Support alignment conversion from/to CIGAR

doc/apidoc.json

@@ -152,6 +152,11 @@
             "Permutation",
             "RandomPermutation",
             "FrequencyPermutation"
+        ],
+        "CIGAR strings" : [
+            "CigarOp",
+            "read_alignment_from_cigar",
+            "write_alignment_to_cigar"
         ]
     },
 

doc/examples/scripts/sequence/gene_counts.py

@@ -305,8 +305,13 @@ def read_iter(fastq_path):
 # displayed.
 # The alignment itself is also discarded here, but note that it could
 # also be used in downstream analysis.
+#
 # Read alignments are typically stored in file formats like SAM/BAM
 # :footcite:`Li2009`.
+# The package `pysam <https://pysam.readthedocs.io/en/latest/>`_
+# provides an interface to these formats.
+# To convert an alignment into a CIGAR string, the function
+# :func:`write_alignment_to_cigar()` can be used.
 
 counts = np.zeros(len(sequences), dtype=int)
 for gene_index, alignment in mapping_results:

src/biotite/sequence/align/__init__.py

@@ -35,6 +35,7 @@
 from .alignment import *
 from .banded import *
 from .buckets import *
+from .cigar import *
 from .kmeralphabet import *
 from .kmertable import *
 from .kmersimilarity import *