Name
	TRhist - profiling all tandem repeats in personal genomes

Input: (gzipped) fastq file
Output: histogram.list (default): CSV file of all tandem repeat histograms
        paired.fasta (default)  : fasta file for finding tandem repeat loci (optional: option -p)
	repeat.list (default)   : All tandem repeats in each reads (optional: option -d)

Synopsis:
	java -jar TRhist.jar -z reads.fastq.gz 
	java -jar TRhist.jar -p -z -output_fasta reads.fasta reads1.fastq.gz reads2.fastq.gz
	
Option
	-z                 Input file fomat is gzipped fastq (Default: fastq format)
	-a                 Output histogram of approximate tandem repeats (Default: exact tandem repeats)
        -output STR  Output file name for all tandem repeat histograms (Default: histogram.list)
	-p                 Input is paired-end reads (fastq format). Paired-end reads should be same lengths.
	-output_fasta STR  Output file name for finding tandem repeat loci if option -p is used (Default: paired.fasta)
                           If all bases are tandem repeats in a read, output pairedend sequence in fasta file format.
        -output_debug STR  Output file name for all tandem repeats if option -d is used (Default: repeat.list)


* Java requirement
	TRhist.jar on this web site is compiled with java version 1.7.0_05. 
        You need Java Runtime Environment version 1.7.0_05 or newer version to run this jar file. 
	
-------------------------------------------------------------------------------- 
File format of histogram.list


repeat_unit,[repeatUnitSequence1]
length1,frequency1
length2,frequency2
......
repeat_unit,[repeatUnitSequence2]
length1,frequency1
length2,frequency2
......

Example:
repeat_unit,A
1,0
2,41937120
.
.
.
100,0
repeat_unit,C
1,0
2,1321793
.
.
.
100,0

--------------------------------------------------------------------------------
File format of paired.fasta
>[readName]_[readSequence]_[representativeRepeatUnit]_pairedend
ATCACATTCTACTTA...

--------------------------------------------------------------------------------
File format of repeat.list
[readName]
Period: [tandem repeat period] Left : [start position] Right: [end position] repeatition : [repeat unit]
....