Merge pull request #1031 from cfe-lab/complete-cigar-definition

Complete CIGAR string definition
cfe-lab · Nov 7, 2023 · 3984943 · 3984943
2 parents d62ac24 + 70e3f37
commit 3984943
Showing 1 changed file with 2 additions and 1 deletion.
diff --git a/micall/utils/consensus_aligner.py b/micall/utils/consensus_aligner.py
@@ -23,9 +23,10 @@
 # Most codons in an insertion or deletion that is still aligned in amino acids.
 MAXIMUM_AMINO_GAP = 10
 
+# Mapping as defined in https://samtools.github.io/hts-specs/SAMv1.pdf, page 8
 CigarActions = IntEnum(
     'CigarActions',
-    'MATCH INSERT DELETE SKIPPED SOFT_CLIPPED HARD_CLIPPED',
+    'MATCH INSERT DELETE SKIPPED SOFT_CLIPPED HARD_CLIPPED PADDING SEQ_MATCH MISMATCH',
     start=0)