Merge branch 'master' into dev

Author: owlang

README.md

@@ -3,6 +3,10 @@
 
 Scripts are generically categorized within semi-descriptive tabs and are designed to be run in parallel with each other and themselves.
 
+
+### Tutorial to using basic plotting capabilities of ScriptManager
+Open **ScriptManager-Tutorial.docx** available in root directory
+
 ## Build Instructions
 (after cloning this repo):
 ```

ScriptManager-Tutorial.docx

@@ -0,0 +1,20 @@
+# Dependencies
+/node_modules
+
+# Production
+/build
+
+# Generated files
+.docusaurus
+.cache-loader
+
+# Misc
+.DS_Store
+.env.local
+.env.development.local
+.env.test.local
+.env.production.local
+
+npm-debug.log*
+yarn-debug.log*
+yarn-error.log*

docusaurus/.gitignore

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+# Website
+
+This website is built using [Docusaurus 2](https://v2.docusaurus.io/), a modern static website generator.
+
+### Installation
+
+```
+$ yarn
+```
+
+### Local Development
+
+```
+$ yarn start
+```
+
+This command starts a local development server and open up a browser window. Most changes are reflected live without having to restart the server.
+
+### Build
+
+```
+$ yarn build
+```
+
+This command generates static content into the `build` directory and can be served using any static contents hosting service.
+
+### Deployment
+
+```
+$ GIT_USER=<Your GitHub username> USE_SSH=true yarn deploy
+```
+
+If you are using GitHub pages for hosting, this command is a convenient way to build the website and push to the `gh-pages` branch.

docusaurus/README.md

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+module.exports = {
+  presets: [require.resolve('@docusaurus/core/lib/babel/preset')],
+};

docusaurus/babel.config.js

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+---
+slug: hola
+title: Hola
+author: Gao Wei
+author_title: Docusaurus Core Team
+author_url: https://github.com/wgao19
+author_image_url: https://avatars1.githubusercontent.com/u/2055384?v=4
+tags: [hola, docusaurus]
+---
+
+Lorem ipsum dolor sit amet, consectetur adipiscing elit. Pellentesque elementum dignissim ultricies. Fusce rhoncus ipsum tempor eros aliquam consequat. Lorem ipsum dolor sit amet

docusaurus/blog/2019-05-28-hola.md

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+---
+slug: hello-world
+title: Hello
+author: Endilie Yacop Sucipto
+author_title: Maintainer of Docusaurus
+author_url: https://github.com/endiliey
+author_image_url: https://avatars1.githubusercontent.com/u/17883920?s=460&v=4
+tags: [hello, docusaurus]
+---
+
+Welcome to this blog. This blog is created with [**Docusaurus 2 alpha**](https://v2.docusaurus.io/).
+
+<!--truncate-->
+
+This is a test post.
+
+A whole bunch of other information.

docusaurus/blog/2019-05-29-hello-world.md

@@ -0,0 +1,13 @@
+---
+slug: welcome
+title: Welcome
+author: Yangshun Tay
+author_title: Front End Engineer @ Facebook
+author_url: https://github.com/yangshun
+author_image_url: https://avatars0.githubusercontent.com/u/1315101?s=400&v=4
+tags: [facebook, hello, docusaurus]
+---
+
+Blog features are powered by the blog plugin. Simply add files to the `blog` directory. It supports tags as well!
+
+Delete the whole directory if you don't want the blog features. As simple as that!

docusaurus/blog/2019-05-30-welcome.md

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+---
+id: bam-to-bed
+title: BAM to BED
+sidebar_label: bam-to-bed
+---
+
+Convert BAM file to BED file
+
+Usage:
+```bash
+java -jar ScriptManager.jar bam-format-converter bam-to-bed [-1 | -2 | -a | -m | -f]
+[-hpsV] [-n=<MIN_INSERT>] [-o=<output>] [-x=<MAX_INSERT>] <bamFile>
+```
+
+### Positional Input
+
+This tool takes a single BAM file for input. As with other tools, this tool requires the BAM file be indexed.
+
+### Output Options
+
+| Option | Description |
+| ------ | ----------- |
+| `-o, --output=<output>` | specify output directory (name will be same as original with .bed ext) |
+| `-s, --stdout` | stream output file to STDOUT (cannot be used with `-o` flag) |
+
+### Filter Options
+These filter options are shared across all the BAM Format Converter tools.
+
+| Option | Description |
+| ------ | ----------- |
+| `-p, --mate-pair` | require proper mate pair (default not required) |
+| `-n, --min-insert=<MIN_INSERT>` | filter by min insert size in bp |
+| `-x, --max-insert=<MAX_INSERT>` | filter by max insert size in bp |
+
+### Read Options
+
+| Option | Description |
+| ------ | ----------- |
+| `-1, --read1` | output read 1 (default) |
+| `-2, --read2` | output read 2 |
+| `-a, --all-reads` | output combined |
+| `-m, --midpoint` | output midpoint (require PE) |
+| `-f, --fragment` | output fragment (requires PE) |

docusaurus/docs/bam-format-converter/bam-to-bed.md

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+---
+id: bam-to-bedgraph
+title: BAM to bedGraph
+sidebar_label: bam-to-bedgraph
+---
+
+Convert BAM file to bedGraph file
+
+Usage:
+```bash
+java -jar ScriptManager.jar bam-format-converter bam-to-bedgraph [-1 | -2 | -a | -m]
+[-hpV] [-n=<MIN_INSERT>] [-o=<outputBasename>] [-x=<MAX_INSERT>]
+<bamFile>
+```
+
+### Positional Input
+
+This tool takes a single BAM file for input. As with other tools, this tool requires the BAM file be indexed.
+
+### Output Options
+
+| Option | Description |
+| ------ | ----------- |
+| `-o, --output=<outputBasename>` | specify output directory (name will be same as original with `_<strand>.bedgraph` ext) |
+| `-s, --stdout` | stream output file to STDOUT (cannot be used with `-o` flag) |
+
+### Filter Options
+These filter options are shared across all the BAM Format Converter tools.
+
+| Option | Description |
+| ------ | ----------- |
+| `-p, --mate-pair` | require proper mate pair (default not required) |
+| `-n, --min-insert=<MIN_INSERT>` | filter by min insert size in bp |
+| `-x, --max-insert=<MAX_INSERT>` | filter by max insert size in bp |
+
+### Read Options
+
+| Option | Description |
+| ------ | ----------- |
+| `-1, --read1` | output read 1 (default) |
+| `-2, --read2` | output read 2 |
+| `-a, --all-reads` | output combined |
+| `-m, --midpoint` | output midpoint (require PE) |