gts-infix - infix input sequence(s) into the host sequence(s)
gts-infix [--version] [-h | --help] [args] locator host guest
gts-infix takes two sequence inputs: a host sequence input and a guest
sequence input, and inserts the sequences contained in the host sequence
input into the sequences contained in the guest sequence input. If the guest
sequence input is omitted, standard input will be read instead. For each
sequence in the guest sequence input, a copy of each of the host sequence
input will be created. Each guest sequence will then be inserted into the
location(s) specified by the locator in the host sequence.
A locator consists of a location specifier and a modifier. A location specifier
may be a modifier, a point location, a range location, or a selector.
The syntax for a locator is [specifier][@modifier]. See gts-locator(7) for a
more in-depth explanation of a locator. Refer to the EXAMPLES for some examples
to get started.
Features that were present at the point of insertion will be split to form
a joined location. Such features can be instead expanded if the -e or
--embed option is provided. Any features present in the guest sequence
will be transferred to the corresponding locations after being inesrted into
the host sequence.
There is also a similar command in gts(1) designated gts-insert(1), While gts-infix inserts the primary sequence input into the host sequences, gts-insert(1) inserts guest sequences into the primary sequence input. Use gts-infix when you want a insert the sequence that you are working on in a pipeline into another sequence. Note that all of the host sequences will be read into memory when using gts-infix and all of the guest sequences will be read into memory when using gts-insert(1). If memory availability may be an issue, make sure to use the command that will read in the smaller file.
<locator>A locator string ([specifier][@modifier]). See gts-locator(7) for more
details.
<host>Host sequence file. See gts-seqin(7) for a list of currently supported list of sequence formats.
<seqin>Input sequence file (may be omitted if standard input is provided).
-e, --embedExtend existing feature locations when inserting instead of splitting them.
-F <format>, --format=<format>Output file format (defaults to same as input).
--no-cacheDo not use or create cache.
-o <output>, --output=<output>Output sequence file (specifying - will force standard output).
gts-infix currently has no known bugs.
gts-infix is written and maintained by @AUTHOR@.