update ghpages

Author: hiruna72

CODE_OF_CONDUCT.md

@@ -0,0 +1,128 @@
+# Contributor Covenant Code of Conduct
+
+## Our Pledge
+
+We as members, contributors, and leaders pledge to make participation in our
+community a harassment-free experience for everyone, regardless of age, body
+size, visible or invisible disability, ethnicity, sex characteristics, gender
+identity and expression, level of experience, education, socio-economic status,
+nationality, personal appearance, race, religion, or sexual identity
+and orientation.
+
+We pledge to act and interact in ways that contribute to an open, welcoming,
+diverse, inclusive, and healthy community.
+
+## Our Standards
+
+Examples of behavior that contributes to a positive environment for our
+community include:
+
+* Demonstrating empathy and kindness toward other people
+* Being respectful of differing opinions, viewpoints, and experiences
+* Giving and gracefully accepting constructive feedback
+* Accepting responsibility and apologizing to those affected by our mistakes,
+  and learning from the experience
+* Focusing on what is best not just for us as individuals, but for the
+  overall community
+
+Examples of unacceptable behavior include:
+
+* The use of sexualized language or imagery, and sexual attention or
+  advances of any kind
+* Trolling, insulting or derogatory comments, and personal or political attacks
+* Public or private harassment
+* Publishing others' private information, such as a physical or email
+  address, without their explicit permission
+* Other conduct which could reasonably be considered inappropriate in a
+  professional setting
+
+## Enforcement Responsibilities
+
+Community leaders are responsible for clarifying and enforcing our standards of
+acceptable behavior and will take appropriate and fair corrective action in
+response to any behavior that they deem inappropriate, threatening, offensive,
+or harmful.
+
+Community leaders have the right and responsibility to remove, edit, or reject
+comments, commits, code, wiki edits, issues, and other contributions that are
+not aligned to this Code of Conduct, and will communicate reasons for moderation
+decisions when appropriate.
+
+## Scope
+
+This Code of Conduct applies within all community spaces, and also applies when
+an individual is officially representing the community in public spaces.
+Examples of representing our community include using an official e-mail address,
+posting via an official social media account, or acting as an appointed
+representative at an online or offline event.
+
+## Enforcement
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be
+reported to the community leaders responsible for enforcement at
+.
+All complaints will be reviewed and investigated promptly and fairly.
+
+All community leaders are obligated to respect the privacy and security of the
+reporter of any incident.
+
+## Enforcement Guidelines
+
+Community leaders will follow these Community Impact Guidelines in determining
+the consequences for any action they deem in violation of this Code of Conduct:
+
+### 1. Correction
+
+**Community Impact**: Use of inappropriate language or other behavior deemed
+unprofessional or unwelcome in the community.
+
+**Consequence**: A private, written warning from community leaders, providing
+clarity around the nature of the violation and an explanation of why the
+behavior was inappropriate. A public apology may be requested.
+
+### 2. Warning
+
+**Community Impact**: A violation through a single incident or series
+of actions.
+
+**Consequence**: A warning with consequences for continued behavior. No
+interaction with the people involved, including unsolicited interaction with
+those enforcing the Code of Conduct, for a specified period of time. This
+includes avoiding interactions in community spaces as well as external channels
+like social media. Violating these terms may lead to a temporary or
+permanent ban.
+
+### 3. Temporary Ban
+
+**Community Impact**: A serious violation of community standards, including
+sustained inappropriate behavior.
+
+**Consequence**: A temporary ban from any sort of interaction or public
+communication with the community for a specified period of time. No public or
+private interaction with the people involved, including unsolicited interaction
+with those enforcing the Code of Conduct, is allowed during this period.
+Violating these terms may lead to a permanent ban.
+
+### 4. Permanent Ban
+
+**Community Impact**: Demonstrating a pattern of violation of community
+standards, including sustained inappropriate behavior,  harassment of an
+individual, or aggression toward or disparagement of classes of individuals.
+
+**Consequence**: A permanent ban from any sort of public interaction within
+the community.
+
+## Attribution
+
+This Code of Conduct is adapted from the [Contributor Covenant][homepage],
+version 2.0, available at
+https://www.contributor-covenant.org/version/2/0/code_of_conduct.html.
+
+Community Impact Guidelines were inspired by [Mozilla's code of conduct
+enforcement ladder](https://github.com/mozilla/diversity).
+
+[homepage]: https://www.contributor-covenant.org
+
+For answers to common questions about this code of conduct, see the FAQ at
+https://www.contributor-covenant.org/faq. Translations are available at
+https://www.contributor-covenant.org/translations.

