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### =========================================================================
### quickBamFlagSummary()
### -------------------------------------------------------------------------
.runlen <- function(x) runLength(Rle(x))
.printSummaryHeader <- function(width1, width2, width3)
{
printHeaderLine <- function(h1, h2, h3, h4)
{
cat(format(h1, width=width1, justify="right"),
" |", format(h2, width=width2, justify="right"),
" |", format(h3, width=width3, justify="right"),
" | ", h4, "\n", sep="")
}
printHeaderLine( "group", "nb of", "nb of", "mean / max")
printHeaderLine( "of", "records", "unique", "records per")
printHeaderLine("records", "in group", "QNAMEs", "unique QNAME")
}
.printSummaryLine <- function(group, group_desc,
N_rec_per_uqname, width2, width3)
{
N_rec <- sum(N_rec_per_uqname)
N_uqname <- length(N_rec_per_uqname)
if (N_uqname == 0L) {
mean_N_rec_per_uqname <- max_N_rec_per_uqname <- NA
} else {
mean_N_rec_per_uqname <- mean(N_rec_per_uqname)
max_N_rec_per_uqname <- max(N_rec_per_uqname)
}
cat(group_desc, " ", group,
" |", format(N_rec, width=width2),
" |", format(N_uqname, width=width3),
" | ", format(mean_N_rec_per_uqname, digits=3L, width=4L),
" / ", max_N_rec_per_uqname,
"\n", sep="")
}
.printMainSummary <- function(N_rec_per_uqname,
N_1seg_rec_per_uqname,
N_mseg_rec_per_uqname,
N_first_rec_per_uqname,
N_last_rec_per_uqname,
N_other_rec_per_uqname)
{
GROUP2DESC <- c(
A="All records........................",
S=" o template has single segment....",
M=" o template has multiple segments.",
F=" - first segment..............",
L=" - last segment...............",
O=" - other segment.............."
)
width1 <- nchar(GROUP2DESC[1L]) + 2L
width2 <- width3 <- 9L
.printSummaryHeader(width1, width2, width3)
.printSummaryLine("A", GROUP2DESC[["A"]],
N_rec_per_uqname, width2, width3)
.printSummaryLine("S", GROUP2DESC[["S"]],
N_1seg_rec_per_uqname, width2, width3)
.printSummaryLine("M", GROUP2DESC[["M"]],
N_mseg_rec_per_uqname, width2, width3)
.printSummaryLine("F", GROUP2DESC[["F"]],
N_first_rec_per_uqname, width2, width3)
.printSummaryLine("L", GROUP2DESC[["L"]],
N_last_rec_per_uqname, width2, width3)
.printSummaryLine("O", GROUP2DESC[["O"]],
N_other_rec_per_uqname, width2, width3)
cat("\nNote that (S, M) is a partitioning of A, and (F, L, O) ",
"is a partitioning of M.\n", "Indentation reflects this.\n", sep="")
}
.printDetailedSummary <- function(group,
N_mapped_rec_per_uqname,
N_primary_rec_per_uqname,
N_secondary_rec_per_uqname,
N_unmapped_rec_per_uqname)
{
SUBGROUP2DESC <- c(
`1`=" o record is mapped..............",
`2`=" - primary alignment.........",
`3`=" - secondary alignment.......",
`4`=" o record is unmapped............"
)
## width1 <- nchar(SUBGROUP2DESC[1L]) + 3L
width2 <- width3 <- 9L
cat("\nDetails for group ", group, ":\n", sep="")
#.printSummaryHeader(width1, width2, width3)
.printSummaryLine(paste0(group, "1"), SUBGROUP2DESC[["1"]],
N_mapped_rec_per_uqname, width2, width3)
.printSummaryLine(paste0(group, "2"), SUBGROUP2DESC[["2"]],
N_primary_rec_per_uqname, width2, width3)
.printSummaryLine(paste0(group, "3"), SUBGROUP2DESC[["3"]],
N_secondary_rec_per_uqname, width2, width3)
.printSummaryLine(paste0(group, "4"), SUBGROUP2DESC[["4"]],
N_unmapped_rec_per_uqname, width2, width3)
}
.detailedSummary <- function(group, qnameid, flag)
{
## 'N_mapped_rec_per_uqname' and 'N_unmapped_rec_per_uqname':
rec_is_unmapped <- as.logical(bamFlagAsBitMatrix(flag, "isUnmappedQuery"))
rec_is_mapped <- !rec_is_unmapped
N_mapped_rec_per_uqname <- .runlen(qnameid[rec_is_mapped])
N_unmapped_rec_per_uqname <- .runlen(qnameid[rec_is_unmapped])
## 'N_primary_rec_per_uqname' and 'N_secondary_rec_per_uqname':
rec_is_secondary <- as.logical(bamFlagAsBitMatrix(flag,
"isSecondaryAlignment"))
## The notion of primary/secondary alignment only applies to mapped
## seqments:
stopifnot(!any(rec_is_secondary & rec_is_unmapped))
rec_is_primary <- rec_is_mapped & !rec_is_secondary
N_primary_rec_per_uqname <- .runlen(qnameid[rec_is_primary])
N_secondary_rec_per_uqname <- .runlen(qnameid[rec_is_secondary])
.printDetailedSummary(group,
N_mapped_rec_per_uqname,
N_primary_rec_per_uqname,
N_secondary_rec_per_uqname,
N_unmapped_rec_per_uqname)
}
setMethod(quickBamFlagSummary, "list",
function(file, ..., param=ScanBamParam(), main.groups.only=FALSE)
{
what0 <- c("qname", "flag")
if (!isTRUEorFALSE(main.groups.only)) {
stop("'main.groups.only' must be TRUE or FALSE")
} else if (!all(what0 %in% names(file))) {
stop("'file' must contain elements ",
paste(sQuote(what0), collapse=" "))
