comparison rmarkdown_samtools_flagstat.Rmd @ 4:ec39bfeaf496 draft

update

3:106ab5f33970

---
title: 'HTML report title'
output:
    html_document:
      number_sections: true
      toc: true
      theme: cosmo

  error = TRUE
)
```


# Code for computational analysis

```{r 'step 1'}
command = paste0('samtools flagstat ', opt$input_bam, ' > report.csv')
system(command)
read.csv('report.csv')
```

4:ec39bfeaf496

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

  error = TRUE
)
```


# Reads alignment stats

```{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)
```