inputs>
     <page>
         <param format="bcf_bgzip" name="input1" type="data" label="Choose bcf_bgzip file"/>
diff --git a/lib/galaxy/datatypes/converters/bcf_to_bcf_bgzip_converter.py b/lib/galaxy/datatypes/converters/bcf_to_bcf_bgzip_converter.py
new file mode 100644
index 00000000000..ba52f0116dc
--- /dev/null
+++ b/lib/galaxy/datatypes/converters/bcf_to_bcf_bgzip_converter.py
@@ -0,0 +1,22 @@
+#!/usr/bin/env python
+
+"""
+Uses bcftools to compress a bcf into a bcf.gz
+
+usage: %prog in_file out_file
+"""
+import optparse
+import subprocess
+
+
+def main():
+    # Read options, args.
+    parser = optparse.OptionParser()
+    (options, args) = parser.parse_args()
+    input_fname, output_fname = args
+
+    subprocess.call(["bcftools", "view", input_fname, "-o", output_fname, "-O", "b"])
+
+
+if __name__ == "__main__":
+    main()
diff --git a/lib/galaxy/datatypes/converters/bcf_to_bcf_bgzip_converter.xml b/lib/galaxy/datatypes/converters/bcf_to_bcf_bgzip_converter.xml
new file mode 100644
index 00000000000..5aea96fc5b7
--- /dev/null
+++ b/lib/galaxy/datatypes/converters/bcf_to_bcf_bgzip_converter.xml
@@ -0,0 +1,14 @@
+<tool id="CONVERTER_bcf_to_bcf_bgzip" name="Convert BCF to BCF_BGZIP" version="0.0.1" hidden="false">
+<!--  <description>__NOT_USED_CURRENTLY_FOR_CONVERTERS__</description> -->
+  <command interpreter="python">bcf_to_bcf_bgzip_converter.py '$input1' '$output1'</command>
+  <inputs>
+    <page>
+        <param format="bcf" name="input1" type="data" label="Choose bcf file"/>
+    </page>
+   </inputs>
+  <outputs>
+    <data format="bcf_bgzip" name="output1"/>
+  </outputs>
+  <help>
+  </help>
+</tool>