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Merge pull request #89 from CEGRcode/ying-website
ScriptManager Homepage Merge major changes to homepage of docusaurus website to master so that they can be deployed. 1. add background image+user interface screen shot 2. change the logo and falvicon 3. change the nav bar github text link to icon link 4. add plotting sample 5. add icons and user interface screenshot to each tool 6. add tool index description and update Tool name links. NOTE: I didn't delete any original code. I just commented them
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‎docusaurus/docs/bam-format-converter/bam-to-bed.md‎

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sidebar_label: bam-to-bed
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---
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<!-- <img src={image} alt="" style={{width:70+'%'}}/> -->
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![bam-to-bed](/../static/icons/bam-format-converter/BAM-FormatConverter:BAMtoBED.svg)
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Convert BAM file to BED file
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<img src={require('/../static/md-img/BAMFormatConverter/BAM-FormatConverter_BAMtoBED.png').default} style={{width:70+'%'}}/>
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Usage:
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```bash
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java -jar ScriptManager.jar bam-format-converter bam-to-bed [-1 | -2 | -a | -m | -f]
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[-hpsV] [-n=<MIN_INSERT>] [-o=<output>] [-x=<MAX_INSERT>] <bamFile>
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### Output Options
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| Option | Description |
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| ------ | ----------- |
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| Option | Description |
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| ----------------------- | ---------------------------------------------------------------------- |
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| `-o, --output=<output>` | specify output directory (name will be same as original with .bed ext) |
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| `-s, --stdout` | stream output file to STDOUT (cannot be used with `-o` flag) |
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| `-s, --stdout` | stream output file to STDOUT (cannot be used with `-o` flag) |
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### Filter Options
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These filter options are shared across all the BAM Format Converter tools.
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| Option | Description |
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| ------ | ----------- |
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| `-p, --mate-pair` | require proper mate pair (default not required) |
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| `-n, --min-insert=<MIN_INSERT>` | filter by min insert size in bp |
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| `-x, --max-insert=<MAX_INSERT>` | filter by max insert size in bp |
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| Option | Description |
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| ------------------------------- | ----------------------------------------------- |
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| `-p, --mate-pair` | require proper mate pair (default not required) |
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| `-n, --min-insert=<MIN_INSERT>` | filter by min insert size in bp |
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| `-x, --max-insert=<MAX_INSERT>` | filter by max insert size in bp |
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### Read Options
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| Option | Description |
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| ------ | ----------- |
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| `-1, --read1` | output read 1 (default) |
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| `-2, --read2` | output read 2 |
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| `-a, --all-reads` | output combined |
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| `-m, --midpoint` | output midpoint (require PE) |
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| `-f, --fragment` | output fragment (requires PE) |
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| Option | Description |
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| ----------------- | ----------------------------- |
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| `-1, --read1` | output read 1 (default) |
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| `-2, --read2` | output read 2 |
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| `-a, --all-reads` | output combined |
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| `-m, --midpoint` | output midpoint (require PE) |
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| `-f, --fragment` | output fragment (requires PE) |

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

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title: BAM to bedGraph
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sidebar_label: bam-to-bedgraph
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---
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![bam-to-bedgraph](/../static/icons/bam-format-converter/BAM-format-converter:BAMtobedgraph.svg)
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Convert BAM file to bedGraph file
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<img src={require('/../static/md-img/BAMFormatConverter/BAM-format-converter:BAMtobedgraph.png').default} style={{width:70+'%'}}/>
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Usage:
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```bash
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java -jar ScriptManager.jar bam-format-converter bam-to-bedgraph [-1 | -2 | -a | -m]

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

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title: BAM to GFF
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sidebar_label: bam-to-gff
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---
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![bam-to-gff](/../static/icons/bam-format-converter/BAM-Format-Converter:BAMtoGFF.svg)
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Convert BAM file to GFF file
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<img src={require('/../static/md-img/BAMFormatConverter/BAM-Format-Converter_BAMtoGFF.png').default} style={{width:70+'%'}}/>
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Usage:
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```bash
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java -jar ScriptManager.jar bam-format-converter bam-to-gff [-1 | -2 | -a | -m | -f]

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

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title: BAM to scIDX
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sidebar_label: bam-to-scidx
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---
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![bam-to-scidx](/../static/icons/bam-format-converter/BAM-format-converter:BAMtoscIDX.svg)
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Convert BAM file to scIDX file
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<img src={require('/../static/md-img/BAMFormatConverter/BAM-format-converter:BAMtobedgraph.png').default} style={{width:70+'%'}}/>
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Usage:
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```bash
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java -jar ScriptManager.jar bam-format-converter bam-to-scidx [-1 | -2 | -a | -m]

