git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/basecallQC@130196 bc3139a8-67e5-0310-9ffc-ced21a209358
Tom Carroll authored on 08/06/2017 16:16:28
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new file mode 100644 |
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@@ -0,0 +1,487 @@ |
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+readPattern <- function(bcl2fastqparams){
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| 2 |
+ c(readlengths(bcl2fastqparams)[1],indexlengths(bcl2fastqparams)[1], |
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+ indexlengths(bcl2fastqparams)[2],readlengths(bcl2fastqparams)[2]) |
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+} |
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+readBCLStatFile <- function(read.filename){
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+ read.filename <- file(read.filename, "rb") |
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+ clusterNumber <- readBin(read.filename,"int",size=4,n = 1) |
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+ ACI <- readBin(read.filename,"double",size=8,n = 1) |
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+ AIAOverAIAA <- readBin(read.filename,"double",size=8,n = 1) |
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+ AICOverAICA <- readBin(read.filename,"double",size=8,n = 1) |
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+ AIGOverAIGA <- readBin(read.filename,"double",size=8,n = 1) |
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+ AITOverAITA <- readBin(read.filename,"double",size=8,n = 1) |
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+ AIAOverA <- readBin(read.filename,"double",size=8,n = 1) |
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+ AICOverC <- readBin(read.filename,"double",size=8,n = 1) |
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+ AIGOverG <- readBin(read.filename,"double",size=8,n = 1) |
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+ AITOverT <- readBin(read.filename,"double",size=8,n = 1) |
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+ NCA <- readBin(read.filename,"int",size=4,n = 1) |
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+ NCC <- readBin(read.filename,"int",size=4,n = 1) |
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+ NCG <- readBin(read.filename,"int",size=4,n = 1) |
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+ NCT <- readBin(read.filename,"int",size=4,n = 1) |
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+ NCX <- readBin(read.filename,"int",size=4,n = 1) |
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+ NCIA <- readBin(read.filename,"int",size=4,n = 1) |
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+ NCIC <- readBin(read.filename,"int",size=4,n = 1) |
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+ NCIG <- readBin(read.filename,"int",size=4,n = 1) |
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+ NCIT <- readBin(read.filename,"int",size=4,n = 1) |
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+ |
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+ |
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+ bclClusterTileStats <- c(clusterNumber,ACI,AIAOverAIAA,AICOverAICA,AIGOverAIGA, |
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+ AITOverAITA,AIAOverA,AICOverC,AIGOverG, |
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+ AITOverT,NCA,NCC,NCG,NCT,NCX,NCIA,NCIC,NCIG,NCIT) |
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+ close(read.filename) |
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+ return(bclClusterTileStats) |
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+} |
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+readBCLStatFiles <- function(read.filenames){
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+ bclStatList <- lapply(read.filenames,readBCLStatFile) |
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+ bclStatMat <- do.call(rbind,bclStatList) |
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+} |
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| 38 |
+readExtractionMetrics <- function(extractionMetricsBin){
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+ bytesOfFile <- file.info(extractionMetricsBin)$size |
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+ read.filename <- file(extractionMetricsBin, "rb") |
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+ bytesRead <- 0 |
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+ k <- 1 |
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+ versionNumber <- readBin(read.filename,"int",size=1,n = 1) |
