Update glossary entry for CIGAR
@@ -6,10 +6,14 @@ Glossary
:sorted:
cigar
- An alignment format string. In the python API, the cigar alignment is
- presented as a list of tuples ``(operation,length)``. For example, the tuple
- ``[ (0,3), (1,5), (0,2) ]`` refers to an alignment with 3 matches, 5 insertions
- and another 2 matches.
+ Stands for Compact Idiosyncratic Gapped Alignment Report and
+ represents a compressed (run-length encoded) pairwise alignment
+ format. It was first defined by the Exonerate Aligner, but was alter
+ adapted and adopted as part of the :term:`SAM` standard and many other
+ aligners. In the Python API, the cigar alignment is presented as a
+ list of tuples ``(operation,length)``. For example, the tuple ``[
+ (0,3), (1,5), (0,2) ]`` refers to an alignment with 3 matches, 5
+ insertions and another 2 matches.
region
A genomic region, stated relative to a reference sequence. A
@@ -31,9 +35,12 @@ Glossary
entries within the sequence dictionary in the header section of
a :term:`TAM` file or :term:`BAM` file.
- Reference
+ contig
The sequence that a :term:`tid` refers to. For example ``chr1``, ``contig123``.
+ Reference
+ Synonym for contig
+
SAM
A textual format for storing genomic alignment information.
