trim_paired now can work on a combined input file

Instead of having files separate ("*.PE.1.fastq" and "*.PE.2.fastq"),
you can have a single combined input file where the reads are already
interleaved.

Added a test directory and some test fastq files.

Added a .gitignore mask
Added a .gitignore
updated usage messages and fixed param logic
Merge branch 'combined_input'
updated markdown readme
Merge pull request #6 from bcthomas/master

altered to work with combined paired-end input files
changed sickle.xml so that output format is taken from input format
changed zlib compilation order in Makefile, changed range of Sanger encoded values
change Makefile to add LIBS
fixed 5 prime trimming bug
Merge pull request #1 from najoshi/master

pull request