expose pair support args

AmpliconSuite-pipeline.py

@@ -279,6 +279,9 @@ def run_AA(amplified_interval_bed, AA_outdir, sname, args):
     insert_sdevs = args.AA_insert_sdevs
     sv_vcf = args.sv_vcf
     sv_vcf_no_filter = args.sv_vcf_no_filter
+    pair_support = args.pair_support_min
+    fb_pair_support = args.foldback_pair_support_min
+
 
     AA_version = \
     Popen([AA_interpreter, AA_SRC + "/AmpliconArchitect.py", "--version"], stdout=PIPE, stderr=PIPE).communicate()[0].rstrip()
@@ -304,6 +307,12 @@ def run_AA(amplified_interval_bed, AA_outdir, sname, args):
         if sv_vcf_no_filter:
             cmd += " --sv_vcf_no_filter"
 
+    if pair_support:
+        cmd += " --pair_support_min {}".format(str(pair_support))
+
+    if fb_pair_support:
+        cmd += " --foldback_pair_support_min {}".format(str(fb_pair_support))
+
     logging.info(cmd + "\n")
     aa_exit_code = call(cmd, shell=True)
     if aa_exit_code != 0:
@@ -619,6 +628,13 @@ def contains_spaces(file_path):
     parser.add_argument("--AA_insert_sdevs", help="Number of standard deviations around the insert size. May need to "
                         "increase for sequencing runs with high variance after insert size selection step. (default "
                         "3.0)", metavar="FLOAT", type=float, default=None)
+    parser.add_argument('--pair_support_min', dest='pair_support_min', help="Number of read pairs for "
+                        "minimum breakpoint support (default 2 but typically becomes higher due to coverage-scaled "
+                        "cutoffs)", metavar='INT', action='store', type=int, default=2)
+    parser.add_argument('--foldback_pair_support_min', help="Number of read pairs for minimum foldback SV support "
+                        "(default 2 but typically becomes higher due to coverage-scaled cutoffs). Used value will be the maximum"
+                        " of pair_support and this argument. Raising to 3 will help dramatically in heavily artifacted samples.",
+                        metavar='INT', action='store', type=int, default=2)
     parser.add_argument("--normal_bam", metavar='FILE', help="Path to matched normal bam for CNVKit (optional)")
     parser.add_argument("--ploidy", metavar='FLOAT', type=float, help="Ploidy estimate for CNVKit (optional). This is not used outside of CNVKit.",
                         default=None)

docker/run_paa_docker.py

@@ -64,6 +64,13 @@ def metadata_helper(metadata_args):
 parser.add_argument("--AA_insert_sdevs", help="Number of standard deviations around the insert size. May need to "
                     "increase for sequencing runs with high variance after insert size selection step. (default "
                     "3.0)", type=float, default=None)
+parser.add_argument('--pair_support_min', dest='pair_support_min', help="Number of read pairs for "
+                        "minimum breakpoint support (default 2 but typically becomes higher due to coverage-scaled "
+                        "cutoffs)", metavar='INT', action='store', type=int, default=2)
+parser.add_argument('--foldback_pair_support_min', help="Number of read pairs for minimum foldback SV support "
+                        "(default 2 but typically becomes higher due to coverage-scaled cutoffs). Used value will be the maximum"
+                        " of pair_support and this argument. Raising to 3 will help dramatically in heavily artifacted samples.",
+                        metavar='INT', action='store', type=int, default=2)
 parser.add_argument(
     "--normal_bam", help="Path to matched normal bam for CNVKit (optional)", default=None)
 parser.add_argument("--ploidy", type=int,
@@ -238,6 +245,12 @@ def metadata_helper(metadata_args):
 if args.AA_insert_sdevs:
     argstring += " --AA_insert_sdevs " + str(args.AA_insert_sdevs)
 
+if args.pair_support_min:
+    argstring += " --pair_support_min " + str(args.pair_support_min)
+
+if args.foldback_pair_support_min:
+    argstring += " --foldback_pair_support_min " + str(args.foldback_pair_support_min)
+
 # To use, would need to mount the directory of this file. Users should just modify as needed afterwards.
 # if args.sample_metadata:
 # 	args.sample_metadata = os.path.abspath(args.sample_metadata)

singularity/run_paa_singularity.py

@@ -71,6 +71,13 @@ def metadata_helper(metadata_args):
 parser.add_argument("--AA_insert_sdevs", help="Number of standard deviations around the insert size. May need to "
                     "increase for sequencing runs with high variance after insert size selection step. (default "
                     "3.0)", type=float, default=None)
+parser.add_argument('--pair_support_min', dest='pair_support_min', help="Number of read pairs for "
+                        "minimum breakpoint support (default 2 but typically becomes higher due to coverage-scaled "
+                        "cutoffs)", metavar='INT', action='store', type=int, default=2)
+parser.add_argument('--foldback_pair_support_min', help="Number of read pairs for minimum foldback SV support "
+                        "(default 2 but typically becomes higher due to coverage-scaled cutoffs). Used value will be the maximum"
+                        " of pair_support and this argument. Raising to 3 will help dramatically in heavily artifacted samples.",
+                        metavar='INT', action='store', type=int, default=2)
 parser.add_argument(
     "--normal_bam", help="Path to matched normal bam for CNVKit (optional)", default=None)
 parser.add_argument("--ploidy", type=int,
@@ -236,6 +243,12 @@ def metadata_helper(metadata_args):
 if args.AA_insert_sdevs:
     argstring += " --AA_insert_sdevs " + str(args.AA_insert_sdevs)
 
+if args.pair_support_min:
+    argstring += " --pair_support_min " + str(args.pair_support_min)
+
+if args.foldback_pair_support_min:
+    argstring += " --foldback_pair_support_min " + str(args.foldback_pair_support_min)
+
 # To use, would need to mount the directory of this file. Users should just modify as needed afterwards.
 # if args.sample_metadata:
 # 	args.sample_metadata = os.path.abspath(args.sample_metadata)