### Install Minimap2 and Download Data

Source: https://github.com/ablab/quast/blob/master/quast_libs/minimap2/cookbook.md

Installs minimap2 executables and downloads example datasets for the cookbook. Ensure the current directory is added to the PATH.

```sh
# install minimap2 executables
curl -L https://github.com/lh3/minimap2/releases/download/v2.28/minimap2-2.28_x64-linux.tar.bz2 | tar jxf -
cp minimap2-2.28_x64-linux/{minimap2,k8,paftools.js} .
export PATH="$PATH:`pwd`" # put the current directory on PATH
# download example datasets
curl -L https://github.com/lh3/minimap2/releases/download/v2.10/cookbook-data.tgz | tar zxf -
```

--------------------------------

### Install Mappy from source

Source: https://github.com/ablab/quast/blob/master/quast_libs/minimap2/python/README.rst

Install mappy from the minimap2 GitHub repository. Requires Cython. This method involves cloning the repository and running the setup script.

```shell
git clone https://github.com/lh3/minimap2
cd minimap2
python setup.py install
```

--------------------------------

### Install and Basic Mapping with Minimap2

Source: https://github.com/ablab/quast/blob/master/quast_libs/minimap2/README.md

Clone the repository, build minimap2, and perform a basic alignment. This example shows mapping long sequences against a reference genome.

```sh
git clone https://github.com/lh3/minimap2
cd minimap2 && make
# long sequences against a reference genome
./minimap2 -a test/MT-human.fa test/MT-orang.fa > test.sam
```

--------------------------------

### Install QUAST (Basic)

Source: https://github.com/ablab/quast/blob/master/README.md

Installs the basic QUAST package. This is the recommended method for most users.

```bash
./setup.py install
```

--------------------------------

### Flot Example: Real-time Line Chart

Source: https://github.com/ablab/quast/blob/master/quast_libs/html_saver/static/flot/NEWS.txt

A new example demonstrating a real-time line chart.

```javascript
real-time line chart example
```

--------------------------------

### Install Barrnap

Source: https://github.com/ablab/quast/blob/master/quast_libs/barrnap/README.md

Steps to install Barrnap from a tarball and add its binary directory to the PATH.

```bash
cd $HOME
tar zxvf barrnap-0.X.tar.gz
echo "PATH=$PATH:$HOME/barrnap-0.x/bin" >> .bashrc
(logout and log back in)
```

--------------------------------

### Install zlib on Ubuntu

Source: https://github.com/ablab/quast/blob/master/manual.html

Installs the zlib development files required by QUAST on Ubuntu systems.

```bash
sudo apt-get install zlib1g-dev
```

--------------------------------

### Install QUAST (Full)

Source: https://github.com/ablab/quast/blob/master/README.md

Installs the full QUAST package, including tools for SV detection and reference genome detection in metagenomic datasets.

```bash
./setup.py install_full
```

--------------------------------

### Install Mappy using pip

Source: https://github.com/ablab/quast/blob/master/quast_libs/minimap2/python/README.rst

Install the mappy library using pip. This is the recommended method for most users.

```shell
pip install --user mappy
```

--------------------------------

### Install QUAST via pip

Source: https://github.com/ablab/quast/blob/master/manual.html

Installs the QUAST package using pip, the Python package installer.

```bash
pip install quast
```

--------------------------------

### Install Minimap2 from Release

Source: https://github.com/ablab/quast/blob/master/quast_libs/minimap2/README.md

Download and extract precompiled Minimap2 binaries for Linux x86-64. Ensure you have curl and tar installed.

```shell
curl -L https://github.com/lh3/minimap2/releases/download/v2.28/minimap2-2.28_x64-linux.tar.bz2 | tar -jxvf -
./minimap2-2.28_x64-linux/minimap2
```

--------------------------------

### Install QUAST via Homebrew

Source: https://github.com/ablab/quast/blob/master/manual.html

Installs the QUAST package using Homebrew, a package manager for macOS.

```bash
brew install quast
```