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+ recordSize <- readBin(read.filename,"int",size=1,n = 1,signed = FALSE) |
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+ bytesRead <- bytesRead+1+1 |
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+ extractionMetricsOut <- list() |
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| 47 |
+ while(bytesRead < bytesOfFile){
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| 48 |
+ laneNumber <- readBin(read.filename,"int",size=2,n = 1) |
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+ tileNumber <- readBin(read.filename,"int",size=2,n = 1) |
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| 50 |
+ cycleNumber <- readBin(read.filename,"int",size=2,n = 1) |
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+ focusForChannelA <- readBin(read.filename,"double",size=4,n = 1) |
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+ focusForChannelC <- readBin(read.filename,"double",size=4,n = 1) |
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| 53 |
+ focusForChannelG <- readBin(read.filename,"double",size=4,n = 1) |
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+ focusForChannelT <- readBin(read.filename,"double",size=4,n = 1) |
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+ maxIntensityForChannelA <- readBin(read.filename,"int",size=2,n = 1,signed = FALSE) |
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| 56 |
+ maxIntensityForChannelC <- readBin(read.filename,"int",size=2,n = 1,signed = FALSE) |
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+ maxIntensityForChannelG <- readBin(read.filename,"int",size=2,n = 1,signed = FALSE) |
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| 58 |
+ maxIntensityForChannelT <- readBin(read.filename,"int",size=2,n = 1,signed = FALSE) |
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+ timeStamp <- readBin(read.filename,"int",size=8,n = 1) |
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+ bytesRead <- bytesRead+(2*3)+(4*4)+(2*4)+8 |
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+ extractionMetricsOut[[k]] <- c( |
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+ laneNumber,tileNumber,cycleNumber, |
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+ focusForChannelA,focusForChannelC, |
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+ focusForChannelG,focusForChannelT, |
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+ maxIntensityForChannelA,maxIntensityForChannelC, |
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+ maxIntensityForChannelG,maxIntensityForChannelT, |
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+ timeStamp |
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+ ) |
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+ k <- k+1 |
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+ } |
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+ extractionMetricsOutMat <- do.call(rbind,extractionMetricsOut) |
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+ colnames(extractionMetricsOutMat) <- c( |
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+ "laneNumber","tileNumber","cycleNumber", |
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+ "focusForChannelA","focusForChannelC", |
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+ "focusForChannelG","focusForChannelT", |
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+ "maxIntensityForChannelA","maxIntensityForChannelC", |
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+ "maxIntensityForChannelG","maxIntensityForChannelT", |
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+ "timeStamp" |
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+ ) |
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+ close(read.filename) |
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| 81 |
+ extractionMetricsOutMat <- tbl_df(extractionMetricsOutMat) |
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+} |
|
| 83 |
+readIndexMetrics <- function(indexMetricsBin){
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+ bytesOfFile <- file.info(indexMetricsBin)$size |
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+ indexMetricsBin <- file(indexMetricsBin, "rb") |
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+ |
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+ bytesRead <- 0 |
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+ versionNumber <- readBin(indexMetricsBin,"int",size=1,n = 1) |
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| 89 |
+ bytesRead <- bytesRead+1 |
|
| 90 |
+ k <- 1 |
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| 91 |
+ IndexMetricsOut <- list() |
|
| 92 |
+ while(bytesRead < bytesOfFile){
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| 93 |
