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how_to [2022/08/04 11:52] – [Add only modified changes and ignore untracked files using git?] javadhow_to [2022/08/10 02:20] – [Run simultaneous jobs (on multiple files) in a single mpi on a cluster?] mohsen
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 This is a collection of short answers and links to some miscellaneous questions that we have had while doing research in Oncinfo. This can also be a useful resource for other scholars in the field of computational biology with similar interests and challenges. This is a collection of short answers and links to some miscellaneous questions that we have had while doing research in Oncinfo. This can also be a useful resource for other scholars in the field of computational biology with similar interests and challenges.
 +
 +----
 +
 +==== Extend   bam  reads to a fixed fragment size to better view peaks with   igv   ====
 +
 +Assume you have ''input.bam'' which contains mapped short single-end sequence reads, but you know the fragment size=''100''. With the following command, you can make a bam file that have the extended reads, but you will miss the actual reads. This helps to better visualize the actual read signal:
 +<code>
 +bedtools bamtobed -i input.bam | \
 +awk -F'\t' 'BEGIN {OFS = FS} {if ($6=="+") {$3=$2+99} else {$2=$3-99}; if ($2<0) {$2=0}; print $0;}' | \
 +bedtools bedtobam -i -> extended_input.bam
 +</code>
  
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-===== Add only modified changes and ignore untracked files using git. =====+===== Add only modified changes and ignore untracked files using git? ===== 
 + 
 +Using newer version of `git` (e.g., >=2.32.1),
  
 <code> <code>
-git ls-files --modified | xargs git add; git commit -m 'minor changes'; git push+git commit -am 'minor changes'; git push
 </code> </code>
  
-The [[https://stackoverflow.com/questions/7124726/git-add-only-modified-changes-and-ignore-untracked-files|above]] should work if there is no conflict. If there is a conflict at push time, first pull. Now, you need to look for ">>>" in the code, and manually fix the conflict. Then, push again. +⚠️ <font inherit/inherit;;#e74c3c;;inherit>Caution</font>: With older versions the -a option will add all files in the directory, which is usually NOT what you want. Instead, use following command, which would have the same effect as above:
- +
-PS: +
- +
-by the new version of `git` the following would have the same effect as above:+
  
 <code> <code>
-git commit -am 'minor changes'; git push+git ls-files --modified | xargs git add; git commit -m 'minor changes'; git push
 </code> </code>
 +
 +The [[https://stackoverflow.com/questions/7124726/git-add-only-modified-changes-and-ignore-untracked-files|above]] should work if there is no conflict. If there is a conflict at push time, first pull. Now, you need to look for ">>>" in the code, and manually fix the conflict. Then, push again.
  
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