‎docusaurus/docs/bam-manipulation/bam-indexer.md‎

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title: BAM Indexer
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sidebar_label: BAM Indexer
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---
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![bam-indexer](/../static/icons/bam-manipulation/BamManipulation:BAMIndexer.svg)
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For most tools using BAM inputs (both within and without ScriptManager), a BAM index file (`.bai`) file is required so that the tool can efficiently query the file for alignment records. _Read more in the [Picard documentation][picard-index]_.
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ScriptManager's [TagPileup][tag-pileup], [Merge BAM replicates][merge-bam], [BAM Correlation][bam-correlation], and BAM Format Converter tools ([bam-to-bed][bam-to-bed], [bam-to-gff][bam-to-gff], [bam-to-bedgraph][bam-to-bedgraph], and [bam-to-scidx][bam-to-scidx]) are some example tools that require a `.bai` file.
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![BAIIndexerWindow](/../static/md-img/BAIIndexerWindow.png)
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![BAIIndexerWindow](/../static/md-img/BAMManipulation/BAIIndexerWindow.png)
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After clicking "Index", ScriptManager will index all of the loaded index files and save them to the "Output Directory" location with the `.bai` extension. Output files follow convention in naming the `.bai` file. If you are indexing the file `sample123.bam`, then the index file will be called `sample123.bam.bai`.
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‎docusaurus/docs/bam-manipulation/filter-pip-seq.md‎

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sidebar_label: filter-pip-seq
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![filter-pip-seq](/../static/icons/bam-manipulation/FilterPIP-seq_square.svg)
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Usage:
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```bash
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java -jar ScriptManager.jar bam-manipulation filter-pip-seq [-hV] [-f=<filterString>]
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Filter BAM file by -1 nucleotide. Requires genome FASTA file. Note this program does not index the resulting BAM file and user must use appropriate samtools command to generate BAI.
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<img src={require('/../static/md-img/BAMManipulation/FilterPIPseq.png').default} style={{width:70+'%'}}/>
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### Output Options
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‎docusaurus/docs/bam-manipulation/merge-bam.md‎

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![merge-bam](/../static/icons/bam-manipulation/BAMReplicateMerge_square.svg)
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CommandLine tools already exist for this function. This tool only exists as a GUI wrapper in ScriptManager.
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Please see the [Samtools merge tool][samtools-merge] or the [Picard MergeBamAlignment tool][picard-merge].
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<img src={require('/../static/md-img/BAMManipulation/MergeBAM.png').default} style={{width:70+'%'}}/>
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[samtools-merge]:http://www.htslib.org/doc/samtools-merge.html
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[picard-merge]:https://broadinstitute.github.io/picard/command-line-overview.html#MergeBamAlignment

‎docusaurus/docs/bam-manipulation/remove-duplicates.md‎

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![remove-duplicates](/../static/icons/bam-manipulation/MarkDuplicates_square.svg)
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CommandLine tools already exist for this function. This tool only exists as a GUI wrapper in ScriptManager.
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Please see the [Samtools markdup tool][samtools-markdup] or the [Picard MarkDuplicates tool][picard-markdup].
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<img src={require('/../static/md-img/BAMManipulation/BamManipulation:remove-duplicaites.png').default} style={{width:70+'%'}}/>
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[samtools-markdup]:http://www.htslib.org/doc/samtools-markdup.html
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[picard-markdup]:https://broadinstitute.github.io/picard/command-line-overview.html#MarkDuplicates

‎docusaurus/docs/bam-manipulation/sort-bam.md‎

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title: Sort BAM
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![sort-bam](/../static/icons/bam-manipulation/BamManipulation:SortBAM.svg)
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![sort-bam](/../static/md-img/BAMManipulation/BamManipulation_SortBAM.png)
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CommandLine tools already exist for this function. This tool only exists as a GUI wrapper in ScriptManager.
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‎docusaurus/docs/bam-statistics/bam-correlation.md‎

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![bam-correlation](/../static/icons/BAMStatistics/BAMCorrelation_square.svg)
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_Output BAM Header including alignment statistics and parameters given any indexed (BAI) BAM File._
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<img src={require('/../static/md-img/BAMStatistics/BAMCorrelation.png').default} style={{width:70+'%'}}/>
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## Command Line (bam-correlation)
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Compare a list of BAM files to get a matrix of correlations between them. Outputs both a text file of matrix correlation scores and a heatmap PNG.

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