+ laneNumber <- readBin(indexMetricsBin,"int",size=2,n = 1) |
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| 94 |
+ tileNumber <- readBin(indexMetricsBin,"int",size=2,n = 1) |
|
| 95 |
+ readNumber <- readBin(indexMetricsBin,"int",size=2,n = 1) |
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| 96 |
+ indexNameLength <- readBin(indexMetricsBin,"int",size=2,n = 1) |
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| 97 |
+ indexName <- rawToChar(readBin(indexMetricsBin,"raw",n=indexNameLength)) |
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| 98 |
+ identifiedAsIndex <- readBin(indexMetricsBin,"int",size=4,n = 1) |
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| 99 |
+ sampleNameLength <- readBin(indexMetricsBin,"int",size=2,n = 1) |
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| 100 |
+ sampleName <- rawToChar(readBin(indexMetricsBin,"raw",n=sampleNameLength)) |
|
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+ projectNameLength <- readBin(indexMetricsBin,"int",size=2,n = 1) |
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+ projectName <- rawToChar(readBin(indexMetricsBin,"raw",n=projectNameLength)) |
|
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+ bytesRead <- bytesRead + 2+2+2+2+indexNameLength+4+2+sampleNameLength+2+projectNameLength |
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+ IndexMetricsOut[[k]] <- c( |
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+ laneNumber,tileNumber,readNumber,indexName,identifiedAsIndex,sampleName, projectName |
|
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+ ) |
|
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+ k <- k+1 |
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+ } |
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+ close(indexMetricsBin) |
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+ IndexMetricsFrame <- do.call(rbind,IndexMetricsOut) |
|
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+ colnames(IndexMetricsFrame) <- c( |
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+ "laneNumber","tileNumber","readNumber","indexName","identifiedAsIndex","sampleName","projectName" |
|
| 113 |
+ ) |
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+ tbl_df(IndexMetricsFrame) |
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+} |
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+readQMetrics <- function(qMetricsBin){
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| 117 |
+ bytesOfFile <- file.info(qMetricsBin)$size |
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+ read.filename <- file(qMetricsBin, "rb") |
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| 119 |
+ bytesRead <- 0 |
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| 120 |
+ versionNumber <- readBin(read.filename,"int",size=1,n = 1) |
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| 121 |
+ recordSize <- readBin(read.filename,"int",size=1,n = 1,signed = FALSE) |
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| 122 |
+ hasBins <- readBin(read.filename,"logical",size=1,n = 1) |
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| 123 |
+ numberOfBins <- readBin(read.filename,"int",size=1,n = 1,signed = FALSE) |
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| 124 |
+ lowEndsOfBins <- readBin(read.filename,"int",size=1,n = numberOfBins,signed = FALSE) |
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| 125 |
+ highEndsOfBins <- readBin(read.filename,"int",size=1,n = numberOfBins,signed = FALSE) |
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| 126 |
+ valueOfBins <- readBin(read.filename,"int",size=1,n = numberOfBins,signed = FALSE) |
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| 127 |
+ bytesRead <- bytesRead+1+1+1+1+numberOfBins*3 |
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+ k <- 1 |
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| 129 |
+ qMetricsOut <- list() |
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| 130 |
+ while(bytesRead < bytesOfFile){
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| 131 |
+ Lane <- readBin(read.filename,"int",size=2,n = 1,signed = FALSE) |
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| 132 |
+ Tile <- readBin(read.filename,"int",size=2,n = 1,signed = FALSE) |
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| 133 |
+ Cycle <- readBin(read.filename,"int",size=2,n = 1,signed = FALSE) |
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| 134 |
+ qhist <- readBin(read.filename,"integer",size=4,n = 50) |
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+ qMetricsOut[[k]] <- |
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+ c(Lane,Tile,Cycle,qhist) |
