merge master

LICENSE.txt

@@ -1,11 +1,15 @@
-Copyright (c) 2020, Battelle National Biodefense Institute (BNBI);
-all rights reserved. Authored by Rebecca Mitchell.
+Copyright (c) 2020, DHS.
 
 This Software was prepared for the Department of Homeland Security
 (DHS) by the Battelle National Biodefense Institute, LLC (BNBI) as
 part of contract HSHQDC-15-C-00064 to manage and operate the National
 Biodefense Analysis and Countermeasures Center (NBACC), a Federally
-Funded Research and Development Center.
+Funded Research and Development Center. All rights in the computer
+software are reserved by DHS on behalf of the United States Government
+and the Contractor as provided in the Contract. NEITHER THE GOVERNMENT
+NOR BNBI MAKES ANY WARRANTY, EXPRESS OR IMPLIED, OR ASSUMES ANY
+LIABILITY FOR THE USE OF THIS SOFTWARE. This notice including this
+sentence must appear on any copies of this computer software.
 
 Redistribution and use in source and binary forms, with or without
 modification, are permitted provided that the following conditions are

README.md

@@ -77,6 +77,7 @@ analysis_software: ```uas``` (```uas/straitrazor/genemarker```); indicates the a
 sex: ```False``` (True/False); include sex-chromosome STRs (invoke ```--sex``` flag)  
 samp_input: ```/path/to/input/directory/or/samples``` input directory or sample; if not provided, will be current working directory (indicate using ```--input path/to/dir``` )  
 output: ```lusstr_output``` output file/directory name (indicate using ```--out dir/sampleid e.g. --out test_030923```)
+custom: ```False``` (True/False); use custom sequence ranges as defined in the STR markers json file (```str_markers.json```).
 
 ### convert settings  
 kit: ```forenseq``` (forenseq/powerseq) (invoke the ```--powerseq``` flag if using PowerSeq data)  

lusSTR/cli/config.py

@@ -93,6 +93,8 @@ def edit_str_config(config, args):
         data["output_type"] = args.software
     if args.strand:
         data["strand"] = args.strand
+    if args.custom:
+        data["custom_ranges"] = args.custom
     return data
 
 
@@ -175,3 +177,7 @@ def subparser(subparsers):
         help="Specify the strand orientation for the final output files. UAS orientation is "
         "default for STRs; forward strand is default for SNPs."
     )
+    p.add_argument(
+        "--custom", action="store_true",
+        help="Specifying custom sequence ranges."
+    )

lusSTR/data/config.yaml

@@ -9,6 +9,7 @@ output: "lusstr_output" ## output file/directory name; Example: "test_030923"
 
 ##convert settings
 kit: "forenseq" ## forenseq/powerseq
+custom_ranges: False ## True/False; use custom ranges, for PowerSeq sequences only
 nocombine: False ## True/False; do not combine identical sequences (if using STRait Razor data)
 
 ##filter settings