--------------------------------

### Complete Data Specification Example

Source: https://github.com/ablab/quast/blob/master/quast_libs/html_saver/static/flot/API.txt

An example showing an array of series objects, each with a label and associated data points. This format is used for plotting multiple series.

```javascript
[ { label: "Foo", data: [ [10, 1], [17, -14], [30, 5] ] },
  { label: "Bar", data: [ [11, 13], [19, 11], [30, -7] ] } ]
```

--------------------------------

### Install and Basic Usage of BWA

Source: https://github.com/ablab/quast/blob/master/quast_libs/bwa/README.md

Steps to clone the BWA repository, compile it, index a reference genome, and perform alignments for single-end and paired-end reads.

```bash
git clone https://github.com/lh3/bwa.git
cd bwa; make
./bwa index ref.fa
./bwa mem ref.fa read-se.fq.gz | gzip -3 > aln-se.sam.gz
./bwa mem ref.fa read1.fq read2.fq | gzip -3 > aln-pe.sam.gz
```

--------------------------------

### Install minimap2 and k8 Javascript shell

Source: https://github.com/ablab/quast/blob/master/quast_libs/minimap2/misc/README.md

Installs minimap2 via git clone and make, and downloads the k8 Javascript shell. Ensure k8 is on your PATH for paftools.js execution.

```sh
# install minimap2
git clone https://github.com/lh3/minimap2
cd minimap2 && make
# install the k8 javascript shell
curl -L https://github.com/attractivechaos/k8/releases/download/v0.2.4/k8-0.2.4.tar.bz2 | tar -jxf -
cp k8-0.2.4/k8-`uname -s` k8              # or copy it to a directory on your $PATH
# export PATH="$PATH:`pwd`:`pwd`/misc"    # run this if k8, minimap2 or paftools.js not on your $PATH
```

--------------------------------

### Plugin Usage Example

Source: https://github.com/ablab/quast/blob/master/quast_libs/html_saver/static/flot/PLUGINS.txt

Illustrates how to include and use the 'simpledebug' plugin in an HTML page with specific options.

```javascript
$.plot($("#placeholder"), [...], { debug: 2 });
```

--------------------------------

### Download and Setup Bwakit, Generate Reference, and Map Reads

Source: https://github.com/ablab/quast/blob/master/quast_libs/bwa/bwakit/README.md

This snippet demonstrates the complete workflow: downloading Bwakit, generating a human reference genome with ALT and HLA information, creating a BWA index, and performing read mapping using `run-bwamem`. The mapping command is piped to `sh` for execution.

```bash
# Download the bwa-0.7.11 binary package (download link may change)
wget -O- http://sourceforge.net/projects/bio-bwa/files/bwakit/bwakit-0.7.12_x64-linux.tar.bz2/download \
  | gzip -dc | tar xf -
# Generate the GRCh38+ALT+decoy+HLA and create the BWA index
bwa.kit/run-gen-ref hs38DH   # download GRCh38 and write hs38DH.fa
bwa.kit/bwa index hs38DH.fa  # create BWA index
# mapping
bwa.kit/run-bwamem -o out -H hs38DH.fa read1.fq read2.fq | sh
```

--------------------------------

### Install QUAST via Bioconda

Source: https://github.com/ablab/quast/blob/master/manual.html

Installs the QUAST package using Bioconda, a channel for bioinformatics software on Conda.

```bash
conda install -c bioconda quast
```

--------------------------------

### Basic Mappy Usage Example

Source: https://github.com/ablab/quast/blob/master/quast_libs/minimap2/python/README.rst

