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*********
Glossary
*********
.. 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.
region
A genomic region, stated relative to a reference sequence. A region consists of
reference name ('chr1'), start (100000), and end (200000).
0-based coordinates. Can be expressed as a string ('chr1:10000:20000')
column
Reads that are aligned to a base in the :term:`reference` sequence.
tid
The :term:`target` id. The target id is 0 or a positive integer mapping to
entries within the sequence dictionary in the header section of
a :term:`TAM` file or :term:`BAM` file.
Reference
The sequence that a :term:`tid` refers to. For example ``chr1``, ``contig123``.
SAM
A textual format for storing genomic alignment information.
BAM
Binary SAM format. BAM files are binary formatted, indexed and
allow random access.
TAM
Text SAM file. TAM files are human readable files of
tab-separated fields. TAM files do not allow random access.
sam file
A file containing aligned reads. The :term:`sam file` can either
be a :term:`BAM` file or a :term:`TAM` file.
pileup
Pileup
samtools
The samtools_ package.
csamtools
The samtools_ C-API.
fetching
Retrieving all mapped reads mapped to a :term:`region`.
target
The sequence that a read has been aligned to. Target
sequences have bot a numerical identifier (:term:`tid`)
and an alphanumeric name (:term:`Reference`).
tabix file
A sorted, compressed and indexed tab-separated file created
by the command line tool :file:`tabix` or the commands
:meth:`tabix_compress` and :meth:`tabix_index`. The file
is indexed by chromosomal coordinates.
tabix row
A row in a :term:`tabix file`. Fields within a row are
tab-separated.
.. _samtools: http://samtools.sourceforge.net
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