From a40e25dc5e86d545db189ae5a9dda621f1db1e3a Mon Sep 17 00:00:00 2001
From: Meng Wang <wangm0855@gmail.com>
Date: Wed, 9 Dec 2020 20:28:04 -0500
Subject: [PATCH 1/2] Add --fixedStep option for bigwigCompare

---
 deeptools/bigwigCompare.py            |  8 +++++++-
 deeptools/writeBedGraph_bam_and_bw.py | 14 +++++++-------
 2 files changed, 14 insertions(+), 8 deletions(-)

diff --git a/deeptools/bigwigCompare.py b/deeptools/bigwigCompare.py
index e4d69da20..aa0b17e47 100644
--- a/deeptools/bigwigCompare.py
+++ b/deeptools/bigwigCompare.py
@@ -93,6 +93,11 @@ def parse_arguments(args=None):
                         'zeros may be wrong and this option should be used ',
                         action='store_true')
 
+    parser.add_argument('--fixedStep',
+                        help='Output in fixed step of bin size (as specified by --binSize), not merging '
+                        'neighboring bins with same values in the output file',
+                        action='store_true')
+
     return parser
 
 
@@ -168,7 +173,8 @@ def main(args=None):
         format=args.outFileFormat,
         smoothLength=False,
         missingDataAsZero=not args.skipNonCoveredRegions,
-        extendPairedEnds=False)
+        extendPairedEnds=False,
+        fixedStep=args.fixedStep)
 
     # Clean up temporary bigWig files, if applicable
     if not args.deepBlueKeepTemp:
diff --git a/deeptools/writeBedGraph_bam_and_bw.py b/deeptools/writeBedGraph_bam_and_bw.py
index 61cd47a42..7410470f2 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,
-        skipZeroOverZero=False, missingDataAsZero=False, fixed_step=False):
+        skipZeroOverZero=False, missingDataAsZero=False, fixedStep=False):
     r"""
     Writes a bedgraph having as base a number of bam files.
 
@@ -103,12 +103,12 @@ def writeBedGraph_worker(
 
         value = func(tileCoverage, funcArgs)
 
-        if fixed_step:
+        if fixedStep:
             writeStart = start + tileIndex * tileSize
             writeEnd = min(writeStart + tileSize, end)
             try:
-                _file.write(toBytes("%s\t%d\t%d\t%.2f\n" % (chrom, writeStart,
-                                                            writeEnd, value)))
+                _file.write(toBytes("{0}\t{1}\t{2}\t{3:g}\n".format(chrom, writeStart,
+                                                                    writeEnd, value)))
             except TypeError:
                 _file.write(toBytes("{}\t{}\t{}\t{}\n".format(chrom, writeStart,
                                                               writeEnd, value)))
@@ -130,7 +130,7 @@ def writeBedGraph_worker(
                 writeStart = writeEnd
                 writeEnd = min(writeStart + tileSize, end)
 
-    if not fixed_step:
+    if not fixedStep:
         # write remaining value if not a nan
         if previousValue and writeStart != end and \
                 not np.isnan(previousValue):
@@ -146,7 +146,7 @@ def writeBedGraph(
         bamOrBwFileList, outputFileName, fragmentLength,
         func, funcArgs, tileSize=25, region=None, blackListFileName=None, numberOfProcessors=1,
         format="bedgraph", extendPairedEnds=True, missingDataAsZero=False,
-        skipZeroOverZero=False, smoothLength=0, fixed_step=False, verbose=False):
+        skipZeroOverZero=False, smoothLength=0, fixedStep=False, verbose=False):
     r"""
     Given a list of bamfiles, a function and a function arguments,
     this method writes a bedgraph file (or bigwig) file
@@ -205,7 +205,7 @@ def writeBedGraph(
 
     res = mapReduce.mapReduce((tileSize, fragmentLength, bamOrBwFileList,
                                func, funcArgs, extendPairedEnds, smoothLength,
-                               skipZeroOverZero, missingDataAsZero, fixed_step),
+                               skipZeroOverZero, missingDataAsZero, fixedStep),
                               writeBedGraph_wrapper,
                               chromNamesAndSize,
                               genomeChunkLength=genomeChunkLength,

From 430c161447a2be374fea5b89bafb5aa7704bd99a Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bj=C3=B6rn=20Gr=C3=BCning?= <bjoern@gruenings.eu>
Date: Tue, 4 Apr 2023 19:14:19 +0200
Subject: [PATCH 2/2] trigger new build

---
 deeptools/bigwigCompare.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/deeptools/bigwigCompare.py b/deeptools/bigwigCompare.py
index aa0b17e47..fd427f0cc 100644
--- a/deeptools/bigwigCompare.py
+++ b/deeptools/bigwigCompare.py
@@ -97,7 +97,6 @@ def parse_arguments(args=None):
                         help='Output in fixed step of bin size (as specified by --binSize), not merging '
                         'neighboring bins with same values in the output file',
                         action='store_true')
-
     return parser