Added CNV comparison feature

Input segments.txt files will be compared based on chr, start, stop, CNV type columns and matching and mismatching intervals will be reported.

With implicit VCF indexing for VCF BED intersection

In previous version the VCF needs to be indexed with some tool like IGV tools or Tabix to run the utility.
Now the tool itself takes care of the VCF index generation with intermediate temporary index file.
One prerequisite is that the input VCF must have contig information in header in below format for all the applicable chromosomes.
##contig=<ID=chr1,length=249250621,assembly=hg19>

With median amplification level calculation fix

In previous builds the median amplification level was calculated based on the histogram values alone.
Now the Histogram values are multiplied with amplification level are used.

BED intersect

Added below features

1. One can specify the VCF comparison output to a folder
2. Added new tool to intersect two BED files
3. Added colors to tabs for easy traversal

VCF BED intersection

Added VCF BED intersection utility to existing suite.
VCF needs to be indexed before use for faster processing.

With overlapping indel fix

Issue is fixed where indels are counted missing even if present in both files.

First release with 4 utilities

This release contains below utilities;

1. VCF comparison utility: To compare SNP, Indels, CNVs in VCF_4.2 format.
2. Duplicate metrics utility: To calculate %duplicates from a BAM file.
3. VCF Ts/Tv util: To calculate transition and transversion ratio from given VCF file
4. Comparison of QC metrics in the form of .properties file.