Merge pull request #50 from tyler5huang/master

SMuRFv2.0.6
skandlab · Nov 18, 2020 · bce10eb · bce10eb
2 parents c391d5d + 14f42f2
commit bce10eb
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Showing 2 changed files with 13 additions and 12 deletions.
diff --git a/smurf/R/parsevcf_allfeaturesall.R b/smurf/R/parsevcf_allfeaturesall.R
@@ -327,19 +327,19 @@ parsevcf_allfeaturesall = function(x, tbi, roi=F, roi.dir=NULL, t.label=NULL){
   meta_data=data.frame(snv_pass)[,1:3]
   meta_data[c(names_m2,names_f,names_vs,names_vd,names_s2)]=NA
   #do not merge when the 1st row is all NAs + last column PASSED/REJECT
-  if ((rowSums(is.na(data.frame(mcols(gr_m2)[1,1:length(mcols(gr_m2))-1])))!=ncol(data.frame(mcols(gr_m2)[1,-1]))-1)==TRUE) {
+  if ((rowSums(is.na(data.frame(mcols(gr_m2)[1,1:length(mcols(gr_m2))-1])))!=ncol(data.frame(mcols(gr_m2)[1,1:length(mcols(gr_m2))-1])))==TRUE) {
     meta_data[Biostrings::match(gr_m2, snv_pass), names_m2]=data.frame(mcols(gr_m2)[,-1])
   }
-  if ((rowSums(is.na(data.frame(mcols(gr_f)[1,1:length(mcols(gr_f))-1])))!=ncol(data.frame(mcols(gr_f)[1,-1]))-1)==TRUE) {
+  if ((rowSums(is.na(data.frame(mcols(gr_f)[1,1:length(mcols(gr_f))-1])))!=ncol(data.frame(mcols(gr_f)[1,1:length(mcols(gr_f))-1])))==TRUE) {
     meta_data[Biostrings::match(gr_f, snv_pass), names_f]=data.frame(mcols(gr_f)[,-1])
   }
-  if ((rowSums(is.na(data.frame(mcols(gr_vs)[1,1:length(mcols(gr_vs))-1])))!=ncol(data.frame(mcols(gr_vs)[1,-1]))-1)==TRUE) {
+  if ((rowSums(is.na(data.frame(mcols(gr_vs)[1,1:length(mcols(gr_vs))-1])))!=ncol(data.frame(mcols(gr_vs)[1,1:length(mcols(gr_vs))-1])))==TRUE) {
     meta_data[Biostrings::match(gr_vs, snv_pass), names_vs]=data.frame(mcols(gr_vs)[,-1])
   }
-  if ((rowSums(is.na(data.frame(mcols(gr_vd)[1,1:length(mcols(gr_vd))-1])))!=ncol(data.frame(mcols(gr_vd)[1,-1]))-1)==TRUE) {
+  if ((rowSums(is.na(data.frame(mcols(gr_vd)[1,1:length(mcols(gr_vd))-1])))!=ncol(data.frame(mcols(gr_vd)[1,1:length(mcols(gr_vd))-1])))==TRUE) {
     meta_data[Biostrings::match(gr_vd, snv_pass), names_vd]=data.frame(mcols(gr_vd)[,-1])
   }
-  if ((rowSums(is.na(data.frame(mcols(gr_s2)[1,1:length(mcols(gr_s2))-1])))!=ncol(data.frame(mcols(gr_s2)[1,-1]))-1)==TRUE) {
+  if ((rowSums(is.na(data.frame(mcols(gr_s2)[1,1:length(mcols(gr_s2))-1])))!=ncol(data.frame(mcols(gr_s2)[1,1:length(mcols(gr_s2))-1])))==TRUE) {
     meta_data[Biostrings::match(gr_s2, snv_pass), names_s2]=data.frame(mcols(gr_s2)[,-1])
   }
 