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+ bytesRead <- bytesRead+2+2+2+4*50 |
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+ k <- k+1 |
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| 139 |
+ } |
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+ |
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+ close(read.filename) |
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| 142 |
+ qMetricsFrame <- do.call(rbind,qMetricsOut) |
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+ colnames(qMetricsFrame) <- c("Lane","Tile","Cycle",paste0("Q",1:50))
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+ tbl_df(qMetricsFrame) |
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+} |
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| 146 |
+readCorrectedIntMetrics <- function(correctedIntMetricsBin){
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| 147 |
+ bytesOfFile <- file.info(correctedIntMetricsBin)$size |
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| 148 |
+ read.filename <- file(correctedIntMetricsBin, "rb") |
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| 149 |
+ bytesRead <- 0 |
|
| 150 |
+ k <- 1 |
|
| 151 |
+ versionNumber <- readBin(read.filename,"int",size=1,n = 1) |
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| 152 |
+ recordSize <- readBin(read.filename,"int",size=1,n = 1,signed = FALSE) |
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+ bytesRead <- bytesRead+1+1 |
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| 154 |
+ correctedIntMetricsOut <- list() |
|
| 155 |
+ while(bytesRead < bytesOfFile){
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| 156 |
+ laneNumber <- readBin(read.filename,"int",size=2,n = 1) |
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| 157 |
+ tileNumber <- readBin(read.filename,"int",size=2,n = 1) |
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| 158 |
+ cycleNumber <- readBin(read.filename,"int",size=2,n = 1) |
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| 159 |
+ averageCycleIntensity <- readBin(read.filename,"int",size=2,n = 1) |
|
| 160 |
+ averageCorrectedIntensityForChannelA <- readBin(read.filename,"int",size=2,n = 1) |
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| 161 |
+ averageCorrectedIntensityForChannelC <- readBin(read.filename,"int",size=2,n = 1) |
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| 162 |
+ averageCorrectedIntensityForChannelG <- readBin(read.filename,"int",size=2,n = 1) |
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| 163 |
+ averageCorrectedIntensityForChannelT <- readBin(read.filename,"int",size=2,n = 1) |
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+ averageCorrectedIntForCalledClustersForBaseA <- readBin(read.filename,"int",size=2,n = 1) |
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+ averageCorrectedIntForCalledClustersForBaseC <- readBin(read.filename,"int",size=2,n = 1) |
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| 166 |
+ averageCorrectedIntForCalledClustersForBaseG <- readBin(read.filename,"int",size=2,n = 1) |
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| 167 |
+ averageCorrectedIntForCalledClustersForBaseT <- readBin(read.filename,"int",size=2,n = 1) |
|
| 168 |
+ numberOfBaseCallsForNoCall <- readBin(read.filename,"int",size=4,n = 1) |
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| 169 |
+ numberOfBaseCallsForBaseA <- readBin(read.filename,"int",size=4,n = 1) |
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| 170 |
+ numberOfBaseCallsForBaseC <- readBin(read.filename,"int",size=4,n = 1) |
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| 171 |
+ numberOfBaseCallsForBaseG <- readBin(read.filename,"int",size=4,n = 1) |
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| 172 |
+ numberOfBaseCallsForBaseT <- readBin(read.filename,"int",size=4,n = 1) |
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| 173 |
+ signalToNoiseRatio <- readBin(read.filename,"double",size=4,n = 1) |
|
| 174 |
+ bytesRead <- bytesRead+(2*3)+(2*9)+(4*5)+4 |
|
| 175 |
+ correctedIntMetricsOut[[k]] <- c(laneNumber,tileNumber,cycleNumber,averageCycleIntensity, |
|
| 176 |
+ averageCorrectedIntensityForChannelA,averageCorrectedIntensityForChannelC, |
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+ averageCorrectedIntensityForChannelG,averageCorrectedIntensityForChannelT, |
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| 178 |
+ averageCorrectedIntForCalledClustersForBaseA,averageCorrectedIntForCalledClustersForBaseC, |
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+ averageCorrectedIntForCalledClustersForBaseG,averageCorrectedIntForCalledClustersForBaseT, |