}
## Order records by QNAME.
qname0 <- file[["qname"]]
flag0 <- file[["flag"]]
qnameid0 <- match(qname0, qname0) # assign unique id to each unique QNAME
oo <- order(qnameid0)
qnameid <- qnameid0[oo]
flag <- flag0[oo]
## 'N_rec_per_uqname':
N_rec_per_uqname <- .runlen(qnameid)
## 'N_mseg_rec_per_uqname' and 'N_1seg_rec_per_uqname':
rec_is_mseg <- as.logical(bamFlagAsBitMatrix(flag, "isPaired"))
rec_is_1seg <- !rec_is_mseg
N_1seg_rec_per_uqname <- .runlen(qnameid[rec_is_1seg])
N_mseg_rec_per_uqname <- .runlen(qnameid[rec_is_mseg])
stopifnot(identical(length(N_1seg_rec_per_uqname) +
length(N_mseg_rec_per_uqname),
length(N_rec_per_uqname)))
## 'N_first_rec_per_uqname' and 'N_last_rec_per_uqname' and
## 'N_other_rec_per_uqname':
is_first_mate <- as.logical(bamFlagAsBitMatrix(flag, "isFirstMateRead"))
is_second_mate <- as.logical(bamFlagAsBitMatrix(flag, "isSecondMateRead"))
rec_is_first <- rec_is_mseg & is_first_mate & !is_second_mate
rec_is_last <- rec_is_mseg & is_second_mate & !is_first_mate
rec_is_other <- rec_is_mseg & (is_first_mate == is_second_mate)
N_first_rec_per_uqname <- .runlen(qnameid[rec_is_first])
N_last_rec_per_uqname <- .runlen(qnameid[rec_is_last])
N_other_rec_per_uqname <- .runlen(qnameid[rec_is_other])
stopifnot(identical(sum(N_first_rec_per_uqname) +
sum(N_last_rec_per_uqname) +
sum(N_other_rec_per_uqname),
sum(N_mseg_rec_per_uqname)))
.printMainSummary(N_rec_per_uqname,
N_1seg_rec_per_uqname,
N_mseg_rec_per_uqname,
N_first_rec_per_uqname,
N_last_rec_per_uqname,
N_other_rec_per_uqname)
if (main.groups.only)
return(invisible(NULL))
if (length(N_1seg_rec_per_uqname) != 0L &&
length(N_mseg_rec_per_uqname != 0L))
.detailedSummary("A", qnameid, flag)
if (length(N_1seg_rec_per_uqname) != 0L)
.detailedSummary("S", qnameid[rec_is_1seg], flag[rec_is_1seg])
if (length(N_mseg_rec_per_uqname) != 0L)
.detailedSummary("M", qnameid[rec_is_mseg], flag[rec_is_mseg])
if (length(N_first_rec_per_uqname) != 0L)
.detailedSummary("F", qnameid[rec_is_first], flag[rec_is_first])
if (length(N_last_rec_per_uqname) != 0L)
.detailedSummary("L", qnameid[rec_is_last], flag[rec_is_last])
if (length(N_other_rec_per_uqname) != 0L)
.detailedSummary("O", qnameid[rec_is_other], flag[rec_is_other])
invisible(NULL)
})
setMethod(quickBamFlagSummary, "character",
function(file, index=file, ..., param=ScanBamParam(),
main.groups.only=FALSE)
{
file <- BamFile(index)
quickBamFlagSummary(file, param=param, main.groups.only=main.groups.only)
})
### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
### Old stuff.
###
quickCountBam <- function(file, ..., param=ScanBamParam(),
mainGroupsOnly=FALSE)
{
.Deprecated("quickBamFlagSummary", "Rsamtools")
if (is.null(param))
param <- ScanBamParam()
file <- BamFile(file, ...)
quickBamFlagSummary(file, param=param, main.groups.only=mainGroupsOnly)
}
quickBamCounts <- function(file, index=file, param=NULL,
main.groups.only=FALSE)
{
.Defunct("quickBamFlagSummary", "Rsamtools")
}
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