From 70e3f37865b456557c5bf502152919e0155449f7 Mon Sep 17 00:00:00 2001
From: Vitaliy Mysak <vmysak@bccfe.ca>
Date: Wed, 1 Nov 2023 09:28:22 -0700
Subject: [PATCH] Complete CIGAR string definition

---
 micall/utils/consensus_aligner.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/micall/utils/consensus_aligner.py b/micall/utils/consensus_aligner.py
index ab0bbdbc9..66e9ca6bf 100644
--- 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)