Demonstrates key mappy functionalities: loading an index, retrieving a subsequence, computing its reverse complement, and aligning sequences from a FASTA/FASTQ file.

```python
import mappy as mp
a = mp.Aligner("test/MT-human.fa")  # load or build index
if not a: raise Exception("ERROR: failed to load/build index")
s = a.seq("MT_human", 100, 200)     # retrieve a subsequence from the index
print(mp.revcomp(s))                # reverse complement
for name, seq, qual in mp.fastx_read("test/MT-orang.fa"): # read a fasta/q sequence
		for hit in a.map(seq): # traverse alignments
			print("{}\t{}\t{}\t{}".format(hit.ctg, hit.r_st, hit.r_en, hit.cigar_str))
```

--------------------------------

### Install Matplotlib on Ubuntu

Source: https://github.com/ablab/quast/blob/master/manual.html

Installs the Matplotlib Python library and its dependencies on Ubuntu systems, required for generating PDF plots.

```bash
sudo apt-get install -y pkg-config libfreetype6-dev libpng-dev python-matplotlib
```

--------------------------------

### Complete Debug Plugin Example

Source: https://github.com/ablab/quast/blob/master/quast_libs/html_saver/static/flot/PLUGINS.txt

A comprehensive example of a debug plugin that alerts series information. It utilizes options to control debug level and hooks into 'processDatapoints' and 'processOptions'.

```javascript
(function ($) {
    function init(plot) {
      var debugLevel = 1;
    
      function checkDebugEnabled(plot, options) {
        if (options.debug) {
          debugLevel = options.debug;
            
          plot.hooks.processDatapoints.push(alertSeries);
        }
      }

      function alertSeries(plot, series, datapoints) {
        var msg = "series " + series.label;
        if (debugLevel > 1)
          msg += " with " + series.data.length + " points";
        alert(msg);
      }
    
      plot.hooks.processOptions.push(checkDebugEnabled);
    }

    var options = { debug: 0 };
    
    $.plot.plugins.push({
        init: init,
        options: options,
        name: "simpledebug",
        version: "0.1"
    });
  })(jQuery);
```

--------------------------------

### Example Contig with Multiple Misassemblies

Source: https://github.com/ablab/quast/blob/master/manual.html

This example illustrates a contig with multiple extensive misassemblies, specifically relocations, and also a local misassembly. It provides details on the contig, its length, and the types and counts of misassemblies.

```text
CONTIG: **Contig_753 (140518bp)** Top Length: 121089  Top ID: 99.98     Skipping redundant alignments after choosing the best set of alignments     Skipping redundant alignment 273398 273468 | 18977 18907 | 71 71 | 100.0 | Escherichia_coli Contig_753     _...._     Skipping redundant alignment 3363797 3363867 | 18977 18907 | 71 71 | 100.0 | Escherichia_coli Contig_753     This contig is misassembled. 14 total aligns.         Real Alignment 1: 1425621 1426074 | 19431 18978 | 454 454 | 100.0 | Escherichia_coli Contig_753             _Gap between these two alignments (local misassembly)_. Inconsistency = 148         Real Alignment 2: 1426295 1426818 | 18905 18382 | 524 524 | 100.0 | Escherichia_coli Contig_753             **Extensive misassembly ( relocation, inconsistency = 2224055 )** between these two alignments         Real Alignment 3: 3650278 3650348 | 18977 18907 | 71 71 | 100.0 | Escherichia_coli Contig_753             **Extensive misassembly ( relocation, inconsistency = 236807 )** between these two alignments         Real Alignment 4: 3765544 3886652 | 140518 19430 | 121109 121089 | 99.98 | Escherichia_coli Contig_753             **Extensive misassembly ( relocation, inconsistency = -1052 )** between these two alignments         Real Alignment 5: 3886649 3905037 | 18381 1 | 18389 18381 | 99.96 | Escherichia_coli Contig_753
```

--------------------------------

### Install k8 Javascript shell

Source: https://github.com/ablab/quast/blob/master/quast_libs/minimap2/misc/README.md