README.md

@@ -5,21 +5,31 @@ signals (**squig**gles) + vis**ualiser** = **squigualiser**
 
 Google Chrome is the recommended web browser to visualise these plots.
 
+Watch [the video](https://youtu.be/kClYH4KpOjk) to learn a few tricks to get the best out of the plots.
+
 ![PyPI Downloads](https://img.shields.io/pypi/dm/squigualiser?label=pypi%20downloads)
 [![PyPI](https://img.shields.io/pypi/v/squigualiser.svg?style=flat)](https://pypi.python.org/pypi/squigualiser)
 [![Snake CI](https://github.com/hiruna72/squigualiser/actions/workflows/snake.yml/badge.svg)](https://github.com/hiruna72/squigualiser/actions/workflows/snake.yml)
+[![GitHub Downloads](https://img.shields.io/github/downloads/hiruna72/squigualiser/total?logo=GitHub)](https://github.com/hiruna72/squigualiser/releases)
+<!---
+[![BioConda Install](https://img.shields.io/conda/dn/bioconda/slow5tools.svg?style=flag&label=BioConda%20install)](https://anaconda.org/bioconda/slow5tools)
+-->
+
+Squigualiser preprint - https://www.biorxiv.org/content/10.1101/2024.02.19.581111v2
 
 ![image](docs/figures/different_aligments/method_eventalign.png)
-*Figure - A [pileup view](#pileup-view) of DNA R10.4.1 signals that align to the region `chr1:92,783,745-92,783,946`. Click the [link](https://hiruna72.github.io/squigualiser/docs/figures/different_aligments/dna_r10.4.1_e8.2_400bps_sup.cfg_evligned_vs_sim.html) to open it on your browser.* Go to Section [Examples](#examples) for more examples.
+* Figure - A [pileup view](#pileup-view) of DNA R10.4.1 signals that align to the region `chr1:92,783,745-92,783,946`.
+* Click the [link](https://hiruna72.github.io/squigualiser/docs/figures/different_aligments/dna_r10.4.1_e8.2_400bps_sup.cfg_evligned_vs_sim.html) to open it on your browser.
+* Go to Section [Examples](#examples) for more examples.
 
 # Table of Contents
 1. [Quickstart](#quickstart)
 2. [Advanced Setup](#advanced-setup)
-3. [Signal to read visualisation](#signal-to-read-visualisation)
+3. [Signal-to-read visualisation](#signal-to-read-visualisation)
    1. [Option 1 - Using f5c resquiggle](#option-1---f5c-resquiggle)
    2. [Option 2 - Using basecaller move table](#option-2---basecaller-move-table)
    3. [Option 3 - Using squigulator signal simulation](#option-3---squigulator-signal-simulation)
-5. [Signal to reference visualisation](#signal-to-reference-visualisation)
+5. [Signal-to-reference visualisation](#signal-to-reference-visualisation)
    1. [Option 1 - Using f5c eventalign](#option-1-f5c-eventalign)
    2. [Option 2 - Using basecaller move table](#option-2---basecaller-move-table-1)
    3. [Option 3 - Using squigulator signal simulation](#option-3---squigulator-signal-simulation-1)
@@ -173,13 +183,13 @@ SLOW5 files compressed with *zstd* offer smaller file size and better performanc
 </div>
 </details>
 
-## Signal to read visualisation
+## Signal-to-read visualisation
 
 This section explains how you can use squigualiser to visualise a raw signal alignment against its basecalled read. Click on the arrow to expand the revalent method.
 
