From f409a5339fe96e0e47d1de88dd7ecbd94e2a3324 Mon Sep 17 00:00:00 2001
From: Devon Ryan <dpryan79@gmail.com>
Date: Sun, 31 Mar 2019 12:33:53 +0200
Subject: [PATCH 1/7] Implement #816

---
 deeptools/bigwigCompare.py            | 7 +++++++
 deeptools/writeBedGraph_bam_and_bw.py | 6 +++++-
 2 files changed, 12 insertions(+), 1 deletion(-)

diff --git a/deeptools/bigwigCompare.py b/deeptools/bigwigCompare.py
index bfce8a80c..80738840c 100644
--- a/deeptools/bigwigCompare.py
+++ b/deeptools/bigwigCompare.py
@@ -61,6 +61,12 @@ def parse_arguments(args=None):
                         type=float,
                         required=False)
 
+    parser.add_argument('--skipZeroOverZero',
+                        help='Skip bins where BOTH BAM files lack coverage. '
+                        'This is determined BEFORE any applicable pseudocount '
+                        'is added.',
+                        action='store_true')
+
     parser.add_argument('--operation',
                         help='The default is to output the log2ratio of the '
                         'two samples. The reciprocal ratio returns the '
@@ -159,6 +165,7 @@ def main(args=None):
         blackListFileName=args.blackListFileName,
         verbose=args.verbose,
         numberOfProcessors=args.numberOfProcessors,
+        skipZeroOverZero=args.skipZeroOverZero,
         format=args.outFileFormat,
         smoothLength=False,
         missingDataAsZero=not args.skipNonCoveredRegions,
diff --git a/deeptools/writeBedGraph_bam_and_bw.py b/deeptools/writeBedGraph_bam_and_bw.py
index 67cfa9b43..c7abf1535 100644
--- a/deeptools/writeBedGraph_bam_and_bw.py
+++ b/deeptools/writeBedGraph_bam_and_bw.py
@@ -45,7 +45,7 @@ def writeBedGraph_wrapper(args):
 def writeBedGraph_worker(
         chrom, start, end, tileSize, defaultFragmentLength,
         bamOrBwFileList, func, funcArgs, extendPairedEnds=True, smoothLength=0,
-        missingDataAsZero=False, fixed_step=False):
+        skipZeroOverZero=False, missingDataAsZero=False, fixed_step=False):
     r"""
     Writes a bedgraph having as base a number of bam files.
 
@@ -102,6 +102,10 @@ def writeBedGraph_worker(
                              "files. Remove this chromosome from the bigwig file "
                              "to continue".format(chrom))
 
+        if skipZeroOverZero and np.sum(tileCoverage) == 0:
+            previousValue = None
+            continue
+
         value = func(tileCoverage, funcArgs)
 
         if fixed_step:

From 18af2b6d02dd592491d76cc330915529874ba1d9 Mon Sep 17 00:00:00 2001
From: Devon Ryan <dpryan79@gmail.com>
Date: Sun, 31 Mar 2019 13:28:32 +0200
Subject: [PATCH 2/7] expose option

---
 deeptools/writeBedGraph_bam_and_bw.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/deeptools/writeBedGraph_bam_and_bw.py b/deeptools/writeBedGraph_bam_and_bw.py
index c7abf1535..000b6b288 100644
--- a/deeptools/writeBedGraph_bam_and_bw.py
+++ b/deeptools/writeBedGraph_bam_and_bw.py
@@ -151,7 +151,7 @@ def writeBedGraph(
         bamOrBwFileList, outputFileName, fragmentLength,
         func, funcArgs, tileSize=25, region=None, blackListFileName=None, numberOfProcessors=1,
         format="bedgraph", extendPairedEnds=True, missingDataAsZero=False,
-        smoothLength=0, fixed_step=False, verbose=False):
+        skipZeroOverZero=False, smoothLength=0, fixed_step=False, verbose=False):
     r"""
     Given a list of bamfiles, a function and a function arguments,
     this method writes a bedgraph file (or bigwig) file
@@ -210,7 +210,7 @@ def writeBedGraph(
 
     res = mapReduce.mapReduce((tileSize, fragmentLength, bamOrBwFileList,
                                func, funcArgs, extendPairedEnds, smoothLength,
-                               missingDataAsZero, fixed_step),
+                               skipZeroOverZero, missingDataAsZero, fixed_step),
                               writeBedGraph_wrapper,
                               chromNamesAndSize,
                               genomeChunkLength=genomeChunkLength,