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| 180 |
+ numberOfBaseCallsForNoCall, |
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| 181 |
+ numberOfBaseCallsForBaseA,numberOfBaseCallsForBaseC, |
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| 182 |
+ numberOfBaseCallsForBaseG,numberOfBaseCallsForBaseT) |
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| 183 |
+ k <- k+1 |
|
| 184 |
+ } |
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| 185 |
+ close(read.filename) |
|
| 186 |
+ correctedIntMetricsMat <- do.call(rbind,correctedIntMetricsOut) |
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| 187 |
+} |
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| 188 |
+readImageMetrics <- function(imageMetricsBin){
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| 189 |
+ bytesOfFile <- file.info(imageMetricsBin)$size |
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| 190 |
+ read.filename <- file(imageMetricsBin, "rb") |
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+ bytesRead <- 0 |
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| 192 |
+ k <- 1 |
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| 193 |
+ versionNumber <- readBin(read.filename,"int",size=1,n = 1) |
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| 194 |
+ recordSize <- readBin(read.filename,"int",size=1,n = 1,signed = FALSE) |
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+ bytesRead <- bytesRead+1+1 |
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| 196 |
+ imageMetricsOut <- list() |
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| 197 |
+ while(bytesRead < bytesOfFile){
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| 198 |
+ laneNumber <- readBin(read.filename,"int",size=2,n = 1) |
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+ tileNumber <- readBin(read.filename,"int",size=2,n = 1) |
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| 200 |
+ cycleNumber <- readBin(read.filename,"int",size=2,n = 1) |
|
| 201 |
+ channelNumber <- readBin(read.filename,"int",size=2,n = 1,signed = FALSE) |
|
| 202 |
+ minimumContrast <- readBin(read.filename,"int",size=2,n = 1,signed = FALSE) |
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| 203 |
+ maximumContrast <- readBin(read.filename,"int",size=2,n = 1,signed = FALSE) |
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| 204 |
+ bytesRead <- bytesRead+(2*3)+(2*3) |
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| 205 |
+ imageMetricsOut[[k]] <- c(laneNumber,tileNumber,cycleNumber, |
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+ channelNumber,minimumContrast,maximumContrast) |
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+ k <- k+1 |
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| 208 |
+ } |
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| 209 |
+ close(read.filename) |
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| 210 |
+ imageMetricsMat <- do.call(rbind,imageMetricsOut) |
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+} |
|
| 212 |
+readTileMetrics <- function(tileMetricsBin){
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| 213 |
+ bytesOfFile <- file.info(tileMetricsBin)$size |
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| 214 |
+ read.filename <- file(tileMetricsBin, "rb") |
|
| 215 |
+ bytesRead <- 0 |
|
| 216 |
+ k <- 1 |
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| 217 |
+ versionNumber <- readBin(read.filename,"int",size=1,n = 1) |
|
| 218 |
+ recordSize <- readBin(read.filename,"int",size=1,n = 1,signed = FALSE) |
|
| 219 |
+ bytesRead <- bytesRead+1+1 |
|
| 220 |
+ tileMetricsOut <- list() |
|
| 221 |
+ while(bytesRead < bytesOfFile){
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| 222 |
+ laneNumber <- readBin(read.filename,"int",size=2,n = 1) |
|
| 223 |
+ tileNumber <- readBin(read.filename,"int",size=2,n = 1) |
|
| 224 |
+ codeTile <- readBin(read.filename,"int",size=2,n = 1,signed = FALSE) |
|
| 225 |
+ valueTile <- readBin(read.filename,"double",size=4,n = 1) |
|
| 226 |
+ bytesRead <- bytesRead+(2*2)+2+4 |
|
| 227 |
+ tileMetricsOut[[k]] <- c(laneNumber,tileNumber, |
|
| 228 |
+ codeTile,valueTile) |
|
| 229 |
+ k <- k+1 |
|
| 230 |
+ } |
|
| 231 |
+ close(read.filename) |
|
| 232 |
+ tileMetricsMat <- do.call(rbind,tileMetricsOut) |
|
| 233 |
+ colnames(tileMetricsMat) <- c( |
|
| 234 |
+ "laneNumber","tileNumber", |
|
| 235 |
+ "code","value" |
|
| 236 |
+ ) |
|
| 237 |
+ tbl_df(tileMetricsMat) %>% |
|
| 238 |
+ mutate(code = str_c("c",code)) %>%
|
|
| 239 |
+ group_by(laneNumber,tileNumber,code) %>% |
|
| 240 |
+ summarise_all(max) %>% |
|
| 241 |
+ ungroup() %>% |
