Implemented standalone split_fastq.py script.

First commit of standalone split_fastq.py script. Needs more
comprehensive testing and performance benchmarking, but seems to work
well.
Added trim_reads.py

Also fixed handling of FASTQ files with different lengths in
split_fastq.py (should be an error).
Created fastq_util.py and moved FASTQ-handling functions to this library.
Added filtering function to read_fastq()

read_fastq accepts an optional filtering function that limits which
FASTQ records are yielded.
Improved FASTQ file handling.

Added a new read_fastq_multi function for reading multiple FASTQ files
in parallel. Documented fastq_util.py
Committed work-in-progress version of EnrichLibrary classes.

Added additional fastq_util.py functions.
Continuing development of the EnrichLibrary classes.

Settled on a reasonable object interface. Implemented the
BasicEnrichLibrary and OverlapEnrichLibrary classes. Needs commenting
and testing!
Fire alarm
Finished aligner implementation.

Commit before extensive testing of the SeqLib implementations.
Testable versions of SeqLib and derivatives.

Needs more testing, especially efficiency/memory use testing.
Fixed Aligner code.

Aligner also combines adjacent indels and properly calls multi-base
duplications.
Added chastity filtering.
Implemented barcode.py
Fixed some errors in overlap.py

Aligner now handles N's. Other minor fixes. Thanks, msr.
Minor changes to overlap.py
Changed overlap.py alignment conditions.

Alignment is now based on a percentage of mismatches in the overlap
region, rather than a number of consecutive mismatch. Should help
reduce unnecessary aligner calls.
Added first version of Selection class.

Also includes minor updates to overlap and seqlib.
SeqLib now stores wild type counts.

Wild type instances are counted under the special key "wt"
Modifications to Counter storage.

Counters are now stored in a dictionary, to better accomodate different
experimental designs.
Many updates, including new FQRead class for FASTQ data.

Switched over to FQRead from tuples. Allows named fields and editing of
FASTQ data in-place (instead of requiring copies).