Fixes in mergeSTR

RELEASE_NOTES.rst

@@ -12,7 +12,7 @@ Functionality Changes:
 
 Misc:
 
-* mergeutils: function GetMinHarmonizedRecords was transformed into GetRecordComparabilityAndIncrement, which allows the caller
+* mergeutils: function GetMinHarmonizedRecords was transformed into GetIncrementAndComparability, which allows the caller
   to define custom predicate that decides whether records are comparable.
 
 4.0.2

trtools/compareSTR/compareSTR.py

@@ -899,8 +899,8 @@ def main(args):
                               range(len(current_records))]
         # increments contains information about which record should be
         # skipped in next iteration
-        increment, comparable = mergeutils.GetRecordComparabilityAndIncrement(harmonized_records, chroms,
-                                                                              handle_overlaps)
+        increment, comparable = mergeutils.GetIncrementAndComparability(harmonized_records, chroms,
+                                                                        handle_overlaps)
 
         if args.verbose: mergeutils.DebugPrintRecordLocations(current_records, increment)
         if mergeutils.CheckMin(increment): return 1

trtools/mergeSTR/mergeSTR.py

@@ -624,12 +624,17 @@ def main(args: Any) -> int:
                     ", e.g.: bcftools reheader -f hg19.fa.fai -o myvcf-readher.vcf.gz myvcf.vcf.gz")
                 return 1
         harmonized_records = HarmonizeIfNotNone(current_records, vcftype)
-        is_min = mergeutils.GetMinHarmonizedRecords(harmonized_records, chroms)
-        if args.verbose: mergeutils.DebugPrintRecordLocations(current_records, is_min)
-        if mergeutils.CheckMin(is_min): return 1
-        MergeRecords(vcfreaders, vcftype, num_samples, harmonized_records, is_min, vcfw, useinfo,
+
+        # mergeSTR doesnt provide custom comparability handler. By default, only the increment is necessary to decide
+        # which records should be merged during single iteration. This is because the merge is based on the position
+        # of the records. If this behaviour changes in the future, custom mergability handler will have to be created.
+        increment, _ = mergeutils.GetIncrementAndComparability(harmonized_records, chroms)
+
+        if args.verbose: mergeutils.DebugPrintRecordLocations(current_records, increment)
+        if mergeutils.CheckMin(increment): return 1
+        MergeRecords(vcfreaders, vcftype, num_samples, harmonized_records, increment, vcfw, useinfo,
                      useformat, format_type)
-        current_records = mergeutils.GetNextRecords(vcfreaders, current_records, is_min)
+        current_records = mergeutils.GetNextRecords(vcfreaders, current_records, increment)
         done = mergeutils.DoneReading(current_records)
     return 0
 

trtools/utils/mergeutils.py

@@ -16,6 +16,7 @@
 
 CYVCF_RECORD = cyvcf2.Variant
 CYVCF_READER = cyvcf2.VCF
+COMPARABILITY_CALLBACK = Callable[[List[Optional[trh.TRRecord]], List[int], int], Union[bool, List[bool]]]
 
 
 def LoadReaders(vcffiles: List[str], region: Optional[str] = None) -> List[CYVCF_READER]:
@@ -248,13 +249,18 @@ def GetMinRecords(record_list: List[Optional[trh.TRRecord]], chroms: List[str])
     return [CheckPos(r, chroms[min_chrom], min_pos) for r in record_list]
 
 
+def default_callback(records: List[trh.TRRecord], chrom_order: List[int], min_chrom_index: int) -> bool:
+    return True
+
+
+def GetIncrementAndComparability(record_list: List[Optional[trh.TRRecord]],
+                                 chroms: List[str],
+                                 overlap_callback: COMPARABILITY_CALLBACK = default_callback) \
+        -> Tuple[List[bool], Union[bool, List[bool]]]:
 
-def GetRecordComparabilityAndIncrement(record_list: List[Optional[trh.TRRecord]],
-                                       chroms: List[str],
-                                       overlap_callback: Callable[[List[Optional[trh.TRRecord]], List[int], int], bool]) \
-        -> Tuple[List[bool], bool]:
     r"""Get list that says which records should be skipped in the next
-     iteration, and whether they are all comparable with each other
+     iteration (increment), and whether they are all comparable / mergable
+     The value of increment elements is determined by the (harmonized) position of corresponding records
 
