humburg

---
title: "Main Document"
author: "Author Name"
date: "`r format(Sys.time(), '%a %d %b %Y')`"
output:
  reportMD::multi_document:
    toc: true
    fig_caption: true
    highlight: atom-one-dark
    use_namespace: true

humburg

---
title: "Test file"
author: Tester
output:
  knitrBootstrap::bootstrap_document:
    toc: true
    theme: amelia
    highlight: sunburst
---

humburg

import pysam
import tempfile

header = { 'HD': {'VN': '1.0'},
            'SQ': [{'LN': 1575, 'SN': 'chr1'},
                   {'LN': 1584, 'SN': 'chr2'}] }

tmp_file = tempfile.NamedTemporaryFile()
outfile = pysam.AlignmentFile(tmp_file.name, "wh", header=header)
a = pysam.AlignedSegment()

humburg

---
title: Caption test 
output:
  knitrBootstrap::bootstrap_document:
    fig_caption: true
    keep_md: true
  rmarkdown::html_document:
    fig_caption: true
    keep_md: true
    self_contained: false