feat: first version in the new repository

README.md

@@ -17,7 +17,7 @@ Install with the Conda or Mamba package manager after setting your [Bioconda cha
 ❯ conda install neodisambiguate
 ```
 
-#### Introduction
+### Introduction
 
 Disambiguation of aligned reads is performed per-template and all information across primary, secondary, and supplementary alignments is used as evidence.
 Alignment disambiguation is commonly required when analyzing sequencing data from transduction, transfection, transgenic, or xenographic (including patient derived xenograft) experiments.
@@ -31,21 +31,21 @@ Input BAMs of arbitrary sort order are accepted, however, an internal sort to qu
 All output BAM files will be written in the same sort order as the input BAM files.
 Although paired-end reads will give the most discriminatory power for disambiguation of short-read sequencing data, this tool accepts paired, single-end (fragment), and mixed pairing input data.
 
-#### Features
+### Features
 
 - Accepts SAM/BAM sources of any sort order
 - Will disambiguate an arbitrary number of BAMs, all aligned to different references
 - Writes the ambiguous alignments to a separate directory
 - Extensible implementation which supports alternative disambiguation strategies
 - Benchmarks show high accuracy: [Click Here](benchmarks/disambiguate.md)
 
-#### Command Line Usage
+### Command Line Usage
 
 ```bash
 ❯ neodisambiguate -i infile1.bam infile2.bam -p out/disambiguated
 ```
 
-#### Example Usage
+### Example Usage
 
 To disambiguate templates for sample `dna00001` that are aligned to human (A) and mouse (B):
 
@@ -67,7 +67,7 @@ To disambiguate templates for sample `dna00001` that are aligned to human (A) an
   └── dna00001.mm10.bam
 ```
 
-#### Local Installation
+### Local Installation
 
 Bootstrap compilation and build the executable with:
 
@@ -76,7 +76,7 @@ Bootstrap compilation and build the executable with:
 ./bin/neodisambiguate --help
 ```
 
-#### Prior Art
+### Prior Art
 
 This project was inspired by AstraZeneca's `disambiguate`:
 

benchmarks/disambiguate.md

@@ -15,7 +15,7 @@ As a preliminary test, we will attempt to disambiguate simulated paired-end read
 [mm10-reference]:   https://rgd.mcw.edu/rgdweb/report/gene/main.html?id=1332211
 [rn6-reference]:    https://rgd.mcw.edu/rgdweb/report/gene/main.html?id=1584969
 
-#### Dependencies
+### Dependencies
 
 - [`bwa`](https://bioconda.github.io/recipes/bwa/README.html)
 - [`dwgsim`](https://anaconda.org/bioconda/dwgsim)