feat(mi): add generic VCF length-based calculator

davidlougheed · Dec 5, 2024 · ad9015f · ad9015f
1 parent 697c7be
commit ad9015f
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Showing 3 changed files with 7 additions and 4 deletions.
diff --git a/strkit/constants.py b/strkit/constants.py
@@ -20,6 +20,7 @@
 CALLER_HIPSTR = "hipstr"
 CALLER_LONGTR = "longtr"
 CALLER_GANGSTR = "gangstr"
+CALLER_GENERIC_VCF_AL = "generic-vcf-al"
 CALLER_REPEATHMM = "repeathmm"
 CALLER_STRAGLR = "straglr"
 CALLER_STRKIT = "strkit"
@@ -47,6 +48,7 @@
 MI_CALLERS = (
     CALLER_EXPANSIONHUNTER,
     CALLER_GANGSTR,
+    CALLER_GENERIC_VCF_AL,
     CALLER_LONGTR,
     CALLER_REPEATHMM,
     CALLER_STRAGLR,

diff --git a/strkit/entry.py b/strkit/entry.py
@@ -391,7 +391,7 @@ def _exec_mi(p_args) -> None:
     from strkit.mi.base import BaseCalculator
     from strkit.mi.expansionhunter import ExpansionHunterCalculator
     from strkit.mi.gangstr import GangSTRCalculator
-    from strkit.mi.longtr import LongTRCalculator
+    from strkit.mi.generic_vcf import GenericVCFLengthCalculator
     from strkit.mi.repeathmm import RepeatHMMCalculator
     from strkit.mi.straglr import StraglrCalculator
     from strkit.mi.strkit import StrKitCalculator, StrKitJSONCalculator, StrKitVCFCalculator
@@ -401,7 +401,8 @@ def _exec_mi(p_args) -> None:
     calc_classes: dict[str, Type[BaseCalculator]] = {
         c.CALLER_EXPANSIONHUNTER: ExpansionHunterCalculator,
         c.CALLER_GANGSTR: GangSTRCalculator,
-        c.CALLER_LONGTR: LongTRCalculator,
+        c.CALLER_GENERIC_VCF_AL: GenericVCFLengthCalculator,
+        c.CALLER_LONGTR: GenericVCFLengthCalculator,
         c.CALLER_REPEATHMM: RepeatHMMCalculator,
         c.CALLER_STRAGLR: StraglrCalculator,
         c.CALLER_STRKIT: StrKitCalculator,

diff --git a/strkit/mi/longtr.py → strkit/mi/generic_vcf.py b/strkit/mi/longtr.py → strkit/mi/generic_vcf.py
@@ -6,10 +6,10 @@
 from .result import MIContigResult, MILocusData
 from .vcf_utils import VCFCalculatorMixin
 
-__all__ = ["LongTRCalculator"]
+__all__ = ["GenericVCFLengthCalculator"]
 
 
-class LongTRCalculator(BaseCalculator, VCFCalculatorMixin):
+class GenericVCFLengthCalculator(BaseCalculator, VCFCalculatorMixin):
     def _get_sample_contigs(self) -> tuple[set, set, set]:
         contigs = self.get_contigs_from_files(self._mother_call_file, self._father_call_file, self._child_call_file)
         self._logger.debug(