 #### Option 1 - f5c resquiggle
 <details>
-<summary>Steps for using f5c resquiggle signal-read alignment</summary>
+<summary>Steps for using f5c resquiggle signal-to-read alignment</summary>
 <div markdown=1>
 
 1. Install f5c [v1.3 or higher](https://github.com/hasindu2008/f5c/releases) as explained in [f5c documentation](https://github.com/hasindu2008/f5c/#quick-start).
@@ -196,7 +206,7 @@ f5c resquiggle -c ${FASTQ} ${SIGNAL_FILE} -o ${ALIGNMENT}
 * Refer [Note(2)](#notes) for more information about `--kmer-model [KMER_MODEL]`, which is optional.
 * Refer [Note(3)](#notes) for more information about RNA.
 
-3. Plot signal to read alignment
+3. Plot signal-to-read alignment
 
 ````
 OUTPUT_DIR=output_dir
@@ -238,7 +248,7 @@ squigualiser reform --sig_move_offset 0 --kmer_length 1 -c --bam basecalls.sam -
 * Refer [Note(5)](#notes) for a description about `sig_move_offset`.
 * Refer [Note(6)](#notes) for handling a potential SAM/BAM error.
 
-3. Plot signal to read alignment
+3. Plot signal-to-read alignment
 
 ````
 FASTA_FILE=read.fasta
@@ -266,13 +276,13 @@ squigualiser plot --file ${FASTA_FILE} --slow5 ${SIGNAL_FILE} --alignment ${ALIG
 ````
 REF=ref.fasta          #reference
 READ=sim.fasta         #simulated reads
-ALIGNMENT=sim.paf      #contains signal-read alignment
+ALIGNMENT=sim.paf      #contains signal-to-read alignment
 SIGNAL_FILE=sim.blow5  #simultated raw signal data
 
 squigulator -x dna-r10-prom ${REF} -n 1 -o ${SIGNAL_FILE} -q ${READ} -c ${ALIGNMENT} # instead of dna-r10-prom, you can specify any other profile
 ````
 
-3. Plot signal to read alignment.
+3. Plot signal-to-read alignment.
 
 ````
 OUTPUT_DIR=output_dir
@@ -282,7 +292,7 @@ squigualiser plot -f ${READ} -s ${SIGNAL_FILE} -a ${ALIGNMENT} -o ${OUTPUT_DIR}
 </div>
 </details>
 
-## Signal to reference visualisation
+## Signal-to-reference visualisation
 
 This section explains how you can use squigualiser to visualise a raw signal alignment against a reference. Click on the arrow to expand the relevant method.
 
@@ -386,7 +396,7 @@ REALIGN_BAM=realign_output.bam
 squigualiser realign --bam ${MAPP_SAM} --paf ${REFORMAT_PAF} -o ${REALIGN_BAM}
 ````
 
-5. Plot signal to reference alignment
+5. Plot signal-to-reference alignment
 
 ````
 REGION=chr1:6811404-6811443
@@ -417,7 +427,7 @@ NUM_READS=50 #number of reads to simulate
 squigulator -x dna-r10-prom ${REF} -o ${SIGNAL_FILE} -a sim.sam -n ${NUM_READS} && samtools sort sim.sam -o ${ALIGNMENT} && samtools index ${ALIGNMENT}
 ```
 
-3. Plot signal to reference alignment.
+3. Plot signal-to-reference alignment.
 ````
 OUTPUT_DIR=output_dir
 REGION=chr1:6811404-6811443
@@ -460,10 +470,10 @@ tabix -0 -b 9 -e 8 -s 6 ${ALIGNMENT}
 ![image](docs/figures/pileup/pileup_plot.png)
 
 Similar to IGV pileup view now you can view the signal pileup view. To create a pileup view the following conditions should be met.
-1. The plot is a signal to reference visualisation, not a signal to read.
+1. The plot is a signal-to-reference visualisation, not a signal-to-read.
 2. A genomic region should be specified using the argument `--region`
 
-First, create an alignment file by following the steps mentioned in [Signal to reference visualisation](#signal-to-reference-visualisation)
+First, create an alignment file by following the steps mentioned in [Signal-to-reference visualisation](#signal-to-reference-visualisation)
 
 ````
 REGION=chr1:6811011-6811198
@@ -535,7 +545,7 @@ However, the user is adviced to use `--profile` (documented [here](docs/profiles
 For more information please refer [base_shift and eventalignment](docs/base_shift_and_eventalignment.md) and [base_shift and reverse mapped reads](docs/base_shift_of_reverse_mapped_reads.md).
 