@@ -833,22 +833,23 @@ parsevcf_allfeaturesall = function(x, tbi, roi=F, roi.dir=NULL, t.label=NULL){
   meta_indel=data.frame(indel_pass)[,1:3]
   meta_indel[c(names_m2,names_f,names_vs,names_vd,names_s2)]=NA
   #do not merge when the 1st row is all NAs + last column PASSED/REJECT
-  if ((rowSums(is.na(data.frame(mcols(gr_m2)[1,1:length(mcols(gr_m2))-1])))!=ncol(data.frame(mcols(gr_m2)[1,-1]))-1)==TRUE) {
+  if ((rowSums(is.na(data.frame(mcols(gr_m2)[1,1:length(mcols(gr_m2))-1])))!=ncol(data.frame(mcols(gr_m2)[1,1:length(mcols(gr_m2))-1])))==TRUE) {
     meta_indel[Biostrings::match(gr_m2, indel_pass), names_m2]=data.frame(mcols(gr_m2)[,-1])
   }
-  if ((rowSums(is.na(data.frame(mcols(gr_f)[1,1:length(mcols(gr_f))-1])))!=ncol(data.frame(mcols(gr_f)[1,-1]))-1)==TRUE) {
+  if ((rowSums(is.na(data.frame(mcols(gr_f)[1,1:length(mcols(gr_f))-1])))!=ncol(data.frame(mcols(gr_f)[1,1:length(mcols(gr_f))-1])))==TRUE) {
     meta_indel[Biostrings::match(gr_f, indel_pass), names_f]=data.frame(mcols(gr_f)[,-1])
   }
-  if ((rowSums(is.na(data.frame(mcols(gr_vs)[1,1:length(mcols(gr_vs))-1])))!=ncol(data.frame(mcols(gr_vs)[1,-1]))-1)==TRUE) {
+  if ((rowSums(is.na(data.frame(mcols(gr_vs)[1,1:length(mcols(gr_vs))-1])))!=ncol(data.frame(mcols(gr_vs)[1,1:length(mcols(gr_vs))-1])))==TRUE) {
     meta_indel[Biostrings::match(gr_vs, indel_pass), names_vs]=data.frame(mcols(gr_vs)[,-1])
   }
-  if ((rowSums(is.na(data.frame(mcols(gr_vd)[1,1:length(mcols(gr_vd))-1])))!=ncol(data.frame(mcols(gr_vd)[1,-1]))-1)==TRUE) {
+  if ((rowSums(is.na(data.frame(mcols(gr_vd)[1,1:length(mcols(gr_vd))-1])))!=ncol(data.frame(mcols(gr_vd)[1,1:length(mcols(gr_vd))-1])))==TRUE) {
     meta_indel[Biostrings::match(gr_vd, indel_pass), names_vd]=data.frame(mcols(gr_vd)[,-1])
   }
-  if ((rowSums(is.na(data.frame(mcols(gr_s2)[1,1:length(mcols(gr_s2))-1])))!=ncol(data.frame(mcols(gr_s2)[1,-1]))-1)==TRUE) {
+  if ((rowSums(is.na(data.frame(mcols(gr_s2)[1,1:length(mcols(gr_s2))-1])))!=ncol(data.frame(mcols(gr_s2)[1,1:length(mcols(gr_s2))-1])))==TRUE) {
     meta_indel[Biostrings::match(gr_s2, indel_pass), names_s2]=data.frame(mcols(gr_s2)[,-1])
   }
-
+
+
   end.time=Sys.time()
   print(end.time-start.time)
 

diff --git a/smurf/R/smurf.R b/smurf/R/smurf.R
@@ -98,7 +98,7 @@ smurf = function(directory=NULL, mode=NULL, nthreads = -1,
                  check.packages=T, file.exclude=NULL){
 
   #SMuRF version announcement
-  print("SMuRFv2.0.5 (2nd Nov 2020)")
+  print("SMuRFv2.0.6 (18th Nov 2020)")
 
 
   if(is.null(directory)){