Mercurial > repos > mingchen0919 > rmarkdown_samtools_flagstat
comparison rmarkdown_samtools_flagstat.Rmd @ 4:ec39bfeaf496 draft
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author | mingchen0919 |
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date | Wed, 27 Dec 2017 15:14:47 -0500 |
parents | a0f0effea707 |
children | 1c16536c70f5 |
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3:106ab5f33970 | 4:ec39bfeaf496 |
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1 --- | 1 --- |
2 title: 'HTML report title' | 2 title: 'Reads alignment stats' |
3 output: | 3 output: |
4 html_document: | 4 html_document: |
5 number_sections: true | 5 number_sections: true |
6 toc: true | 6 toc: true |
7 theme: cosmo | 7 theme: cosmo |
14 error = TRUE | 14 error = TRUE |
15 ) | 15 ) |
16 ``` | 16 ``` |
17 | 17 |
18 | 18 |
19 # Code for computational analysis | 19 # Reads alignment stats |
20 | 20 |
21 ```{r 'step 1'} | 21 ```{r 'flagstat'} |
22 command = paste0('samtools flagstat ', opt$input_bam, ' > report.csv') | 22 command = paste0('samtools flagstat ', opt$input_bam, ' > ', paste0(opt$report_dir, '/report.txt')) |
23 system(command) | 23 system(command) |
24 read.csv('report.csv') | 24 df = readLines(paste0(opt$report_dir, '/report.txt')) %>% |
25 str_replace('(\\d+\\s+\\+\\s+\\d+)\\s+', '\\1,') %>% | |
26 str_split(',') %>% | |
27 as.data.frame() %>% t() | |
28 rownames(df) = NULL | |
29 colnames(df) = c('PASS + FAIL', 'Description') | |
30 knitr::kable(df) | |
25 ``` | 31 ``` |
26 | 32 |
27 | |
28 |