From 1eccf65770bcf541c45d3e09c21ec192fe115d3a Mon Sep 17 00:00:00 2001
From: Devon Ryan <dpryan79@gmail.com>
Date: Sun, 31 Mar 2019 16:43:54 +0200
Subject: [PATCH 3/7] Add a test using pseudocounts and skipZeroOverZero

---
 .../test_bigwigCompare_and_multiBigwigSummary.py     | 12 ++++++++++++
 1 file changed, 12 insertions(+)

diff --git a/deeptools/test/test_bigwigCompare_and_multiBigwigSummary.py b/deeptools/test/test_bigwigCompare_and_multiBigwigSummary.py
index 3cd05b940..b567918ea 100644
--- a/deeptools/test/test_bigwigCompare_and_multiBigwigSummary.py
+++ b/deeptools/test/test_bigwigCompare_and_multiBigwigSummary.py
@@ -62,6 +62,18 @@ def test_bigwigCompare_skipnas():
     unlink(outfile)
 
 
+def test_bigwigCompare_skipZeroOverZero():
+    outfile = '/tmp/result.bg"'
+    args = "-b1 {} -b2 {} -o {] --skipZeroOverZero --pseudocount 1 3 --outFileFormat bedgraph".format(BIGWIG_A, BIGWIG_A, outfile).split()
+    bwComp.main(args)
+    _foo = open(outfile, 'r')
+    resp = _foo.readlines()
+    _foo.close()
+    expected = ['3R\t100\t200\t0.25\n']
+    assert resp == expected, "{} != {}".format(resp, expected)
+    unlink(outfile)
+
+
 def test_multiBigwigSummary():
     outfile = '/tmp/result.bg'
     args = "bins -b {} {} --binSize 50 -o {}".format(BIGWIG_A, BIGWIG_B, outfile).split()

From 20797ef2f62c88947b22a31f48ab049fa89f6ca8 Mon Sep 17 00:00:00 2001
From: Devon Ryan <dpryan79@gmail.com>
Date: Sun, 31 Mar 2019 16:49:31 +0200
Subject: [PATCH 4/7] syntax

---
 deeptools/test/test_bigwigCompare_and_multiBigwigSummary.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/deeptools/test/test_bigwigCompare_and_multiBigwigSummary.py b/deeptools/test/test_bigwigCompare_and_multiBigwigSummary.py
index b567918ea..867b2131a 100644
--- a/deeptools/test/test_bigwigCompare_and_multiBigwigSummary.py
+++ b/deeptools/test/test_bigwigCompare_and_multiBigwigSummary.py
@@ -64,7 +64,7 @@ def test_bigwigCompare_skipnas():
 
 def test_bigwigCompare_skipZeroOverZero():
     outfile = '/tmp/result.bg"'
-    args = "-b1 {} -b2 {} -o {] --skipZeroOverZero --pseudocount 1 3 --outFileFormat bedgraph".format(BIGWIG_A, BIGWIG_A, outfile).split()
+    args = "-b1 {} -b2 {} -o {} --skipZeroOverZero --pseudocount 1 3 --outFileFormat bedgraph".format(BIGWIG_A, BIGWIG_A, outfile).split()
     bwComp.main(args)
     _foo = open(outfile, 'r')
     resp = _foo.readlines()

From 0a8fb305d40ce61d9203e63b52784d1bd54e6ec8 Mon Sep 17 00:00:00 2001
From: dpryan79 <dpryan79@gmail.com>
Date: Mon, 1 Apr 2019 11:15:45 +0200
Subject: [PATCH 5/7] Fix tests

---
 deeptools/test/test_bigwigCompare_and_multiBigwigSummary.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/deeptools/test/test_bigwigCompare_and_multiBigwigSummary.py b/deeptools/test/test_bigwigCompare_and_multiBigwigSummary.py
index 867b2131a..831924277 100644
--- a/deeptools/test/test_bigwigCompare_and_multiBigwigSummary.py
+++ b/deeptools/test/test_bigwigCompare_and_multiBigwigSummary.py
@@ -69,7 +69,7 @@ def test_bigwigCompare_skipZeroOverZero():
     _foo = open(outfile, 'r')
     resp = _foo.readlines()
     _foo.close()
-    expected = ['3R\t100\t200\t0.25\n']
+    expected = ['3R\t100\t200\t-1\n']
     assert resp == expected, "{} != {}".format(resp, expected)
     unlink(outfile)
 