Downloads and installs the k8 Javascript shell, a prerequisite for running paftools.js scripts. It is recommended to place the executable in a directory included in your system's PATH.

```sh
curl -L https://github.com/attractivechaos/k8/releases/download/v0.2.4/k8-0.2.4.tar.bz2 | tar -jxf -
cp k8-0.2.4/k8-`uname -s` $HOME/bin/k8  # assuming $HOME/bin in your $PATH
```

--------------------------------

### Basic QUAST Usage Example

Source: https://github.com/ablab/quast/blob/master/README.md

A typical command-line usage of QUAST to evaluate assemblies. It specifies input contigs, a reference genome, gene information, paired-end reads, and an output directory.

```bash
./quast.py test_data/contigs_1.fasta \
               test_data/contigs_2.fasta \
            -r test_data/reference.fasta.gz \
            -g test_data/genes.txt \
            -1 test_data/reads1.fastq.gz -2 test_data/reads2.fastq.gz \
            -o quast_test_output
```

--------------------------------

### Basic Flot Plotting Example

Source: https://github.com/ablab/quast/blob/master/quast_libs/html_saver/static/flot/README.txt

Demonstrates a basic Flot plot with a line from (0,0) to (1,1). Ensure the placeholder div has defined width and height and is not hidden.

```javascript
$.plot($("#placeholder"), [ [[0, 0], [1, 1]] ], { yaxis: { max: 1 } });
```

--------------------------------

### MetaQUAST References List Example

Source: https://github.com/ablab/quast/blob/master/manual.html

A sample file for the --references-list option in MetaQUAST. Each line contains a reference genome name to be searched in the NCBI database.

```text
Lactobacillus_plantarum
Lactobacillus  reuteri DSM 20016
Lactobacillus_psittaci
Harry Potter
```

--------------------------------

### Data Transformation with processDatapoints Hook

Source: https://github.com/ablab/quast/blob/master/quast_libs/html_saver/static/flot/API.txt

Example of the processDatapoints hook for transforming data after normalization but before min/max calculation. This example multiplies all y-coordinates by 2.

```javascript
function multiply(plot, series, datapoints) {
    var points = datapoints.points, ps = datapoints.pointsize;
    for (var i = 0; i < points.length; i += ps)
        points[i + 1] *= 2;
}
```

--------------------------------

### Define and Install a Draw Hook

Source: https://github.com/ablab/quast/blob/master/quast_libs/html_saver/static/flot/API.txt

Install a custom callback function to execute during the drawing phase. Hooks allow for modification of the plotting process by accessing internal data structures.

```javascript
function hellohook(plot, canvascontext) { alert("hello!"); };
var plot = $.plot(placeholder, data, { hooks: { draw: [hellohook] } });
```

--------------------------------

### Get basic alignment statistics

Source: https://github.com/ablab/quast/blob/master/quast_libs/minimap2/misc/README.md

Calculates basic alignment statistics using minimap2 and paftools.js stat.

```sh
minimap2 -c test/MT-human.fa test/MT-orang.fa | paftools.js stat -       # basic alignment statistics
```

--------------------------------

### Download and Extract QUAST Tarball

Source: https://github.com/ablab/quast/blob/master/manual.html

Downloads the QUAST source code tarball and extracts it, preparing for installation or in-place use.

```bash
wget https://github.com/ablab/quast/releases/download/quast_5.3.0/quast-5.3.0.tar.gz
tar -xzf quast-5.3.0.tar.gz
cd quast-5.3.0
```

--------------------------------

### Assemble Reads with Miniasm

Source: https://github.com/ablab/quast/blob/master/quast_libs/minimap2/cookbook.md

If miniasm is installed, it can be used with the generated overlap PAF file to create an assembly graph in GFA format.

```bash
miniasm -f ecoli_p6_25x_canu.fa overlap.paf > asm.gfa
```

--------------------------------

### Configuring Multiple Axes

Source: https://github.com/ablab/quast/blob/master/quast_libs/html_saver/static/flot/API.txt