 ### Signal scaling
-The commands `plot` and `plot_pileup` can take the argument `--sig_scale`. By providing the argument `--sig_scale znorm` or `--sig_scale medmad` the signals will be zscore or median MAD normalized respectively.
+The commands `plot` and `plot_pileup` can take the argument `--sig_scale`. Provide the argument `--sig_scale znorm` to zscore normalize, `--sig_scale medmad` to median MAD normalize, and `--sig_scale scaledpA` to scale the raw signal to the pore model.
 
 
 ## Plot Conventions
@@ -547,15 +557,15 @@ The commands `plot` and `plot_pileup` can take the argument `--sig_scale`. By pr
 
 
 ## Calculate alignment statistics
-Calculate basic statistics of read/reference - signal alignments.
+Calculate basic statistics of signal-to-read/reference alignments.
 Check [here](docs/commands.md/#metric) for the command.
 Check [here](docs/different_alignments.md) for an example.
 
 ## Notes
 
 1. If your FASTQ file is a multi-line file (not to confuse with multi-read), then install [seqtk](https://github.com/lh3/seqtk) and use `seqtk seq -l0 in.fastq > out.fastq`  to convert multi-line FASTQ to 4-line FASTQ.
 2. The optional argument `--kmer-model KMER_MODEL` can be used to specify a custom k-mer model if you wish.
-3. To plot RNA signal-read alignment use the alignment file created using `f5c resquiggle --rna -c ${FASTQ} ${SIGNAL_FILE} -o ${ALIGNMENT}`. Also, provide the argument `--rna` to the visualising command. Currently, there exists no RNA kmer model for r10.4.1 chemistry.
+3. To plot RNA signal-to-read alignment use the alignment file created using `f5c resquiggle --rna -c ${FASTQ} ${SIGNAL_FILE} -o ${ALIGNMENT}`. Also, provide the argument `--rna` to the visualising command. Currently, there exists no RNA kmer model for r10.4.1 chemistry.
 4. The input alignment format accepted by `squigualiser plot` is explained [here](https://hasindu2008.github.io/f5c/docs/output#resquiggle). This standard format made plotting a lot easier.
 5. The argument `sig_move_offset` is the number of moves `n` to skip in the signal to correct the start of the alignment. This will not skip bases in the fastq sequence. For example, to align the first move with the first kmer `--sig_move_offset 0` should be passed. To align from the second move onwards, `--sig_move_offset 1` should be used.
 6. Pysam does not allow reading SAM/BAM files without a `@SQ` line in the header. Hence, `squigualiser reform` script might error out with `NotImplementedError: can not iterate over samfile without header`. Add a fake `@SQ` header line with a zero length reference as follows,
@@ -571,12 +581,12 @@ Check [here](docs/different_alignments.md) for an example.
 
 ![image](docs/figures/preview.png)
 
-1. The first read is a signal-read alignment using guppy_v.6.3.7 move table annotation ([link](https://hiruna72.github.io/squigualiser/docs/figures/sig_to_read/testcase-1.1.html)).
-2. The second read is a signal-read alignment using f5c resquiggle output ([link](https://hiruna72.github.io/squigualiser/docs/figures/sig_to_read/testcase-2.1.html)).
-3. The third read is a signal-read alignment using the squigulator's simulated output ([link](https://hiruna72.github.io/squigualiser/docs/figures/sig_to_read/testcase-1.11.html)).
-4. The fourth read (RNA) is a signal-read alignment using f5c resquiggle output ([link](https://hiruna72.github.io/squigualiser/docs/figures/sig_to_read/testcase-3.2.html)).
+1. The first read is a signal-to-read alignment using guppy_v.6.3.7 move table annotation ([link](https://hiruna72.github.io/squigualiser/docs/figures/sig_to_read/testcase-1.1.html)).
+2. The second read is a signal-to-read alignment using f5c resquiggle output ([link](https://hiruna72.github.io/squigualiser/docs/figures/sig_to_read/testcase-2.1.html)).
+3. The third read is a signal-to-read alignment using the squigulator's simulated output ([link](https://hiruna72.github.io/squigualiser/docs/figures/sig_to_read/testcase-1.11.html)).
+4. The fourth read (RNA) is a signal-to-read alignment using f5c resquiggle output ([link](https://hiruna72.github.io/squigualiser/docs/figures/sig_to_read/testcase-3.2.html)).
 
