Revert "Merge branch 'Multiplex_Major_Patch' into devel"

This reverts commit c5e923d, reversing
changes made to 1463b08.

revert merge

Author: cying111

.github/workflows/check-bioc.yml

@@ -40,7 +40,7 @@ env:
   run_covr: 'false'
   run_pkgdown: 'false'
   has_RUnit: 'false'
-  cache-version: 'cache-v4'
+  cache-version: 'cache-v3'
   run_docker: 'false'
 
 jobs:
@@ -56,7 +56,7 @@ jobs:
         config:
           - { os: ubuntu-latest, r: '4.4.2', bioc: '3.20', cont: "bioconductor/bioconductor_docker:RELEASE_3_20", rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest" }
           - { os: macOS-latest, r: '4.4.2', bioc: '3.20'}
-          ## - { os: windows-latest, r: '4.4', bioc: '3.20'}
+            ##- { os: windows-latest, r: '4.3', bioc: '3.18'}
           ## Check https://github.com/r-lib/actions/tree/master/examples
           ## for examples using the http-user-agent
     env:
@@ -81,7 +81,7 @@ jobs:
       ## https://github.com/r-lib/actions/blob/master/examples/check-standard.yaml
       ## If they update their steps, we will also need to update ours.
       - name: Checkout Repository
-        uses: actions/checkout@v4
+        uses: actions/checkout@v3
 
       ## R is already included in the Bioconductor docker images
       - name: Setup R from r-lib
@@ -104,15 +104,15 @@ jobs:
 
       - name: Restore R package cache
         if: "!contains(github.event.head_commit.message, '/nocache') && runner.os != 'Linux'"
-        uses: actions/cache@v4
+        uses: actions/cache@v3
         with:
           path: ${{ env.R_LIBS_USER }}
           key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE-r-4.4.2-${{ hashFiles('.github/depends.Rds') }}
           restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE-r-4.4.2-
 
       - name: Cache R packages on Linux
         if: "!contains(github.event.head_commit.message, '/nocache') && runner.os == 'Linux' "
-        uses: actions/cache@v4
+        uses: actions/cache@v3
         with:
           path: /home/runner/work/_temp/Library
           key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-devel-r-4.4.2-${{ hashFiles('.github/depends.Rds') }}

.github/workflows/lint.yaml

@@ -15,7 +15,7 @@ jobs:
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v2
 
       - uses: r-lib/actions/setup-r@v2
         with:

.github/workflows/pr-commands.yaml

@@ -14,7 +14,7 @@ jobs:
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v2
 
       - uses: r-lib/actions/pr-fetch@v2
         with:
@@ -49,7 +49,7 @@ jobs:
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v2
 
       - uses: r-lib/actions/pr-fetch@v2
         with:

.github/workflows/test-coverage.yaml

@@ -16,7 +16,7 @@ jobs:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
 
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v3
 
       - uses: r-lib/actions/setup-r@v2
         with:

DESCRIPTION

@@ -86,8 +86,7 @@ Imports:
     Rsamtools,
     methods,
     Rcpp,
-    xgboost,
-    Matrix
+    xgboost
 VignetteBuilder: 
     knitr
 LazyData: true

NAMESPACE

@@ -7,9 +7,7 @@ export(readFromGTF)
 export(transcriptToGeneExpression)
 export(writeBambuOutput)
 export(writeToGTF)
-export(writeAnnotationsToGTF)
 export(trainBambu)
-export(setNDR)
 export(compareTranscripts)
 importFrom(stats,predict)
 importFrom(BiocGenerics,basename)
@@ -75,8 +73,7 @@ import(data.table, except=c(last, first, shift, second, between))
 import(dplyr, except=c(last, first, desc, union, setdiff, intersect, slice))
 import(IRanges, except=c(slice, collapse, setdiff, intersect,cor))
 import(SummarizedExperiment)
-import(Matrix)
-import(S4Vectors, except=c(rename, setequal, setdiff, intersect,cor, unname, expand))
+import(S4Vectors, except=c(rename, setequal, setdiff, intersect,cor))
 useDynLib(bambu, .registration = TRUE)
 import(xgboost)
 import(BSgenome)

R/bambu-assignDist.R

@@ -19,10 +19,6 @@ isore.combineTranscriptCandidates <- function(readClassList,
         min.readCount, min.readFractionByGene, 
         min.txScore.multiExon, min.txScore.singleExon, verbose)
     combinedSplicedTranscripts[,confidenceType := "highConfidenceJunctionReads"]
-    # when single exon min score is greater than 1, skip unspliced transcripts combination
-    # this is a very customized config, useful when data is very big 
-    if (min.txScore.singleExon > 1) 
-        return(combinedSplicedTranscripts)
     combinedUnsplicedTranscripts <- 
         combineUnsplicedTranscriptModels(readClassList, bpParameters, 
         stranded, min.readCount, min.readFractionByGene, 
@@ -39,11 +35,11 @@ isore.combineTranscriptCandidates <- function(readClassList,
 combineSplicedTranscriptModels <- function(readClassList, bpParameters, 
         min.readCount, min.readFractionByGene, min.txScore.multiExon, 
         min.txScore.singleExon, verbose){
-    bpParameters$progressbar <- FALSE
+    bpParameters$progressbar = FALSE
     options(scipen = 999) #maintain numeric basepair locations not sci.notfi.
     start.ptm <- proc.time()
     n_sample <- length(readClassList)
-    nGroups <- max(ceiling(n_sample/10),min(bpworkers(bpParameters), 
+    nGroups = max(ceiling(n_sample/10),min(bpworkers(bpParameters), 
                                             round(n_sample/2)))
     indexList <- sample(rep(seq_len(nGroups), length.out=n_sample))
     indexList <- splitAsList(seq_len(n_sample), indexList)
@@ -132,7 +128,7 @@ combineFeatureTibble <- function(combinedFeatureTibble,
             maxTxScore.noFit, NSampleReadCount, NSampleReadProp,NSampleTxScore, 
             starts_with('start'), starts_with('end'), starts_with('readCount'))
     } else { 
-        combinedTable <- full_join(combinedFeatureTibble, 
+        combinedTable = full_join(combinedFeatureTibble, 
             featureTibbleSummarised, by = c('intronStarts', 'intronEnds', 'chr',
             'strand'), suffix=c('.combined','.new')) %>% 
             mutate(NSampleReadCount=pmax0NA(NSampleReadCount.combined) + 
@@ -212,7 +208,7 @@ combineUnsplicedTranscriptModels <-
             min.readFractionByGene, min.txScore.multiExon,
             min.txScore.singleExon, verbose){
         start.ptm <- proc.time()
-        bpParameters$progressbar <- FALSE
+        bpParameters$progressbar = FALSE
         newUnsplicedSeList <- 
             bplapply(seq_along(readClassList), function(sample_id)
                 extractNewUnsplicedRanges(readClassSe = 
@@ -289,7 +285,7 @@ reduceUnsplicedRanges <- function(rangesList, stranded){
 makeUnsplicedTibble <- function(combinedNewUnsplicedSe,newUnsplicedSeList,
         colDataNames,min.readCount, min.readFractionByGene,
         min.txScore.multiExon, min.txScore.singleExon, bpParameters){
-        bpParameters$progressbar <- FALSE
+        bpParameters$progressbar = FALSE
     newUnsplicedTibble <- as_tibble(combinedNewUnsplicedSe) %>%
         rename(chr = seqnames) %>% select(chr, start, end, strand, row_id) %>%
         separate_rows(row_id, sep = "\\+")