|
| 242 |
+ mutate(Lane=laneNumber,Tile=tileNumber) %>% |
|
| 243 |
+ mutate(code=stringr::str_replace_all(code,"c100","ClusterDensity")) %>% |
|
| 244 |
+ mutate(code=stringr::str_replace_all(code,"c101","ClusterDensityPF")) %>% |
|
| 245 |
+ mutate(code=stringr::str_replace_all(code,"c102","NumberOfClusters")) %>% |
|
| 246 |
+ mutate(code=stringr::str_replace_all(code,"c103","NumberOfClustersPF")) %>% |
|
| 247 |
+ mutate(code=stringr::str_replace_all(code,"c200", |
|
| 248 |
+ paste0("PhasingFor",
|
|
| 249 |
+ names(readPattern(bcl2fastqparams))[readPattern(bcl2fastqparams) != 0][1]))) %>% |
|
| 250 |
+ mutate(code=stringr::str_replace_all(code,"c201", |
|
| 251 |
+ paste0("PrePhasingFor",
|
|
| 252 |
+ names(readPattern(bcl2fastqparams))[readPattern(bcl2fastqparams) != 0][1]))) %>% |
|
| 253 |
+ mutate(code=stringr::str_replace_all(code,"c202", |
|
| 254 |
+ paste0("PhasingFor",
|
|
| 255 |
+ names(readPattern(bcl2fastqparams))[readPattern(bcl2fastqparams) != 0][2]))) %>% |
|
| 256 |
+ mutate(code=stringr::str_replace_all(code,"c203", |
|
| 257 |
+ paste0("PrePhasingFor",
|
|
| 258 |
+ names(readPattern(bcl2fastqparams))[readPattern(bcl2fastqparams) != 0][2]))) %>% |
|
| 259 |
+ mutate(code=stringr::str_replace_all(code,"c204", |
|
| 260 |
+ paste0("PhasingFor",
|
|
| 261 |
+ names(readPattern(bcl2fastqparams))[readPattern(bcl2fastqparams) != 0][3]))) %>% |
|
| 262 |
+ mutate(code=stringr::str_replace_all(code,"c205", |
|
| 263 |
+ paste0("PrePhasingFor",
|
|
| 264 |
+ names(readPattern(bcl2fastqparams))[readPattern(bcl2fastqparams) != 0][3]))) %>% |
|
| 265 |
+ mutate(code=stringr::str_replace_all(code,"c206", |
|
| 266 |
+ paste0("PhasingFor",
|
|
| 267 |
+ names(readPattern(bcl2fastqparams))[readPattern(bcl2fastqparams) != 0][4]))) %>% |
|
| 268 |
+ mutate(code=stringr::str_replace_all(code,"c207", |
|
| 269 |
+ paste0("PrePhasingFor",
|
|
| 270 |
+ names(readPattern(bcl2fastqparams))[readPattern(bcl2fastqparams) != 0][4]))) %>% |
|
| 271 |
+ filter(code!="PrePhasingForNA" & code!="PhasingForNA" ) %>% |
|
| 272 |
+ spread(code,value) %>% |
|
| 273 |
+ dplyr::select(-laneNumber,-tileNumber, |
|
| 274 |
+ -starts_with("c",ignore.case = FALSE))
|
|
| 275 |
+} |
|
| 276 |
+readPhasingMetrics <- function(phasingMetricsBin){
|
|
| 277 |
+ bytesOfFile <- file.info(phasingMetricsBin)$size |
|
| 278 |
+ read.filename <- file(phasingMetricsBin, "rb") |
|
| 279 |
+ bytesRead <- 0 |
|
| 280 |
+ k <- 1 |
|
| 281 |
+ versionNumber <- readBin(read.filename,"int",size=1,n = 1) |
|
| 282 |
+ recordSize <- readBin(read.filename,"int",size=1,n = 1,signed = FALSE) |
|
| 283 |
+ bytesRead <- bytesRead+1+1 |
|
| 284 |
+ phasingMetricsOut <- list() |
|
| 285 |
+ while(bytesRead < bytesOfFile){
|
|
| 286 |
+ laneNumber <- readBin(read.filename,"int",size=2,n = 1) |
|
| 287 |
+ tileNumber <- readBin(read.filename,"int",size=2,n = 1) |
|
| 288 |
+ cycleNumber <- readBin(read.filename,"int",size=2,n = 1,signed = FALSE) |
|
| 289 |
+ phasingWeight <- readBin(read.filename,"double",size=4,n = 1) |
|
| 290 |
+ prephasingWeight <- readBin(read.filename,"double",size=4,n = 1) |
|
| 291 |
+ bytesRead <- bytesRead+(2*3)+(4*2) |
|
| 292 |
+ phasingMetricsOut[[k]] <- c(laneNumber,tileNumber,cycleNumber, |
|
| 293 |
+ phasingWeight,prephasingWeight) |
|
| 294 |
+ k <- k+1 |
|
| 295 |
+ } |
|
| 296 |
+ close(read.filename) |
|
| 297 |
+ phasingMetricsMat <- do.call(rbind,phasingMetricsOut) |
|
| 298 |
+} |
|
| 299 |
+readErrorMetrics <- function(errorMetricsBin){
|
|
| 300 |
+ bytesOfFile <- file.info(errorMetricsBin)$size |
|
| 301 |
+ read.filename <- file(errorMetricsBin, "rb") |
|
| 302 |
+ bytesRead <- 0 |
|
| 303 |
+ k <- 1 |
|
| 304 |
+ versionNumber <- readBin(read.filename,"int",size=1,n = 1) |
|
| 305 |
+ recordSize <- readBin(read.filename,"int",size=1,n = 1,signed = FALSE) |
|
| 306 |
+ bytesRead <- bytesRead+1+1 |
|
| 307 |
+ tileMetricsOut <- list() |
|
| 308 |
+ while(bytesRead < bytesOfFile){
|
|
| 309 |
+ laneNumber <- readBin(read.filename,"int",size=2,n = 1) |
|
| 310 |
+ tileNumber <- readBin(read.filename,"int",size=2,n = 1) |
|
| 311 |
+ cycleNumber <- readBin(read.filename,"int",size=2,n = 1,signed = FALSE) |
|
| 312 |
+ errorRate <- readBin(read.filename,"double",size=4,n = 1) |
|
| 313 |
+ numberOfPerfectReads <- readBin(read.filename,"int",size=4,n = 1) |
|
| 314 |
+ numberOfReadsWithOneError <- readBin(read.filename,"int",size=4,n = 1) |
|
| 315 |
+ numberOfReadsWithTwoError <- readBin(read.filename,"int",size=4,n = 1) |
|
| 316 |
+ numberOfReadsWithThreeError <- readBin(read.filename,"int",size=4,n = 1) |
|
| 317 |
+ numberOfReadsWithFourError <- readBin(read.filename,"int",size=4,n = 1) |
|
| 318 |
