'--corr' option was modified.

README.md

@@ -1,5 +1,5 @@
 # MutMap User Guide
-#### version 2.1.4
+#### version 2.1.5
 
 ## Table of contents
 - [What is MutMap?](#What-is-MutMap)
@@ -74,7 +74,7 @@ $ mutmap -h
 usage: mutmap -r <FASTA> -c <BAM|FASTQ> -b <BAM|FASTQ>
               -n <INT> -o <OUT_DIR> [-T] [-e <DATABASE>]
 
-MutMap version 2.1.4
+MutMap version 2.1.5
 
 optional arguments:
   -h, --help         show this help message and exit
@@ -218,7 +218,7 @@ usage: mutplot -v <VCF> -o <OUT_DIR> -n <INT> [-w <INT>] [-s <INT>]
                [-D <INT>] [-d <INT>] [-N <INT>] [-m <FLOAT>]
                [-S <INT>] [-e <DATABASE>] [--igv] [--corr] [--indel]
 
-MutPlot version 2.1.4
+MutPlot version 2.1.5
 
 optional arguments:
   -h, --help            show this help message and exit
@@ -244,9 +244,10 @@ optional arguments:
   -e , --snpEff         Predict causal variant using SnpEff. Please
                         check available databases in SnpEff.
   --igv                 Output IGV format file to check results on IGV.
-  --corr                Use corrected threshold in Huang et al. (2019).
-                        If you specify this option, the options related to
-                        the simulation ("-N" and "-F") will be ignored.
+  --corr                Use the corrected threshold in Huang et al. (2019).
+                        Please spesify mu_alpha_2 in Huang et al. (2019).
+                        When you specify this option, p99 and p95 has the
+                        same value.
   --indel               Plot SNP-index with INDEL.
   --fig-width           Width allocated in chromosome figure. [7.5]
   --fig-height          Height allocated in chromosome figure. [4.0]

mutmap/__init__.py

@@ -1 +1 @@
-__version__ = "2.1.4"
+__version__ = "2.1.5"

mutmap/params.py

@@ -321,11 +321,13 @@ def mutplot_options(self):
                             help='Output IGV format file to check results on IGV.')
 
         parser.add_argument('--corr',
-                            action='store_true',
-                            default=False,
-                            help=('Use corrected threshold in Huang et al. (2019).\n'
-                                  'If you specify this option, the options related to\n'
-                                  'the simulation ("-N" and "-F") will be ignored.'))
+                            action='store',
+                            type=float,
+                            help=('Use the corrected threshold in Huang et al. (2019).\n'
+                                  'Please spesify mu_alpha_2 in Huang et al. (2019).\n'
+                                  'When you specify this option, p99 and p95 has the\n'
+                                  'same value.'),
+                            metavar='')
 
         parser.add_argument('--indel',
                             action='store_true',

mutmap/vcf2index.py

@@ -25,6 +25,10 @@ def __init__(self, args):
         if self.snpEff is not None:
             self.ANN_re = re.compile(';ANN=(.*);*')
 
+        if self.corr is not None:
+            var_fix = 0.25/(2*self.N_bulk)
+            self.threshold = self.corr*(var_fix**(1/2)) + 0.5
+
     def get_field(self):
         root, ext = os.path.splitext(self.vcf)
         if ext == '.gz':
@@ -101,13 +105,6 @@ def F2_simulation(self, depth):
         p95 = replicates[int(0.95*self.N_replicates) - 1]
         return p99, p95
 
-    def calculate_corrected_threshold(self, depth):
-        var_AF = (2*self.N_bulk + depth)/(8*self.N_bulk*depth)
-
-        p99 = 2.576*(var_AF**(1/2)) + 0.5
-        p95 = 1.960*(var_AF**(1/2)) + 0.5
-        return p99, p95
-
     def calc_SNPindex(self, field_pos):
         root, ext = os.path.splitext(self.vcf)
         if ext == '.gz':
@@ -145,8 +142,8 @@ def calc_SNPindex(self, field_pos):
                 if record['type'] == 'keep':
                     variant = self.check_variant_type(REF, ALT)
 
-                    if self.corr:
-                        p99, p95 = self.calculate_corrected_threshold(record['bulk_depth'])
+                    if self.corr is not None:
+                        p99, p95 = self.threshold, self.threshold
                     else:
                         p99, p95 = self.F2_simulation(record['bulk_depth'])