sliceBamFile function

[mariam16548]

I've put the function into the ctcf folder (sliceBamFunction.R).

[mariam16548]

@paul-shannon

[paul-shannon]

@mariam16548 I am creating a new file sliceBamFile.R based on your function. It will have all of my suggestions, some of which are substantial, some just stylistic. Your code is headed in the right direction!

[paul-shannon]

@mariam16548 see ~/github/chip-seq-motif-study/explore/ctcf/sliceBamFile.R Note that this can be run and tested from the shell:

bash> R -f sliceBamFile.R
--- test_sliceBamFile
[1] TRUE

Lots of stylistic and substantial modifications here. Please absorb them!

[paul-shannon]

@mariam16548 Next task: I suggest a more friendly signature of sliceBamFile:

sliceBamFile <- function(bamFile,  newBamFileName, chrom, start=NA, end=NA)

If you call this function without a start and end, it implies "give me the whole chromosome". In that case, start <-1, and end can be looked up this way:

library(org.Hs.eg.db)
org.Hs.egCHRLENGTHS[[19]]    #  80373285

This is friendly in that it saves the caller the task of looking up the end of the chromosome of interest in those cases where we want an entire chromosome from the bam file.

[mariam16548]

@paul-shannon I've made these requested changes and put them in sliceBamFunction.R. I will continue to look through your suggestions to make sure I understand them!

[paul-shannon]

@mariam16548 - good work! Two stylistic suggestions:

• sliceBamFile.R is a better (more descriptive) name that sliceBamFunction.R in part because Function adds nothing to our understanding: most of the code your write will be functions!!
  • stylistic debates rage, but I prefer to see the terminating curly brace "}" indented the same as the code block it closes.
• also, if your code block has only one line, I prefer omitting the curly brackets: you save a line, you save visual clutter, your code text becomes more expressive

[mariam16548]

Thank you for the feedback (I went back in and applied the suggestions)! -Mariam

On Mon, Aug 26, 2019 at 10:41 AM Paul Shannon notifications@github.com wrote:

@mariam16548 https://github.com/mariam16548 - good work! Two stylistic suggestions:

• sliceBamFile.R is a better (more descriptive) name that sliceBamFunction.R in part because Function adds nothing to our understanding: most of the code your write will be functions!!
• stylistic debates rage, but I prefer to see the terminating curly brace "}" indented the same as the code block it closes.
• also, if your code block has only one line, I prefer omitting the curly brackets: you save a line, you save visual clutter, your code text becomes more expressive

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