altered to work with combined paired-end input files

Hi

Have a look at my fork and see if you're interested in pulling into your master.  I tried to stay faithful to your coding "style."  My changes are almost exclusively in src/trim_paired.c, where I've added the ability to use a single input file with already combined forward/reverse reads.  I also added a .gitignore (sick of seeing git whine at me about compiler intermediate files), and a test directory with a few fastq files I used to test to make sure I didn't break anything.

Anyway, happy to discuss if you want.

Cheers,

bct