Version 0.3.0

- Major changes: now each adapter pair can have its finer control of maximum 
	errors allowed in both 5'-end and 3'-end, and control of the regions 
	where the adapter is expected in the sequence (for both 5'-end adapter 
	and 3'-end adapter).  These controls are specified by extra columns in 
	the "pattern" file given by the "-p" option.

	The details are: now the "pattern" file accepts 6 columns for each 
	line (tab-delimited) in the following format:

	5'-adapter 3'-adapter 5'-max-err 3'-max-err 5'-pos 3'-pos

	For 3'-pos, if negative, it indicates the counts are from the end
	of the sequence.  For example, 5'-pos=20 means the search for the 
	5'-adapter will only be carried out in 0-20 base region, while 
	3'-pos=-10 means the search of 3'-adapter will be in 
	sequence_length-10 to the end of the sequence. 

	An example "pattern" file that can be used to trim Illumina
	AGATCGGAAGAGC adapter is posted in this same web site 
	(illumina_adapter.txt).

	The command line that can be used is like this:
	
	btrim -w 10 -a 25 -p illumina_adapter.txt -3 -P -o output.fastq -l 40\
	-t <(gunzip -c path_to_your_fastq/*.gz ) -C -z

	This setting can routinely achieve 97-99% mapping rate. 
		
	The priority for these parameters are: 
	"pattern" file > command line options (u, v, b, e) > defaults
	
	The old style 2-column "pattern" file is still accepted.

- Added option "-C": this is basically for the program to use named pipes.
	By default, the program checks if the input sequence file is zipped
	or not, but this check seems to cause problem if named pipe is
	used.  When option "-C" is specified, the check is skipped and the
	program assumes the file is unzipped. This option can be used with
	named pipe like this:

	-t <(gunzip -c /path_to_your_fastq/*.gz ) -C 

	
	
Version 0.2.0

- Now accept compressed input files.
- Added option "-T", which searches 3'-end first, then the best match's 
	5'-adaptor is used for 5'-end search.  This is useful when the 
	barcodes are in the 3'-end and option "-B" is used.
- Added option "-k", which keeps all reads in the same output file 
	specified by -o, even for failed reads.
- Added option "-K" to keep failed reads in a separate output file.
- Changed phred_offset=33 as default for the quality scores.  The new version 
	is compatible with the previous versions: the "-S" option is still 
	accepted with the same effect as the default (phred_offset=33).  
	The option "-i" will switch to phred_offset=64.
- Added option "-z" to compress the output file.  The command for compression 
	can be specified by option "-Z", with default="/bin/gzip -f".
- More summary information is added, such as the error distributions for
	each adaptor.