Configure multiple x and y axes using the 'xaxes' and 'yaxes' arrays in the options. This example sets up a top x-axis and a right-positioned y-axis with a minimum value.

```javascript
{
    xaxes: [ { position: "top" } ],
    yaxes: [ { }, { position: "right", min: 20 } ]
  }
```

--------------------------------

### Specify Series Gradient with Opacity and Brightness

Source: https://github.com/ablab/quast/blob/master/quast_libs/html_saver/static/flot/API.txt

Specify a gradient for series colors, controlling opacity and brightness. This example shows bars gradually disappearing.

```javascript
bars: {
      show: true,
      lineWidth: 0,
      fill: true,
      fillColor: { colors: [ { opacity: 0.8 }, { opacity: 0.1 } ] }
  }
```

--------------------------------

### Example SNP Information Line

Source: https://github.com/ablab/quast/blob/master/manual.html

This line represents the format of the .used_snps file, detailing reference genome name, contig name, position, reference nucleotide, contig nucleotide ('.' for deletion), and position on the contig.

```text
Escherichia_coli	contig_15	728803	C	.	3217983
```

--------------------------------

### Real Alignment Format Explanation

Source: https://github.com/ablab/quast/blob/master/manual.html

This example details the structure of a 'Real Alignment' entry in QUAST contigs reports. It breaks down the meaning of each field, including positions, aligned bases, and alignment quality (IDY%).

```text
Real Alignment 1: 19796 20513 | 29511 30228 | 718 718 | 100.0 | ENA|U00096|U00096.2_Escherichia_coli contig-710
```

--------------------------------

### BEDPE Format Example for Translocation

Source: https://github.com/ablab/quast/blob/master/manual.html

An example of a BEDPE file line for a translocation. It specifies different chromosomes for the start and end of the variation, automatically identifying it as a translocation.

```text
chr1	450	550	chr2	100	100	name_does_not_matter_here
```

--------------------------------

### BEDPE Format Example for Deletion

Source: https://github.com/ablab/quast/blob/master/manual.html

An example of a BEDPE file line for a deletion. It includes chromosome, start and end positions for both ends, and 'DEL' in the name to indicate a deletion.

```text
S.aureus	995	1010	S.aureus	1195	1205	DEL
```

--------------------------------

### BEDPE Format Example for Inversion

Source: https://github.com/ablab/quast/blob/master/manual.html

An example of a BEDPE file line for an inversion. It specifies the chromosome, start and end positions for both ends of the variation, and a name containing 'INV'.

```text
E.coli	995	1010	E.coli	1195	1205	This_is_INVersion	The	Rest	Columns	Are	Optional
```

--------------------------------

### Get JavaScript Timestamp

Source: https://github.com/ablab/quast/blob/master/quast_libs/html_saver/static/flot/API.txt

Demonstrates how to get the current JavaScript timestamp in milliseconds.

```javascript
alert((new Date()).getTime())
```

--------------------------------

### Download and Index GRCh38 with ALT Contigs

Source: https://github.com/ablab/quast/blob/master/quast_libs/bwa/README-alt.md

Download BWA-KIT, generate the GRCh38+ALT+decoy+HLA reference, and create the BWA index. This is a prerequisite for mapping reads against the ALT-aware reference.

```sh
# Download bwakit (or from <http://sourceforge.net/projects/bio-bwa/files/bwakit/> manually)
wget -O- http://sourceforge.net/projects/bio-bwa/files/bwakit/bwakit-0.7.12_x64-linux.tar.bz2/download \
  | gzip -dc | tar xf -
# Generate the GRCh38+ALT+decoy+HLA and create the BWA index
bwa.kit/run-gen-ref hs38DH   # download GRCh38 and write hs38DH.fa
bwa.kit/bwa index hs38DH.fa  # create BWA index
# mapping
bwa.kit/run-bwamem -o out -H hs38DH.fa read1.fq read2.fq | sh  # skip "|sh" to show command lines
```