 
     Parameters
@@ -265,15 +271,15 @@ def GetRecordComparabilityAndIncrement(record_list: List[Optional[trh.TRRecord]]
     chroms : list of str
        Ordered list of all chromosomes
 
-    overlap_callback: Callable[[List[Optional[trh.TRRecord]], List[int], int], bool]
+    overlap_callback: Callable[[List[Optional[trh.TRRecord]], List[int], int], Union[bool, List[bool]]
         Function that calculates whether the records are comparable
 
     Returns
     -------
     increment : list of bool
        List or bools, where items are set to True when the record at the index of the item should be
        skipped during VCF file comparison.
-    comparable: bool
+    comparable: bool or list of bool
         Value, that determines whether current records are comparable / mergable, depending on the callback
     """
     chrom_order = [np.inf if r is None else chroms.index(r.chrom) for r in record_list]

trtools/utils/tests/test_mergeutils.py

@@ -110,27 +110,27 @@ def comp_callback_false(x, y, z):
 
 
     pair = [DummyHarmonizedRecord("chr1", 20), DummyHarmonizedRecord("chr1", 20)]
-    assert mergeutils.GetRecordComparabilityAndIncrement(pair, chromosomes, comp_callback_true) == ([True, True], True)
+    assert mergeutils.GetIncrementAndComparability(pair, chromosomes, comp_callback_true) == ([True, True], True)
 
     # these two test cases show that second result of GetRecordComparabilityAndIncrement is
     # entirely dependant on the callback
     pair = [DummyHarmonizedRecord("chr1", 21), DummyHarmonizedRecord("chr1", 20)]
-    assert mergeutils.GetRecordComparabilityAndIncrement(pair, chromosomes, comp_callback_false) == ([False, True], False)
+    assert mergeutils.GetIncrementAndComparability(pair, chromosomes, comp_callback_false) == ([False, True], False)
 
     pair = [DummyHarmonizedRecord("chr1", 21), DummyHarmonizedRecord("chr1", 20)]
-    assert mergeutils.GetRecordComparabilityAndIncrement(pair, chromosomes, comp_callback_true) == ([False, True], True)
+    assert mergeutils.GetIncrementAndComparability(pair, chromosomes, comp_callback_true) == ([False, True], True)
 
     pair = [DummyHarmonizedRecord("chr2", 20), DummyHarmonizedRecord("chr1", 20)]
-    assert mergeutils.GetRecordComparabilityAndIncrement(pair, chromosomes, comp_callback_false) == ([False, True], False)
+    assert mergeutils.GetIncrementAndComparability(pair, chromosomes, comp_callback_false) == ([False, True], False)
 
     pair = [DummyHarmonizedRecord("chr1", 20), DummyHarmonizedRecord("chr1", 21)]
-    assert mergeutils.GetRecordComparabilityAndIncrement(pair, chromosomes, comp_callback_true) == ([True, False], True)
+    assert mergeutils.GetIncrementAndComparability(pair, chromosomes, comp_callback_true) == ([True, False], True)
 
     pair = [None, None]
-    assert mergeutils.GetRecordComparabilityAndIncrement(pair, chromosomes, comp_callback_false) == ([False, False], False)
+    assert mergeutils.GetIncrementAndComparability(pair, chromosomes, comp_callback_false) == ([False, False], False)
 
     pair = [DummyHarmonizedRecord("chr1", 20), None]
-    assert mergeutils.GetRecordComparabilityAndIncrement(pair, chromosomes, comp_callback_false) == ([True, False], False)
+    assert mergeutils.GetIncrementAndComparability(pair, chromosomes, comp_callback_false) == ([True, False], False)
 
     pair = [None, DummyHarmonizedRecord("chr1", 20)]
-    assert mergeutils.GetRecordComparabilityAndIncrement(pair, chromosomes, comp_callback_false) == ([False, True], False)
+    assert mergeutils.GetIncrementAndComparability(pair, chromosomes, comp_callback_false) == ([False, True], False)