--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/customConfigManta.py	Tue Jun 09 06:23:39 2020 -0400
@@ -0,0 +1,80 @@
+import argparse
+
+
+def Parser():
+    the_parser = argparse.ArgumentParser()
+    the_parser.add_argument(
+        '--minCandidateVariantSize', type=int, default=8,
+        help="Run Manta reporting for all SVs/indels at or above this size")
+    the_parser.add_argument(
+        '--rnaMinCandidateVariantSize', type=int, default=1000,
+        help="Separate option (to provide different default) used for \
+              runs in RNA-mode")
+    the_parser.add_argument(
+        '--minEdgeObservations', type=int, default=3,
+        help="Remove all edges from the graph unless they're supported \
+              by this many 'observations'")
+    the_parser.add_argument(
+        '--graphNodeMaxEdgeCount', type=int, default=10,
+        help="If both nodes of an edge have an edge count higher than this, \
+              then skip evaluation of the edge")
+    the_parser.add_argument(
+        '--minCandidateSpanningCount', type=int, default=3,
+        help="Run discovery and candidate reporting for all SVs/indels with \
+              at least this many spanning support observations")
+    the_parser.add_argument(
+        '--minScoredVariantSize', type=int, default=50,
+        help="After candidate identification, only score and report \
+              SVs/indels at or above this size")
+    the_parser.add_argument(
+        '--minDiploidVariantScore', type=int, default=10,
+        help="minimum VCF QUAL score for a variant to be included in \
+              the diploid vcf")
+    the_parser.add_argument(
+        '--minPassDiploidVariantScore', type=int, default=20,
+        help="VCF QUAL score below which a variant is marked as \
+              filtered in the diploid vcf")
+    the_parser.add_argument(
+        '--minPassDiploidGTScore', type=int, default=15,
+        help="minimum genotype quality score below which single samples \
+              are filtered for a variant in the diploid vcf")
+    the_parser.add_argument(
+        '--minSomaticScore', type=int, default=10,
+        help="minimum VCF QUAL score for a variant to be included in the \
+              diploid vcf")
+    the_parser.add_argument(
+        '--minPassSomaticScore', type=int, default=30,
+        help="somatic quality scores below this level are filtered in the \
+              somatic vcf")
+    the_parser.add_argument(
+        '--enableRemoteReadRetrievalForInsertionsInGermlineCallingModes',
+        type=int, default=1,
+        help="includes tumor-normal subtraction and tumor-only calling")
+    the_parser.add_argument(
+        '--enableRemoteReadRetrievalForInsertionsInCancerCallingModes',
+        type=int, default=0,
+        help="GermlineCallingModes includes all other calling modes")
+    the_parser.add_argument(
+        '--useOverlapPairEvidence', type=int, default=0,
+        help="Set 1 if an overlapping read pair will be considered as \
+              evidence. Set to 0 to skip overlapping read pairs")
+    args = the_parser.parse_args()
+    return args
+
+
+if __name__ == "__main__":
+    args = Parser()
+    # recover arguments as a dictionary with keys = argument name and values
+    # are argument values
+    argsDict = args.__dict__
+    ini_lines = []
+    # implement first, hard-coded ini lines
+    ini_lines.append('[manta]')
+    ini_lines.append('referenceFasta = /dummy/path/to/genome.fa')
+    # implement the rest of the ini lines for the argsDict
+    for argument in argsDict:
+        ini_lines.append("%s = %s" % (argument, str(argsDict[argument])))
+    # print ini_lines in configManta.py.ini
+    handler = open('configManta.py.ini', 'w')
+    for line in ini_lines:
+        handler.write("%s\n" % line)