2% faster (total) by using __slots__ in AdapterMatch
2% faster by avoiding tuple pack/unpack
make AdapterMatch.length an attribute instead of a property (tiny bit faster)
support bzip2-compressed files
do not complain about missing bz2 module unless really needed
Print an error when Cython is not available.

The warning appears when cutadapt is checked out from version control.
In that case, the pre-complied cutadapt/calign.c is not included and Cython
is needed.
show read counts per observed no. of errors in statistics
fix incorrect new statistics output
add ability to keep paired end files in sync

note this does not trim the paired end file, just applies the same filtering as to the trimmed file
test separate trimming of paired-end test files
check that two files are given if --paired-output is used
test --paired-output
forgot test files
Fixed typo? in align.py

I think there is a typo in the explanation of the alignment start and stop coordinates.
Merge pull request #4 from mdshw5/patch-1

Fix typo in align.py
document info file format
document that -z option should be used with Bowtie and colorspace
state that pysemiglobalalign is not the Python version of the adapter-trimming algorithm (anymore)
explain how the --paired-output option should be used
Update README.md