split up extendreads & extendreadslen

Author: WardDeb

pydeeptools/deeptools/bamCompare2.py

@@ -258,7 +258,14 @@ def main(args=None):
     if not args.region:
         args.region = 'None'
     if not args.extendReads:
-        args.extendReads = 0
+        args.extendReads = False
+        args.extendReadsLen = 0
+    elif isinstance(args.extendReads, bool):
+        args.extendReadsLen = 0
+        args.extendReads = True
+    elif isinstance(args.extendReads, int):
+        args.extendReadsLen = args.extendReads
+        args.extendReads = True
     if not args.blackListFileName:
         args.blackListFileName = 'None'
     else:
@@ -280,6 +287,7 @@ def main(args=None):
         args.operation,
         args.pseudocount,
         args.extendReads,
+        args.extendReadsLen,
         args.centerReads,
         args.blackListFileName,
         args.minMappingQuality,

pydeeptools/deeptools/bamCoverage2.py

@@ -141,13 +141,19 @@ def main(args=None):
         args.effectiveGenomeSize = 0
     if not args.normalizeUsing:
         args.normalizeUsing = 'None'
-    print(args.Offset)
     if not args.Offset:
         args.Offset = [0, 0]
     elif len(args.Offset) == 1:
         args.Offset = [args.Offset[0], 0]
     if not args.extendReads:
-        args.extendReads = 0
+        args.extendReads = False
+        args.extendReadsLen = 0
+    elif isinstance(args.extendReads, bool):
+        args.extendReadsLen = 0
+        args.extendReads = True
+    elif isinstance(args.extendReads, int):
+        args.extendReadsLen = args.extendReads
+        args.extendReads = True
     if not args.filterRNAstrand:
         args.filterRNAstrand = 'None'
     if not args.blackListFileName:
@@ -179,6 +185,7 @@ def main(args=None):
         args.MNase,
         args.Offset,
         args.extendReads,
+        args.extendReadsLen,
         args.centerReads,
         args.filterRNAstrand,
         args.blackListFileName,

pydeeptools/deeptools/multiBamSummary2.py

@@ -224,6 +224,15 @@ def process_args(args=None):
         args.outRawCounts = "None"
     if not args.scalingFactors:
         args.scalingFactors = "None"
+    if not args.extendReads:
+        args.extendReads = False
+        args.extendReadsLen = 0
+    elif isinstance(args.extendReads, bool):
+        args.extendReadsLen = 0
+        args.extendReads = True
+    elif isinstance(args.extendReads, int):
+        args.extendReadsLen = args.extendReads
+        args.extendReads = True
     # defaults for the filtering options
     if not args.samFlagInclude:
         args.samFlagInclude = 0
@@ -263,6 +272,7 @@ def main(args=None):
         args.blackListFileName,
         args.verbose,
         args.extendReads,
+        args.extendReadsLen,
         args.centerReads,
         args.samFlagInclude,
         args.samFlagExclude,