--------------------------------

### Get Plotting Area Dimensions

Source: https://github.com/ablab/quast/blob/master/quast_libs/html_saver/static/flot/API.txt

Get the width and height of the plotting area inside the grid, excluding space for labels.

```javascript
width()
```

```javascript
height()
```

--------------------------------

### Compile Minimap2 from Source

Source: https://github.com/ablab/quast/blob/master/quast_libs/minimap2/README.md

Compile Minimap2 from source. Requires a C compiler, GNU make, and zlib development files. Use `make sse2only=1` to disable SSE4 if compilation fails.

```shell
make
```

```shell
make sse2only=1
```

--------------------------------

### Example Misassembled Contig Report

Source: https://github.com/ablab/quast/blob/master/manual.html

This example shows a contig identified as having an extensive misassembly (inversion). It details the contig name, length, number of alignments, and the type of misassembly.

```text
CONTIG: **NODE_772 (575bp)** Top Length: 296  Top ID: 100.0     Skipping redundant alignment 1096745 1096882 | 138 1 | 138 138 | 98.55 | Escherichia_coli NODE_772     This contig is misassembled. 3 total aligns.         Real Alignment 1: 924846 925134 | 287 575 | 289 289 | 100.0 | Escherichia_coli NODE_772             **Extensive misassembly ( inversion )** between these two alignments         Real Alignment 2: 924906 925201 | 296 1 | 296 296 | 100.0 | Escherichia_coli NODE_772
```

--------------------------------

### Minimap2 Algorithm Overview: Seeding and Chaining

Source: https://github.com/ablab/quast/blob/master/quast_libs/minimap2/README.md

Steps 3 and 4 describe finding seeds by checking query minimizers against the reference index and then sorting and chaining these seeds by reference position.

```bash
minimap2 -f [=*2e-4*] -K [=*200M*]
```

--------------------------------

### Accessing Minimap2 Manual

Source: https://github.com/ablab/quast/blob/master/quast_libs/minimap2/README.md

View the detailed manual page for minimap2 to understand all command-line options and parameters.

```sh
man ./minimap2.1
```

--------------------------------

### Series-Specific Options Configuration

Source: https://github.com/ablab/quast/blob/master/quast_libs/html_saver/static/flot/PLUGINS.txt

Demonstrates how to define options that are specific to each series within the main options object, using the 'series' key.

```javascript
var options = {
    series: {
      downsample: {
        algorithm: null,
        maxpoints: 1000
      }
    }
  }
```

--------------------------------

### Run QUAST with Custom Metrics

Source: https://github.com/ablab/quast/blob/master/docs_for_devs/how_to_add_a_metric.md

Execute QUAST with your input files to generate a report that includes your newly added metric. Check the `report.txt` file within the generated `quast_results` folder to verify.

```bash
./quast.py test_data/contigs_1.fasta \
               test_data/contigs_2.fasta \
               -r test_data/reference.fasta.gz \
               -g test_data/genes.gff
```

--------------------------------

### Minimap2 Algorithm Overview: Indexing

Source: https://github.com/ablab/quast/blob/master/quast_libs/minimap2/README.md

Step 1 of the Minimap2 algorithm involves reading reference bases, extracting minimizers using -k and -w options, and indexing them in a hash table.

```bash
minimap2 -I [=*4G*] -k [=*21*] -w [=*21*] reference.fasta
```

--------------------------------

### Python Timestamp Generation

Source: https://github.com/ablab/quast/blob/master/quast_libs/html_saver/static/flot/API.txt

Example of generating a JavaScript timestamp in Python for a specific date.

```python
'calendar.timegm(datetime_object.timetuple()) * 1000'
```

--------------------------------

### PHP Timestamp Generation

Source: https://github.com/ablab/quast/blob/master/quast_libs/html_saver/static/flot/API.txt

Example of generating a JavaScript timestamp in PHP for a specific date.

```php
'strtotime("2002-02-20 UTC") * 1000'
```

