Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

read.junctions #58

Merged
merged 3 commits into from
Dec 7, 2021
Merged

read.junctions #58

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
3 commits
Select commit Hold shift + click to select a range
26ec435
stash
zining01 Sep 27, 2021
bdccbab
merge most recent from master
zining01 Dec 7, 2021
f93862c
small fix for testing
zining01 Dec 7, 2021
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
8 changes: 3 additions & 5 deletions R/JaBbA.R
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -3211,8 +3211,6 @@ jbaLP = function(kag.file = NULL,
kag.gg$edges$mark(cn = NULL)
kag.gg$nodes[cn > M]$mark(cn = NA, weight = NA)

## browser()

## add lower bounds depending on ALT junction tier
if (tfield %in% colnames(kag.gg$edges$dt)) {
lbs = ifelse(kag.gg$edges$dt[, ..tfield] == 1, 1, 0)
Expand Down Expand Up @@ -6722,14 +6720,14 @@ read.junctions = function(rafile,
, tier := ifelse(
tier==2, ifelse(grepl("1", this.geno), 2, 3), 3)]
values(this.ra) = this.dt
return(this.ra)
return(verify.junctions(this.ra))
})
loose=FALSE ## TODO: temporary until we figure out how
}
}

if (!get.loose | is.null(vgr$mix)){
return(ra)
return(verify.junctions(ra))
} else {
npix = is.na(vgr$mix)
## these are possible "loose ends" that we will add to the segmentation
Expand All @@ -6744,7 +6742,7 @@ read.junctions = function(rafile,
values(vgr.loose) = cbind(vcf@fixed[bix[npix], ], info(vcf)[bix[npix], ])
}

return(list(junctions = ra, loose.ends = vgr.loose))
return(list(junctions = verify.junctions(ra), loose.ends = vgr.loose))
}
} else{
rafile = data.table::fread(rafile)
Expand Down
3 changes: 2 additions & 1 deletion tests/testthat/test_filterloose.R
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -17,6 +17,7 @@ test_that(desc = "Testing LP JaBbA with .bw coverage input",
slack.penalty = 10,
tilim = 60,
cfield = 'ratio',
reiterate = 2,
verbose = 2,
outdir = 'JaBbA.filter',
overwrite = TRUE,
Expand Down Expand Up @@ -61,7 +62,7 @@ test_that(desc = "Testing LP JaBbA with .bw coverage input",
rescue.all = FALSE,
filter_loose = FALSE))
},
regexp = "Resetting rescue.all to TRUE")
regexp = "Skipping loose end annotation")
})

test_that(desc = "Testing LP JaBbA with .bw coverage input",
Expand Down