---
title: 'Reads alignment stats'
output:
    html_document:
      number_sections: true
      toc: true
      theme: cosmo
      highlight: tango
---

```{r setup, include=FALSE, warning=FALSE, message=FALSE}
knitr::opts_chunk$set(
  echo = ECHO,
  error = TRUE
)
```


# Reads alignment stats on `r opt$input_bam_name`

```{r 'flagstat'}
command = paste0('samtools flagstat ', opt$input_bam, ' > ', paste0(opt$report_dir, '/report.txt'))
system(command)
df = readLines(paste0(opt$report_dir, '/report.txt')) %>%
  str_replace('(\\d+\\s+\\+\\s+\\d+)\\s+', '\\1,') %>% 
  str_split(',') %>% 
  as.data.frame() %>% t()
rownames(df) = NULL
colnames(df) = c('PASS + FAIL', 'Description')
knitr::kable(df)
```