From 925bd123a43076992e034139dd1c91591952ee21 Mon Sep 17 00:00:00 2001
From: caleblareau <caleblareau@g.harvard.edu>
Date: Mon, 21 May 2018 03:33:48 -0400
Subject: [PATCH] v0.3.7 should fix termini

---
 Pypkg/mgatk/mgatk/bin/python/filterClipBam.py | 2 +-
 Pypkg/mgatk/mgatk/bin/python/sumstatsBP.py    | 1 +
 Pypkg/mgatk/mgatk/cli.py                      | 9 ++++++---
 Pypkg/mgatk/setup.py                          | 2 +-
 4 files changed, 9 insertions(+), 5 deletions(-)

diff --git a/Pypkg/mgatk/mgatk/bin/python/filterClipBam.py b/Pypkg/mgatk/mgatk/bin/python/filterClipBam.py
index 4e2a383..074919c 100755
--- a/Pypkg/mgatk/mgatk/bin/python/filterClipBam.py
+++ b/Pypkg/mgatk/mgatk/bin/python/filterClipBam.py
@@ -24,6 +24,7 @@
 
 keepCount = 0
 filtCount = 0
+#proper_pair = "False"
 
 def filterReadTags(intags):
     '''
@@ -49,7 +50,6 @@ def pairing(read):
 def processRead(read):
 	global keepCount
 	global filtCount
-	
 	if(filterReadTags(read.tags) and read.reference_name == mtchr and pairing(read)):
 		keepCount += 1
 		out.write(read)
diff --git a/Pypkg/mgatk/mgatk/bin/python/sumstatsBP.py b/Pypkg/mgatk/mgatk/bin/python/sumstatsBP.py
index 9607e8b..7aae78e 100755
--- a/Pypkg/mgatk/mgatk/bin/python/sumstatsBP.py
+++ b/Pypkg/mgatk/mgatk/bin/python/sumstatsBP.py
@@ -33,6 +33,7 @@ def writeSparseMatrix2(mid, vec1, vec2):
 				V.write(str(i+1)+","+sample+","+str(vec1[i])+","+str(vec2[i])+"\n")
 
 n = int(maxBP)
+
 # BAQ
 # initialize with a pseudo count to avoid dividing by zero
 countsA = [0.00000001] * n 
diff --git a/Pypkg/mgatk/mgatk/cli.py b/Pypkg/mgatk/mgatk/cli.py
index dc1d4af..34bf12a 100644
--- a/Pypkg/mgatk/mgatk/cli.py
+++ b/Pypkg/mgatk/mgatk/cli.py
@@ -117,7 +117,6 @@ def main(mode, input, output, name, mito_genome, ncores,
 		
 		# Handle fasta requirements
 		fastaf, mito_genome, mito_length = handle_fasta_inference(mito_genome, supported_genomes, script_dir, mode, of)
-		
 		# Actually call the external script based on user input
 		if(barcode_known):
 			bc1py = script_dir + "/bin/python/bc1_known.py"
@@ -196,6 +195,9 @@ def main(mode, input, output, name, mito_genome, ncores,
 			sys.exit('ERROR: in `one` mode, the input should be an individual .bam file.')
 		if not os.path.exists(input):
 			sys.exist('ERROR: No file found called "' + input + '"; please specify a valid .bam file')
+		
+		# Define input samples
+		sampleregex = re.compile(r"^[^.]*")
 		samples = [re.search(sampleregex, os.path.basename(input)).group(0)]
 		samplebams = [input]
 	
@@ -239,10 +241,10 @@ def main(mode, input, output, name, mito_genome, ncores,
 		#-------------------
 		# Handle .fasta file
 		#-------------------
-		if(mode == "call" and wasbcall == False):
+		if((mode == "call" and wasbcall == False) or mode == "one"):
 			fastaf, mito_genome, mito_length = handle_fasta_inference(mito_genome, supported_genomes, script_dir, mode, of)
 			click.echo(gettime() + "Found designated mitochondrial chromosome: %s" % mito_genome, logf)
-		
+
 		#----------------		
 		# Determine cores
 		#----------------
@@ -294,6 +296,7 @@ def main(mode, input, output, name, mito_genome, ncores,
 			with open(y_s, 'w') as yaml_file:
 				yaml.dump(dict1, yaml_file, default_flow_style=False, Dumper=yaml.RoundTripDumper)
 			
+			
 			# Call the python script
 			oneSample_py = script_dir + "/bin/python/oneSample.py"
 			pycall = " ".join(['python', oneSample_py, y_s, inputbam, outputbam, sample])
diff --git a/Pypkg/mgatk/setup.py b/Pypkg/mgatk/setup.py
index 64caaa7..db3f2b6 100644
--- a/Pypkg/mgatk/setup.py
+++ b/Pypkg/mgatk/setup.py
@@ -7,7 +7,7 @@
 
 setup(
     name='mgatk',
-    version='0.3.6',
+    version='0.3.7',
     url='https://github.com/aryeelab/mgatk',
     license='MIT',
     author='Caleb Lareau',