From feaaea731adaab78265967123dde76d1c7fe7a8c Mon Sep 17 00:00:00 2001
From: Ahhgust <august.woerner@unthsc.edu>
Date: Thu, 27 Apr 2023 13:06:31 -0500
Subject: [PATCH] Now supports extracting gencall scores (GCALL) as real
 numbers

---
 FormatFactory.py     |  7 +++++
 GencallFormatReal.py | 64 ++++++++++++++++++++++++++++++++++++++++++++
 2 files changed, 71 insertions(+)
 create mode 100644 GencallFormatReal.py

diff --git a/FormatFactory.py b/FormatFactory.py
index c302924..1eb4cdc 100644
--- a/FormatFactory.py
+++ b/FormatFactory.py
@@ -1,5 +1,6 @@
 from GenotypeFormat import GenotypeFormat
 from GencallFormat import GencallFormat
+from GencallFormatReal import GencallFormatReal
 from BAlleleFreqFormat import BAlleleFreqFormat
 from LogRRatioFormat import LogRRatioFormat
 
@@ -31,6 +32,8 @@ def __init__(self, no_samples, formats_to_include, logger):
                 self._format_classes.append(GenotypeFormat)
             if GencallFormat.get_id() in formats_to_include:
                 self._format_classes.append(GencallFormat)
+            if GencallFormatReal.get_id() in formats_to_include:
+                self._format_classes.append(GencallFormatReal)
             if BAlleleFreqFormat.get_id() in formats_to_include:
                 self._format_classes.append(BAlleleFreqFormat)
             if LogRRatioFormat.get_id() in formats_to_include:
@@ -40,6 +43,7 @@ def __init__(self, no_samples, formats_to_include, logger):
     def get_possible_formats():
         valid_classes = [GenotypeFormat.get_id(),
                          GencallFormat.get_id(),
+                         GencallFormatReal.get_id(),
                          BAlleleFreqFormat.get_id(),
                          LogRRatioFormat.get_id()]
         return valid_classes
@@ -98,6 +102,9 @@ def create_formats(self, gtc):
         if GencallFormat.get_id() in self._formats_to_include:
             result.append(GencallFormat(
                 self._logger, gtc.get_genotype_scores()))
+        if GencallFormatReal.get_id() in self._formats_to_include:
+            result.append(GencallFormatReal(
+                self._logger, gtc.get_genotype_scores()))
         if BAlleleFreqFormat.get_id() in self._formats_to_include:
             result.append(BAlleleFreqFormat(
                 self._logger, gtc.get_ballele_freqs()))
diff --git a/GencallFormatReal.py b/GencallFormatReal.py
new file mode 100644
index 0000000..558ace5
--- /dev/null
+++ b/GencallFormatReal.py
@@ -0,0 +1,64 @@
+from vcf.parser import _Format
+
+# Edited by August Woerner; borrowed (heavily) from GencallFormat.py
+
+class GencallFormatReal(object):
+    """
+    Generate GQ format information for VCF
+    """
+
+    def __init__(self, logger, gencall_scores):
+        """
+        Create new GencallFormatReal object
+
+        Args:
+            logger (logging.Logger): Logging object for errors/warnings
+            gencall_scores (list(float)): List of all gencall scores for all loci across sample
+
+        Returns
+            GencallFormatReal
+        """
+        self._logger = logger
+        self._gencall_scores = gencall_scores
+
+    @staticmethod
+    def get_id():
+        return "GCALL"
+
+    @staticmethod
+    def get_description():
+        return "GenCall score as a real number. For merged multi-locus entries, max(GenCall) score is reported."
+
+    @staticmethod
+    def get_format_obj():
+        return _Format(
+            GencallFormatReal.get_id(), 1, "Float", GencallFormatReal.get_description())
+
+    def _get_max_gencall_score(self, bpm_records):
+        """
+        Look up gencall scores for entries defined by bpm_records and report
+        the minimum.
+
+        Args:
+            bpm_records iter(BPMRecord) : Iterable of BPM records
+
+        Returns
+            float : MAX gen call score
+        """
+        return max(self._gencall_scores[record.index_num] for record in bpm_records)
+
+    def generate_sample_format_info(self, bpm_records, vcf_record, sample_name):
+        """
+        Returns sample format info (GQ score)
+
+        Args:
+            bpm_records (iter(BPMRecord)) : BPM records
+            vcf_record (vcf._Record): VCF record
+            sample_name (string): Name of sample
+
+        Returns:
+            float: MAX GenCall score, as a real number [0,1].
+        """
+        gencall_score = self._get_max_gencall_score(bpm_records)
+        #phred_quality_score = int(round(-10*log10(min(1.0, max(0.00001, 1 - min_gencall_score)))))
+        return gencall_score