Read Analysis n Comparison Kit in Java Files

RACKJ (Read Analysis & Comparison Kit in Java) is a set of Java programs that analyze 
and compare RNA-seq data made by NGS (Next-Generation Sequencing) technologies. In 
addition to RPKM (Reads Per Kbp per Million reads) values, RACKJ computes read counts 
for exons and splicing events. In so doing, it is feasible to compare two samples and 
identify genes with most significant difference in exon(splicing)-level. 

Please find usage examples and manual in our website: http://rackj.sourceforge.net/

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CONTENTS
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1. rnaseq.jar: the RACKJ java archive
2. ReleaseNote.txt: release note
3. LICENSE(intervaltree).txt: licence for misc.intervaltree package
4. lgpl.txt: The GNU Lesser General Public License
5. README.txt: this file
6. manual: HTML documents
7. scripts: perl scripts, see documents for description

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CHANGE LOG
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0.99c   (1) fixed a bug for blast2psl.pl for gaps longer than one text line in BLAST output
        (2) Added Promoter annotation to MutationAnnotation.pl
        (3) Added ASnumbers.pl, AScomp_merged.pl, and AScomp_separate.pl for easier
            alternative splicing computation. See https://github.com/wdlingit/rackj/blob/main/walkthrough/Rackj_short_reads_AScomp.md
            for an example walkthrough.

0.99a	(1) Remove a number of subfolders in scripts, moved scripts there to
	    scripts
0.99	(1) Current. Will find someday to document tools useful in works.

someday long time ago
	(1) Revised GffTree for non-parent-first GFF3 files
0.95
	(1) MappingInfoRecover & TranscriptomeRecover for novel region detection
	(2) A set of scripts for cooperation with the MEME suite
	(3) A set of scripts for sample-sensitive alternative splicing detection
	(4) A framework of scripts for read mapping using Bowtie2 & BLAT
	(5) mapping translation functionality of AlignmentFilter
0.75
	(1) FineSpliceCounter for information of detailed splice sites
	(2) multiply applicable -M option for RPKMComputer / GeneTracer / FineSpliceCounter
	(3) option -traceFile for GeneTracer
	(4) unlimited number of traced genes for GeneTracer
	(5) (changed) default paramters of RPKMComputer: -J 2 -contain false -min 8
0.61
	(1) (fixed) java classpath separator problem (: for UN*X, ; for Windows)
	(2) (fixed) possible stack overflow when using SAMReader