Merge d887d75 into 2a62ce0

isovar/locus_reads.py

@@ -65,7 +65,8 @@ def from_pysam_pileup_element(
             base0_position_after_variant,
             use_secondary_alignments,
             use_duplicate_reads,
-            min_mapping_quality):
+            min_mapping_quality,
+            use_soft_clipped_bases=False):
         """
         Parameters
         ----------
@@ -81,6 +82,8 @@ def from_pysam_pileup_element(
 
         min_mapping_quality : int
 
+        use_soft_clipped_bases : bool. Default false; set to true to keep soft-clipped bases
+
         Returns LocusRead or None
         """
         read = pileup_element.alignment
@@ -190,6 +193,15 @@ def from_pysam_pileup_element(
         if isinstance(sequence, bytes):
             sequence = sequence.decode('ascii')
 
+        if not use_soft_clipped_bases:
+            start = read.query_alignment_start
+            end = read.query_alignment_end
+            sequence = sequence[start:end]
+            reference_positions = reference_positions[start:end]
+            base_qualities = base_qualities[start:end]
+            base0_read_position_before_variant -= start
+            base0_read_position_after_variant -= start
+
         return cls(
             name=name,
             sequence=sequence,