From 2d57f5eaabf646817f78f2fd348a6fe776aea160 Mon Sep 17 00:00:00 2001
From: dpryan79 <dpryan79@gmail.com>
Date: Mon, 1 Apr 2019 11:22:00 +0200
Subject: [PATCH 6/7] Make --skipZeroOverZero a galaxy macro and add to
 bigwigCompare

---
 galaxy/wrapper/bamCompare.xml       | 6 +-----
 galaxy/wrapper/bigwigCompare.xml    | 2 ++
 galaxy/wrapper/deepTools_macros.xml | 8 ++++++++
 3 files changed, 11 insertions(+), 5 deletions(-)

diff --git a/galaxy/wrapper/bamCompare.xml b/galaxy/wrapper/bamCompare.xml
index a63210c8f..4c5e45bb1 100644
--- a/galaxy/wrapper/bamCompare.xml
+++ b/galaxy/wrapper/bamCompare.xml
@@ -164,11 +164,7 @@
                 <expand macro="read_processing_options" />
 
                 <expand macro="skipNAs" />
-                <param argument="--skipZeroOverZero" type="select" label="Skip bins of no coverage"
-                    help="Skip bins where BOTH files lack coverage.">
-                    <option value="" selected="true">No</option>
-                    <option value="--skipZeroOverZero">Yes, skip them.</option>
-                </param>
+                <expand macro="skipZeroOverZero" />
 
                 <param argument="--ignoreForNormalization" type="text" value="" size="50"
                     label="regions that should be excluded for calculating the scaling factor"
diff --git a/galaxy/wrapper/bigwigCompare.xml b/galaxy/wrapper/bigwigCompare.xml
index 87deb745e..9609f8366 100644
--- a/galaxy/wrapper/bigwigCompare.xml
+++ b/galaxy/wrapper/bigwigCompare.xml
@@ -28,6 +28,7 @@
             #if $advancedOpt.showAdvancedOpt == "yes":
 
               $advancedOpt.skipNAs
+              $advancedOpt.skipZeroOverZero
               --scaleFactors '$advancedOpt.scaleFactor1:$advancedOpt.scaleFactor2'
               --binSize $advancedOpt.binSize
 
@@ -95,6 +96,7 @@
                     help="Size of the bins in bases for the output of the bigwig/bedgraph file."/>
 
                 <expand macro="skipNAs" />
+                <expand macro="skipZeroOverZero" />
                 <expand macro="scaleFactors" />
                 <expand macro="plotTitle" />
                 <expand macro="blacklist" />
diff --git a/galaxy/wrapper/deepTools_macros.xml b/galaxy/wrapper/deepTools_macros.xml
index 28501c281..13b8fe809 100644
--- a/galaxy/wrapper/deepTools_macros.xml
+++ b/galaxy/wrapper/deepTools_macros.xml
@@ -650,6 +650,14 @@ is vital to you, select Yes below.">
                  (default: False)" />
     </xml>
 
+    <xml name="skipZeroOverZero">
+        <param argument="--skipZeroOverZero" type="select" label="Skip bins of no coverage"
+            help="Skip bins where BOTH files lack coverage.">
+            <option value="" selected="true">No</option>
+            <option value="--skipZeroOverZero">Yes, skip them.</option>
+        </param>
+    </xml>
+
     <xml name="exactScaling">
         <param argument="--exactScaling" type="boolean" truevalue="--exactScaling" falsevalue="" checked="False"
             label="Compute an exact scaling factor"

From f49393283e77e2bfc245ea9ab8816cd4f2f62f69 Mon Sep 17 00:00:00 2001
From: dpryan79 <dpryan79@gmail.com>
Date: Mon, 1 Apr 2019 11:30:08 +0200
Subject: [PATCH 7/7] [ci skip] a bit of formatting

---
 setup.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/setup.py b/setup.py
index 1b7c6982d..ad6256d2e 100755
--- a/setup.py
+++ b/setup.py
@@ -86,8 +86,8 @@ def openREADME():
         "scipy >= 0.17.0",
         "matplotlib >= 2.1.2",
         "pysam >= 0.14.0",
-        "numpydoc >=0.5",
-        "pyBigWig >=0.2.1",
+        "numpydoc >= 0.5",
+        "pyBigWig >= 0.2.1",
         "py2bit >= 0.2.0",
         "plotly >= 2.0.0",
         "deeptoolsintervals >= 0.1.7"