From 26ec435a5240a6ccf77da8b7c10c1ffd179ee3fd Mon Sep 17 00:00:00 2001
From: Zi-Ning Choo <zining01@gmail.com>
Date: Mon, 27 Sep 2021 14:53:30 -0400
Subject: [PATCH 1/2] stash

---
 R/JaBbA.R | 8 +++-----
 1 file changed, 3 insertions(+), 5 deletions(-)

diff --git a/R/JaBbA.R b/R/JaBbA.R
index 75f6022..b480a29 100755
--- a/R/JaBbA.R
+++ b/R/JaBbA.R
@@ -3385,8 +3385,6 @@ 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)
@@ -6896,14 +6894,14 @@ 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
@@ -6918,7 +6916,7 @@ 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)

From f93862ccd76de2258300583b39f7868ba484ddd3 Mon Sep 17 00:00:00 2001
From: Zi-Ning Choo <zining01@gmail.com>
Date: Tue, 7 Dec 2021 17:15:36 -0500
Subject: [PATCH 2/2] small fix for testing

---
 tests/testthat/test_filterloose.R | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/tests/testthat/test_filterloose.R b/tests/testthat/test_filterloose.R
index c6b8328..c7cd5f0 100644
--- a/tests/testthat/test_filterloose.R
+++ b/tests/testthat/test_filterloose.R
@@ -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,
@@ -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",