Answers.Body: <p>I cross-posted this question on the <a href="https://github.com/samtools/samtools/issues/994" rel="nofollow noreferrer">official samtools issue tracker</a>, and finally got a response.</p>
  
  <blockquote>
    <p>Looking at the code for the HTML view, I see <a href="https://github.com/samtools/samtools/blob/develop/bam_tview_html.c#L320" rel="nofollow noreferrer">this</a> and <a href="https://github.com/samtools/samtools/blob/develop/bam_tview_html.c#L348-L352" rel="nofollow noreferrer">this</a>.
    So maybe try</p>
    
    <p><code>COLUMNS=200 samtools tview -d H -p CHR:X-Y aln.bam ref.fasta</code></p>
  </blockquote>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-04-24T14:53:40.727Z
Answers.LastActivityDate: 2019-04-24T14:53:40.727Z
Answers.UserDisplayName: Daniel Standage
Answers.Body: <p>Partially a shameless plug. See if <a href="https://asciigenome.readthedocs.io/en/latest/description.html" rel="nofollow noreferrer">ASCIIGenome</a> can help you with that. </p>
  
  <p>To review a number of regions that you saved in, say, a bed file, you can either process them in <a href="https://asciigenome.readthedocs.io/en/latest/examples.html#batch-and-non-interactive-mode" rel="nofollow noreferrer">batch</a> or load BAM(s) and bed file and jump from one bed interval to the next using the <a href="https://asciigenome.readthedocs.io/en/latest/commandHelp.html#next" rel="nofollow noreferrer"><code>next -start</code></a> command.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2018-12-21T08:36:49.013Z
Answers.LastActivityDate: 2018-12-21T08:36:49.013Z
Answers.UserDisplayName: dariober
Body: <p>I have a large number of loci I would like to examine manually with <code>samtools tview</code>. Rather than typing or copy-n-pasting dozens of coordinates, I was hoping to automate the generation of pileup "images" (text files).</p>
  
  <p>With some experimenting just now, I was happy to learn that if I specify the display option <code>-d H</code> or <code>-d T</code> the output can easily be redirected to a file for later inspection. However, it appears that I cannot control the window captured. Changing the width of the terminal window doesn't change the output, nor does adjusting the <code>-p</code> flag (i.e. <code>-p chr1:501-700</code>). No matter what, <code>tview</code> always reports an 80bp window in text or HTML mode.</p>
  
  <p>Is there any way I can adjust this?</p>
  
Tags: <samtools><read-mapping><visualization>
Title: Control width of samtools tview "snapshot" when redirecting
ThreadText: # Control width of samtools tview "snapshot" when redirecting
  
  (Asked by: username_0 on 2018-12-20)
  
  I have a large number of loci I would like to examine manually with `samtools tview`. Rather than typing or copy-n-pasting dozens of coordinates, I was hoping to automate the generation of pileup "images" (text files).
  
  With some experimenting just now, I was happy to learn that if I specify the display option `-d H` or `-d T` the output can easily be redirected to a file for later inspection. However, it appears that I cannot control the window captured. Changing the width of the terminal window doesn't change the output, nor does adjusting the `-p` flag (i.e. `-p chr1:501-700`). No matter what, `tview` always reports an 80bp window in text or HTML mode.
  
  Is there any way I can adjust this?
  
  **Tags:** samtools, read-mapping, visualization
  
  
  ---
  
  ## 2 answers
  
  ### Answer by username_0 on 2019-04-24. Score: 1 | Accepted answer
  
  I cross-posted this question on the [official samtools issue tracker](https://github.com/samtools/samtools/issues/994), and finally got a response.
  
  > Looking at the code for the HTML view, I see [this](https://github.com/samtools/samtools/blob/develop/bam_tview_html.c#L320) and [this](https://github.com/samtools/samtools/blob/develop/bam_tview_html.c#L348-L352).
  > So maybe try
  >
  > `COLUMNS=200 samtools tview -d H -p CHR:X-Y aln.bam ref.fasta`
  
  
  ---
  
  ### Answer by username_1 on 2018-12-21. Score: 2
  
  Partially a shameless plug. See if [ASCIIGenome](https://asciigenome.readthedocs.io/en/latest/description.html) can help you with that.
  
  To review a number of regions that you saved in, say, a bed file, you can either process them in [batch](https://asciigenome.readthedocs.io/en/latest/examples.html#batch-and-non-interactive-mode) or load BAM(s) and bed file and jump from one bed interval to the next using the [`next -start`](https://asciigenome.readthedocs.io/en/latest/commandHelp.html#next) command.
  
  
  ---
  
  