Needed: Speed-optimized FASTQ to FASTA script

[jorvis]

This script should accept a FASTQ file and and simply convert to FASTA. The only currently needed options are:

• Allow the user to manually append a text string to the end of each header, such as "/1".
• Auto-detect this header format "@SN7001163:78:C0YG5ACXX:6:1101:1241:2178 1:N:0:CCTAGGT" in which the first digit after the whitespace is the mate pair number, then add it to the read ID to make the header like: ">SN7001163:78:C0YG5ACXX:6:1101:1241:2178/1"

While this is trivial itself, what can get more interesting is finding the method to do it that performs the best. Because this will be an important component of a few other projects, speed and proper error handling is important. Most apps assume python, but I'm up for implementations in whatever language will give the best results here as long as they don't open up a huge can of worms dependency-wise.

[jorvis]

Closed because I've added this:

https://github.com/jorvis/biocode/blob/master/fastq/convert_fastq_to_fasta.py

Timing information is found within the script's documentation.

Anyone wishing to offer a faster version (in any language) which provides the same options is certainly welcome.