Ideas/To Do

This is a rather unsorted list of features that would be nice to have, of things that could be improved in the source code, and of possible algorithmic improvements.

• show average error rate
• In colorspace and probably also for Illumina data, gapped alignment is not necessary
• use str.format instead of %
• allow to change scores at runtime (using command-line parameters)
• multi-threading
• --progress
• run pylint, pychecker
• length histogram
• refactor read_sequences (use classes)
• put write_read into a Fast(a|q)Writer class?
• allow .txt input/output
• check whether input is FASTQ although -f fasta is given
• close on StopIteration
• search for adapters in the order in which they are given on the command line
• more tests for the alignment algorithm

Specifying adapters

The idea is to do away with the -b and -g parameters. Only -a is used with a special syntax for each adapter type. This makes it a bit easier to add new adapter types in the feature.

back	-a ADAPTER	-a ADAPTER or -a ...ADAPTER
front	-g ADAPTER	-a ADAPTER...
prefix	-g ^ADAPTER	-a ^ADAPTER...
anywhere	-b ADAPTER	-a ...ADAPTER... ???
paired	(not implemented)	-a ADAPTER...ADAPTER or -a ^ADAPTER...ADAPTER

Or add only -a ADAPTER... as an alias for -g ^ADAPTER and -a ...ADAPTER as an alias for -a ADAPTER.