+ bytesRead <- bytesRead+(2*3)+(4*6) |
|
| 319 |
+ tileMetricsOut[[k]] <- c(laneNumber,tileNumber,cycleNumber, |
|
| 320 |
+ errorRate,numberOfPerfectReads, |
|
| 321 |
+ numberOfReadsWithOneError,numberOfReadsWithTwoError, |
|
| 322 |
+ numberOfReadsWithThreeError,numberOfReadsWithFourError) |
|
| 323 |
+ k <- k+1 |
|
| 324 |
+ } |
|
| 325 |
+ close(read.filename) |
|
| 326 |
+ tileMetricsMat <- do.call(rbind,tileMetricsOut) |
|
| 327 |
+} |
|
| 328 |
+readInterOpsMetrics <- function(bcl2fastqparams,verbose=TRUE, |
|
| 329 |
+ interopsToParse=c("TileMetricsOut","QMetricsOut")){
|
|
| 330 |
+ interOpsMetrics <- list() |
|
| 331 |
+ if(any(interopsToParse %in% "TileMetricsOut")){
|
|
| 332 |
+ if(verbose){message("Parsing InterOps Tile binary file..",appendLF = FALSE)}
|
|
| 333 |
+ tileMetricsFile <- file.path(bcl2fastqparams@RunDir,"InterOp","TileMetricsOut.bin") |
|
| 334 |
+ if(file.exists(tileMetricsFile)){
|
|
| 335 |
+ interOpsMetrics[["tileMet"]] <- readTileMetrics(tileMetricsFile) |
|
| 336 |
+ } |
|
| 337 |
+ if(verbose){message("done",appendLF = TRUE)}
|
|
| 338 |
+ } |
|
| 339 |
+ if(any(interopsToParse %in% "QMetricsOut")){
|
|
| 340 |
+ if(verbose){message("Parsing InterOps QMetrics binary file..",appendLF = FALSE)}
|
|
| 341 |
+ qMetricsFile <- file.path(bcl2fastqparams@RunDir,"InterOp","QMetricsOut.bin") |
|
| 342 |
+ if(file.exists(qMetricsFile)){
|
|
| 343 |
+ interOpsMetrics[["qMet"]] <- readQMetrics(qMetricsFile) |
|
| 344 |
+ } |
|
| 345 |
+ if(verbose){message("done",appendLF = TRUE)}
|
|
| 346 |
+ } |
|
| 347 |
+ return(interOpsMetrics) |
|
| 348 |
+} |
|
| 349 |
+ |
|
| 350 |
+ |
|
| 351 |
+#' Function to parse InterOps files and generate summary reports |
|
| 352 |
+#' |
|
| 353 |
+#' Parses the InterOps binary files produced by Illumina's Real Time Analysis sofware and |
|
| 354 |
+#' used by Illumina's SAV sofware. |
|
| 355 |
+#' InterOp binary files contain information on phasing/prephsing, yield,read numbers |
|
| 356 |
+#' and basecalling quality score distributions per cycle. |
|
| 357 |
+#' This interOpsReport functions parses and summarises the InterOps files, TileMetrics.bin and QMetrics.bin, and the |
|
| 358 |
+#' Stats directory XML files, ConversionStats.xml and DemultiplexingStats.xml. |
|
| 359 |
+#' |
|
| 360 |
+#' |
|
| 361 |
+#' @docType methods |
|
| 362 |
+#' @name interOpsReport |
|
| 363 |
+#' @rdname interOpsReport |
|
| 364 |
+#' |
|
| 365 |
+#' @author Thomas Carroll. |
|
| 366 |
+#' @param bcl2fastqparams A BCL2FastQparams object. |
|
| 367 |
+#' @param verbose TRUE or FALSE . TRUE reports progress through file parsing. |
|
| 368 |
+#' @return A named list of length 3 containing machine and run information, |
|
| 369 |
+#' basecalling quality information and demultiplexing information. |
|
| 370 |
+#' @details The interOpsReport function returns a list of machine and run |
|
| 371 |
+#' information, basecalling quality information and demultiplexing information. |
|
| 372 |
+#' The three named elements are descibed below. |
|
| 373 |
+#' \itemize{
|
|
| 374 |
+#' \item{"machineReport"}{ A data.frame containing information machine and software parameters
|
|
| 375 |
+#' } |
|
| 376 |
+#' \item{"sequencingReport"}{ A data.frame of mean cluster density, percentage clusters passing filter, phasing
|
|
| 377 |
+#' and prephasing percentages, number of reads total/passing filter and percent of reads with mean quality score > Q30 |
|
| 378 |
+#' grouped by lane and read |
|
| 379 |
+#' } |
|
| 380 |
+#' \item{"demuxReport"}{ A data.frame of demultiplexing results containing yield, number of reads, percentage of reads
|
|
| 381 |
+#' with quality scores greater than >Q30 and the percent of total reads per lane. |
|
| 382 |
+#' Results are summarised per lane for samples, underdetermined indexes and all indexes (identifed and unidentified). |
|
| 383 |
+#' } |
|
| 384 |
+#' } |
|
| 385 |
+#' |
|
| 386 |
+#' @import stringr XML RColorBrewer methods raster BiocStyle |
|
| 387 |
+#' @examples |
|
| 388 |
+#' |
|
| 389 |
+ |
|
| 390 |
+#' fileLocations <- system.file("extdata",package="basecallQC")
|
|
| 391 |
+#' runXML <- dir(fileLocations,pattern="runParameters.xml",full.names=TRUE) |
|
| 392 |
+#' config <- dir(fileLocations,pattern="config.ini",full.names=TRUE) |
|
| 393 |
+#' bcl2fastqparams <- BCL2FastQparams(runXML,config,runDir=getwd(),verbose=FALSE) |
|
| 394 |
+#' |
|
| 395 |
+#' # myRes_BCAGJ8ANXX <- interOpsReport(bcl2fastqparams,verbose=TRUE) |
|
| 396 |
+#' @export |
|
| 397 |
+interOpsReport <- function(bcl2fastqparams,verbose=TRUE){
|
|
| 398 |
+ if(verbose){message("Parsing XML files..",appendLF = FALSE)}
|
|
| 399 |
+ basecallmetrics <- baseCallMetrics(bcl2fastqparams) |
|
| 400 |
