From dba08d27256888bf471def0cb804ef860d2da328 Mon Sep 17 00:00:00 2001
From: philippadoherty <94635687+philippadoherty@users.noreply.github.com>
Date: Wed, 12 Jul 2023 13:45:22 -0400
Subject: [PATCH] add -t and --modelonly

---
 MACS3/Utilities/OptValidator.py | 8 ++++----
 bin/macs3                       | 8 ++++----
 2 files changed, 8 insertions(+), 8 deletions(-)

diff --git a/MACS3/Utilities/OptValidator.py b/MACS3/Utilities/OptValidator.py
index 4bc405d..a714f95 100644
--- a/MACS3/Utilities/OptValidator.py
+++ b/MACS3/Utilities/OptValidator.py
@@ -841,8 +841,8 @@ def opt_validate_hmmratac ( options ):
         sys.exit( 1 )
     
     # hmm_training_regions
-    #if options.hmm_training_regions:
-    #    options.argtxt += "# Using -t, --training input to train HMM instead of using fold change settings to select. \n"
+    if options.hmm_training_regions:
+       options.argtxt += "# Using -t, --training input to train HMM instead of using fold change settings to select. \n"
     
     # hmm_zscore non-negative
     #if options.hmm_zscore <0:
@@ -863,8 +863,8 @@ def opt_validate_hmmratac ( options ):
     #    options.argtxt += "# HMM training will be skipped, --model input used instead. \n"
 
     # hmm_modelonly
-    #if options.hmm_modelonly:
-    #    options.argtxt += "# Program will stop after generating model, which can be later applied with '--model'. \n"
+    if options.hmm_modelonly:
+       options.argtxt += "# Program will stop after generating model, which can be later applied with '--model'. \n"
 
 
     # Peak Calling
diff --git a/bin/macs3 b/bin/macs3
index 7479a04..71dbf19 100644
--- a/bin/macs3
+++ b/bin/macs3
@@ -940,8 +940,8 @@ plus an extra option for the HMM model file like `macs3 hmmratac
     group_hmm.add_argument( "--training-flanking", dest = "hmm_training_flanking", type = int, required = False,
                             help = "Training regions will be expanded to both side with this number of basepairs. The purpose is to include more background regions. Default: 1000",
                             default = 1000 )
-    #group_hmm.add_argument( "-t", "--training", dest = "hmm_training_regions", type = str, required = False, 
-    #                        help = "Filename of training regions (previously was BED_file) to use for training HMM, instead of using foldchange settings to select. Default: NA" )
+    group_hmm.add_argument( "-t", "--training", dest = "hmm_training_regions", type = str, required = False, 
+                           help = "Filename of training regions (previously was BED_file) to use for training HMM, instead of using foldchange settings to select. Default: NA" )
     #group_hmm.add_argument( "-z", "--zscore", dest = "hmm_zscore", type = int,
     #                        help = "Zscored read depth to mask during Viterbi decoding. Default: 100",
     #                        default = 100 )
@@ -950,8 +950,8 @@ plus an extra option for the HMM model file like `macs3 hmmratac
     #                        default = 25000000 )
     group_hmm.add_argument( "--model", dest = "hmm_file", type = str, required = False, 
                             help = "A JSON file generated from previous HMMRATAC run to use instead of creating new one. When provided, HMM training will be skipped. Default: NA" )
-    #group_hmm.add_argument( "--modelonly", dest = "hmm_modelonly", action = "store_true", default = False,
-    #                        help = "Stop the program after generating model. Use this option to generate HMM model ONLY, which can be later applied with `--model`. Default: False")
+    group_hmm.add_argument( "--modelonly", dest = "hmm_modelonly", action = "store_true", default = False,
+                           help = "Stop the program after generating model. Use this option to generate HMM model ONLY, which can be later applied with `--model`. Default: False")
 
     # group for peak calling arguments
     group_call = argparser_hmmratac.add_argument_group( "Peak calling/HMM decoding arguments" )
-- 
2.11.4.GIT