--------------------------------

### Compile Minimap2 with SIMDe

Source: https://github.com/ablab/quast/blob/master/quast_libs/minimap2/README.md

Compile Minimap2 using the SIMDe library for cross-platform SIMD support. Use `Makefile.simde`.

```shell
make -f Makefile.simde
```

--------------------------------

### Execute paftools.js script

Source: https://github.com/ablab/quast/blob/master/quast_libs/minimap2/misc/README.md

Demonstrates two methods for executing paftools.js scripts: directly if k8 is in the PATH, or by invoking k8 with the script path.

```sh
path/to/paftools.js             # only if k8 is on your $PATH
k8 path/to/paftools.js
```

--------------------------------

### View Alignment in BLAST-like Format

Source: https://github.com/ablab/quast/blob/master/quast_libs/minimap2/cookbook.md

Display alignment results in a human-readable, BLAST-like format using `paftools.js view`. Requires `--cs` option and minimap2-r741 or higher for `asm20` preset.

```bash
# option "--cs" required; minimap2-r741 or higher required for the "asm20" preset
minimap2 -cx asm20 --cs ecoli_ref.fa ecoli_O104:H4.fa | paftools.js view - | less -S
```

--------------------------------

### Basic Plugin Structure

Source: https://github.com/ablab/quast/blob/master/quast_libs/html_saver/static/flot/PLUGINS.txt

Demonstrates the fundamental structure for creating a Flot plugin by defining an init function and adding it to the $.plot.plugins array.

```javascript
function myCoolPluginInit(plot) {
    plot.coolstring = "Hello!";
  };

  $.plot.plugins.push({ init: myCoolPluginInit, options: { ... } });
```

--------------------------------

### getPlotOffset()

Source: https://github.com/ablab/quast/blob/master/quast_libs/html_saver/static/flot/API.txt

Gets the offset of the grid within the canvas. Returns an object with distances from the canvas edges (left, right, top, bottom).

```APIDOC
## getPlotOffset()

### Description
Gets the offset of the grid within the canvas. Returns an object with distances from the canvas edges (left, right, top, bottom).

### Returns
- Object: An object with `left`, `right`, `top`, and `bottom` properties representing the grid offset.
```

--------------------------------

### Access Axis Information

Source: https://github.com/ablab/quast/blob/master/quast_libs/html_saver/static/flot/API.txt

Get an object containing all axes. Useful for accessing tick information or transformation functions (p2c, c2p).

```javascript
var axes = getAxes();
var ticks = axes.xaxis.ticks;
var canvasX = axes.xaxis.p2c(dataX);
```

--------------------------------

### BamAlignment Construction and Utility

Source: https://github.com/ablab/quast/blob/master/quast_libs/bedtools/src/bedpeToBam/notes.txt

Includes constructor, destructor, and utility functions for building alignment string data and calculating end positions.

```APIDOC
## BamAlignment Construction and Utility Functions

### Description
Provides constructors, a destructor, and utility methods for the BamAlignment class.

### Methods
- `BamAlignment()`: Default constructor.
- `BamAlignment(const BamAlignment &other)`: Copy constructor.
- `~BamAlignment()`: Destructor.
- `bool BuildCharData()`: Populates alignment string fields (read name, bases, qualities, tag data).
- `int GetEndPosition(bool usePadded=false, bool zeroBased=true) const`: Calculates alignment end position, based on starting position and CIGAR data.
```

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### Get Plotting Area Offset

Source: https://github.com/ablab/quast/blob/master/quast_libs/html_saver/static/flot/API.txt

Returns the offset of the plotting area within the grid relative to the document. Useful for calculating mouse positions.

```javascript
offset()
```

--------------------------------

### Get Drawing Canvas

Source: https://github.com/ablab/quast/blob/master/quast_libs/html_saver/static/flot/API.txt

Obtain the canvas element used for drawing. This is useful for advanced customization or direct manipulation of the plot's rendering surface.

```javascript
var canvas = plot.getCanvas();
```