+ demultiplexmetrics <- demultiplexMetrics(bcl2fastqparams) |
|
| 401 |
+ dmx <- demultiplexmetrics$demuxStatsProcessed |
|
| 402 |
+ conv <- basecallmetrics$convStatsProcessed |
|
| 403 |
+ if(verbose){message("done",appendLF = TRUE)}
|
|
| 404 |
+ |
|
| 405 |
+ dmxSum <- dmx %>% |
|
| 406 |
+ tbl_df %>% |
|
| 407 |
+ dplyr::select(Sample,Barcode,Lane) %>% |
|
| 408 |
+ distinct(Sample,Barcode,Lane) %>% |
|
| 409 |
+ mutate(Lane=factor(as.numeric(str_replace_all(Lane,"Lane","")))) |
|
| 410 |
+ |
|
| 411 |
+ convSum <- conv %>% |
|
| 412 |
+ tbl_df %>% |
|
| 413 |
+ group_by(Sample,Lane,Filter) %>% |
|
| 414 |
+ summarise(YieldSum=sum(as.numeric(Yield)), |
|
| 415 |
+ Yield30Sum=sum(as.numeric(Yield30)), |
|
| 416 |
+ Reads=sum(ClusterCount)) %>% |
|
| 417 |
+ filter(Filter=="Pf") %>% |
|
| 418 |
+ group_by(Lane) %>% |
|
| 419 |
+ mutate(PercentageOfGreaterQ30_Bases_PF=(Yield30Sum/YieldSum)*100, |
|
| 420 |
+ PercentOfLane=(Reads/sum(Reads[Sample != "all"]))*100) %>% |
|
| 421 |
+ dplyr::select(-Filter,-Yield30Sum) |
|
| 422 |
+ |
|
| 423 |
+ dmxReport <- full_join(convSum,tbl_df(dmxSum),by = c("Sample", "Lane"))
|
|
| 424 |
+ |
|
| 425 |
+ if(verbose){message("Parsing machine information..",appendLF = FALSE)}
|
|
| 426 |
+ |
|
| 427 |
+ runPReport <- bcl2fastqparams@RunParameters$runParams %>% |
|
| 428 |
+ dplyr::select(ComputerName,RunID,ExperimentName, |
|
| 429 |
+ Flowcell, |
|
| 430 |
+ ChemistryVersion,RunMode, |
|
| 431 |
+ ApplicationName,ApplicationVersion, |
|
| 432 |
+ RTAVersion |
|
| 433 |
+ ) %>% |
|
| 434 |
+ mutate(basecallQC_Version=as.character(packageVersion("basecallQC"))) %>%
|
|
| 435 |
+ t |
|
| 436 |
+ |
|
| 437 |
+ if(verbose){message("done",appendLF = TRUE)}
|
|
| 438 |
+ if(verbose){message("Parsing InterOps binary files..",appendLF = FALSE)}
|
|
| 439 |
+ interOpsMetrics <- readInterOpsMetrics(bcl2fastqparams,verbose = FALSE) |
|
| 440 |
+ tileMet <- interOpsMetrics$tileMet %>% |
|
| 441 |
+ group_by(Lane) %>% |
|
| 442 |
+ summarise(meanClusterDensity=mean(ClusterDensity), |
|
| 443 |
+ sdClusterDensity=sd(ClusterDensity), |
|
| 444 |
+ meanPhasingForRead1=mean(PhasingForRead1,na.rm=TRUE), |
|
| 445 |
+ meanPrePhasingForRead1=mean(PrePhasingForRead1,na.rm=TRUE), |
|
| 446 |
+ NumberOfReads=sum(NumberOfClusters), |
|
| 447 |
+ NumberOfReadsPF=sum(NumberOfClustersPF), |
|
| 448 |
+ percent_PF_Clusters=mean(NumberOfClustersPF/NumberOfClusters)*100, |
|
| 449 |
+ percent_PF_ClustersSD=sd(NumberOfClustersPF/NumberOfClusters)*100, |
|
| 450 |
+ meanPhasingForRead2 = if(exists('PhasingForRead2', where = .)) mean(PhasingForRead2,na.rm=TRUE) else 0,
|
|
| 451 |
+ meanPrePhasingForRead2 = if(exists('PrePhasingForRead2', where = .)) mean(PrePhasingForRead2,na.rm=TRUE) else 0
|
|
| 452 |
+ ) %>% |
|
| 453 |
+ mutate(meanClusterDensity=stringr::str_c(signif(meanClusterDensity/1000,4),"+/-",signif(sdClusterDensity/1000,4)), |
|
| 454 |
+ percent_PF_Clusters=stringr::str_c(signif(percent_PF_Clusters,3),"+/-",signif(percent_PF_ClustersSD,3)), |
|
| 455 |
+ Phasing_PrephasingRead1=stringr::str_c(signif(meanPhasingForRead1*100,3)," / ",signif(meanPrePhasingForRead1*100,3))) %>% |
|
| 456 |
+ {if(exists('meanPhasingForRead2', where = .)) mutate(.,Phasing_PrephasingRead2=stringr::str_c(signif(meanPhasingForRead2*100,3)," / ",signif(meanPrePhasingForRead2*100,3))) else .} %>%
|
|
| 457 |
+ dplyr::select(Lane,meanClusterDensity,percent_PF_Clusters, |
|
| 458 |
+ starts_with("Phasing_Prephasing"),
|
|
| 459 |
+ NumberOfReads,NumberOfReadsPF) |
|
| 460 |
+ |
|
| 461 |
+ |
|
| 462 |
+ qMet <- interOpsMetrics$qMet %>% |
|
| 463 |
+ group_by(Lane,Cycle) %>% |
|
| 464 |
+ dplyr::select(Lane,Cycle,starts_with("Q")) %>%
|
|
| 465 |
+ summarise_all(sum) %>% |
|
| 466 |
+ ungroup() %>% |
|
| 467 |
+ mutate(q30=rowSums(.[32:52])/rowSums(.[3:52])) %>% |
|
| 468 |
+ mutate(Read = cut(Cycle, |
|
| 469 |
+ breaks=unique(cumsum(c(0, |
|
| 470 |
+ readPattern(bcl2fastqparams) |
|
| 471 |
+ ))), |
|
| 472 |
+ labels= names(readPattern(bcl2fastqparams))[readPattern(bcl2fastqparams) !=0] |
|
| 473 |
+ )) %>% |
|
| 474 |
+ group_by(Lane,Read) %>% |
|
| 475 |
+ summarise_all(mean) %>% |
|
| 476 |
+ dplyr::select(Lane,Read,q30) %>% |
|
| 477 |
+ mutate(q30=signif(q30*100,3)) %>% |
|
| 478 |
+ mutate(Read=paste0("Q30-",Read)) %>%
|
|
| 479 |
+ spread(Read,q30) |
|
| 480 |
+ |
|
| 481 |
+ fullSummaryDual <- full_join(tileMet,qMet,by = "Lane") |
|
| 482 |
+ if(verbose){message("done",appendLF = TRUE)}
|
|
| 483 |
+ toReport <- list(machineReport=as.data.frame(runPReport), |
|
| 484 |
+ sequencingReport=as.data.frame(fullSummaryDual), |
|
| 485 |
+ demuxReport=as.data.frame(dmxReport)) |
|
| 486 |
+ return(toReport) |
|
| 487 |
+} |