Conclude merge

Author: manojbhosale

LICENSE

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+MIT License
+
+Copyright (c) 2019 Manojkumar Bhosale
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

README.md

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+# MAutomaton
+
+This is an attempt to tackle the daily tasks in NGS data analysis. This tool is written in Java Swing and has below features.
+
+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.
+
+
+## How to use
+
+### 1. VCF comparator
+
+Prerequisite: **Java 1.8** or **_higher_**
+
+#### Steps
+1. Right click on the jar file and open with java
+2. In **"VCF comparator"** tab select the VCF 1, VCF 2 files to compare.
+3. Click **"Compare"**
+4. Based on size of the VCF files it will take time to compare the VCF. in the mean time the UI will _freeze_ as its a single threaded application.
+5. After comparison is done the UI will update with the comparison results as displayed in below screenshot. The red colored cells indicate non-zero mismatches
+
+
+![alt text](https://github.com/manojbhosale/hello-world/blob/master/MAutomatonScreen.png "MAutomaton screen")
+
+6. If you are interested to find out the actual mismatching and common variants in VCF format visit "C:\gatKAutomator\comparisonResults" directory of your computer, not to mentione you need to have read/write access to this location.The result VCF are named in following way,
+
+* Common variants in both vcf: <VCF 1>_common.vcf
+* Insertion variants only in VCF 1: <VCF 1>_insOld.vcf
+* Insertion variants only in VCF 2: <VCF 2>_insNew.vcf
+* Deletion variants only in VCF 1: <VCF 1>_delOld.vcf
+* Deletion variants only in VCF 2: <VCF 2>_delNew.vcf
+* SNP variants only in VCF 1: <VCF 1>_snpOld.vcf
+* SNP variants only in VCF 2: <VCF 2>_snpNew.vcf
+
+7. If you want ot compare another pair then just select those files and hit "Compare". The results will get appended in the table and the VCFs will get generated at the designated location.
+
+8. If you have miltiple files to compare then use "Multiple files" option. the input is the tab separated mapping file of VCFs to caompare like below.
+create comparison.txt with below content. File paths need to be **_absolute paths_** of the VCFs.
+
+c:\one.vcf c:\two.vcf
+
+c:\a.vcf c:\b.vcf
+
+c:\x.vcf c:\y.vcf