.. glossary::
yaml
Language to serialize objects. Used in the CGAT testing
framework. (`YAML <http://en.wikipedia.org/wiki/YAML>`_).
bam
Format to store genomic alignments in a compressed format.
(`BAM <http://samtools.sourceforge.net/>`_).
bed
File containing genomic intervals.
(`BED <https://genome.ucsc.edu/FAQ/FAQformat.html#format1>`_).
vcf
`Variant call format
<http://www.1000genomes.org/wiki/Analysis/Variant%20Call%20Format/vcf-variant-call-format-version-41>`_.
gtf
`General transfer format
<http://www.ensembl.org/info/website/upload/gff.html>`_.
Format to store genes and transcripts.
gff
`General feature format <http://www.ensembl.org/info/website/upload/gff.html>`_.
bigwig
Compressed format for displaying numerical values across
genomic ranges (`BIGWIG <https://genome.ucsc.edu/goldenPath/help/bigWig.html>`_).
fasta
Sequence format.
wiggle
Format for displaying numerical values across genomic
ranges (`Wiggle <https://genome.ucsc.edu/goldenPath/help/wiggle.html>`_).
psl
Genomic alignment format. The format is described in detail
`(PSL <https://genome.ucsc.edu/FAQ/FAQformat.html#format2>`_.
sam
Format to store genomic alignments
`(SAM <http://samtools.sourceforge.net/>`_).
gdl
gdl
tsv
Tab separated values. In these tables, records are separated by new-line
characters and fields by tab characters. Lines with comments are started
by the ``#`` character and are ignored. The first uncommented line
should contain the column headers. For example::
# This is a comment
gene_id length
gene1 1000
gene2 2000
# Another comment
svg
pass
edge list
pass
fastq
Sequence format containing quality scores, more background is
`here <http://en.wikipedia.org/wiki/FASTQ_format>`_
sra
sra
axt
axt
maf
maf
agp
`AGP format <https://www.ncbi.nlm.nih.gov/assembly/agp/AGP_Specification/>`_
rdf
`Resource description framework <http://en.wikipedia.org/wiki/Resource_Description_Framework>`_
.. glossary::
test directory
Directory that contains the :file:`test.yaml`, input and
reference files for testing scripts.
experiment
experiment
replicate
replicate
graph
graph
track
track
graph
graph
submit host
pass
execution host
pass
edge list
pass
task
pass
sphinxreport
sphinxreport
query
pass
target
pass
code directory
pass
go
pass
goslim
pass
fastq
pass
tss
Transcription start site
production pipeline
A pipeline that performs common tasks on a certain type of
data. The idea of a production pipeline is to provide common
preprocessing of data and a first look. A :term:`project
pipeline` might then take data from one or more
:term:`production pipeline` to glean biological insight.
project pipeline
A pipeline that is project specific. Usually code is developed
first inside a project pipeline. When it becomes generally
useful, it may be refactored into a production pipeline.
stdin
Unix standard input. Most CGAT tools read data from stdin.
stdout
Unix standard output. Most CGAT tools output data to stdout.
stderr
Unix standard error. This is where errors go.
loglevel
Verbosity of logging information. The logging level can be
determined by the ``--verbose`` option. A
level of ``0`` means no logging output, while ``1`` is information
messages only, while ``2`` outputs also debugging information.