-* [This](https://hiruna72.github.io/squigualiser/docs/figures/sig_to_reference/testcase-8.1.html) signal-reference alignment aligns a signal to the region `chr1:4270161-4271160`.
+* [This](https://hiruna72.github.io/squigualiser/docs/figures/sig_to_reference/testcase-8.1.html) signal-to-reference alignment aligns a signal to the region `chr1:4270161-4271160`.
 * [This](https://hiruna72.github.io/squigualiser/docs/figures/sig_to_reference/testcase-8.2.html) is the same plot with a fixed base width.
 
 These examples were generated using the testcases - `1.1, 2.1, 1.11,` and `3.2` respectively in [test_plot_signal_to_read.sh](test/test_plot_signal_to_read.sh).

docs/CONTRIBUTING.md

@@ -0,0 +1,51 @@
+# Contributing to squigualiser
+We love your input! We want to make contributing to this project as easy and transparent as possible, whether it's:
+
+- Reporting a bug
+- Discussing the current state of the code
+- Submitting a fix
+- Proposing new features
+- Becoming a maintainer
+
+## We Develop with Github
+We use github to host code, to track issues and feature requests, as well as accept pull requests.
+
+## We Use [Github Flow](https://guides.github.com/introduction/flow/index.html), So All Code Changes Happen Through Pull Requests
+Pull requests are the best way to propose changes to the codebase (we use [Github Flow](https://guides.github.com/introduction/flow/index.html)). We actively welcome your pull requests:
+
+1. Fork the repo and create your branch from `main`.
+2. If you've added code that should be tested, add tests.
+3. If you've changed APIs, update the documentation.
+4. Ensure the test suite passes.
+5. Make sure your code lints.
+6. Issue that pull request!
+
+## Any contributions you make will be under the MIT Software License
+In short, when you submit code changes, your submissions are understood to be under the same [MIT License](http://choosealicense.com/licenses/mit/) that covers the project. Feel free to contact the maintainers if that's a concern.
+
+## Report bugs using Github's [issues](https://github.com/hiruna72/squigualiser/issues)
+We use GitHub issues to track public bugs. Report a bug by [opening a new issue](); it's that easy!
+
+## Write bug reports with detail, background, and sample code
+Here's [an example from Craig Hockenberry](http://www.openradar.me/11905408).
+
+**Great Bug Reports** tend to have:
+
+- A quick summary and/or background
+- Steps to reproduce
+  - Be specific!
+  - Give sample code if you can. [this stackoverflow question](http://stackoverflow.com/q/12488905/180626) includes sample code that *anyone* with a base R setup can run to reproduce
+- What you expected would happen
+- What actually happens
+- Notes (possibly including why you think this might be happening, or stuff you tried that didn't work)
+
+People *love* thorough bug reports. I'm not even kidding.
+
+## Use a Consistent Coding Style
+Borrowing these from [Facebook's Guidelines](https://github.com/facebook/draft-js/blob/a9316a723f9e918afde44dea68b5f9f39b7d9b00/CONTRIBUTING.md)
+
+## License
+By contributing, you agree that your contributions will be licensed under its MIT License.
+
+## References
+This document was adapted from the open-source contribution guidelines for [Facebook's Draft](https://github.com/facebook/draft-js/blob/a9316a723f9e918afde44dea68b5f9f39b7d9b00/CONTRIBUTING.md) and [from here](https://gist.github.com/briandk/3d2e8b3ec8daf5a27a62)