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Selectable within alignment coordinate options for soft/hard clipped … #35

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60 changes: 44 additions & 16 deletions R/coordinate-mapping-methods.R
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Original file line number Diff line number Diff line change
Expand Up @@ -31,14 +31,20 @@ setGeneric("pmapFromAlignments", signature=c("x", "alignments"),
### mapToAlignments() and mapFromAlignments() methods
###

.mapFromAlignments <- function(x, alignments)
.mapFromAlignments <- function(x, alignments, style = "mapped")
{
if (!length(x) && !length(alignments))
return(GRanges(xHits=integer(), transcriptsHits=integer()))
if (is.null(xNames <- names(x)) ||
is.null(alignmentsNames <- names(alignments)))
stop ("both 'x' and 'alignments' must have names")

style <- switch(style,
mapped = 0,
sequence = 1,
readpos = 2,
stop(paste("specified unsupported style=", style)))

## name matching determines pairs
match0 <- match(alignmentsNames, alignmentsNames)
match1 <- match(xNames, alignmentsNames)
Expand All @@ -53,10 +59,10 @@ setGeneric("pmapFromAlignments", signature=c("x", "alignments"),
alignments <- alignments[alignmentsHits]
s <- .Call("query_locs_to_ref_locs",
start(x), cigar(alignments),
start(alignments), FALSE)
start(alignments), FALSE, style)
e <- .Call("query_locs_to_ref_locs",
end(x), cigar(alignments),
start(alignments), TRUE)
start(alignments), TRUE, style)
e <- pmax(e, s - 1L)

## remove non-hits
Expand All @@ -67,17 +73,23 @@ setGeneric("pmapFromAlignments", signature=c("x", "alignments"),
xHits=xHits[keep], alignmentsHits=alignmentsHits[keep])
}

.mapToAlignments <- function(x, alignments)
.mapToAlignments <- function(x, alignments, style = "sequence")
{
if (!length(x) && !length(alignments))
return(GRanges(xHits=integer(), transcriptsHits=integer()))
if (is.null(names(alignments)))
stop ("'alignments' must have names")

style <- switch(style,
mapped = 0,
sequence = 1,
readpos = 2,
stop(paste("specified unsupported style=", style)))

## map all possible pairs; returns hits only
map <- .Call("map_ref_locs_to_query_locs",
start(x), end(x), cigar(alignments),
start(alignments))
start(alignments), style)
xHits <- map[[3]]
alignmentsHits <- map[[4]]
if (length(xHits))
Expand All @@ -91,30 +103,46 @@ setGeneric("pmapFromAlignments", signature=c("x", "alignments"),

setMethod("mapToAlignments", c("IntegerRanges", "GAlignments"),
function(x, alignments, ...)
ranges(.mapToAlignments(x, alignments))
ranges(.mapToAlignments(x, alignments, ...))
)

setMethod("mapToAlignments", c("GenomicRanges", "GAlignments"),
function(x, alignments, ...)
.mapToAlignments(x, alignments)
.mapToAlignments(x, alignments, ...)
)

setMethod("mapFromAlignments", c("IntegerRanges", "GAlignments"),
function(x, alignments, ...)
ranges(.mapFromAlignments(x, alignments))
ranges(.mapFromAlignments(x, alignments, ...))
)

setMethod("mapFromAlignments", c("GenomicRanges", "GAlignments"),
function(x, alignments, ...)
.mapFromAlignments(x, alignments)
.mapFromAlignments(x, alignments, ...)
)

### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
### pmapToAlignments() and pmapFromAlignments() methods
###

.pmapAlignments <- function(x, alignments, reverse)
.pmapAlignments <- function(x, alignments, reverse, style = "default")
{
if (reverse) {
style <- switch(style,
default = 0,
mapped = 0,
sequence = 1,
readpos = 2,
stop(paste("specified unsupported style=", style)))
} else {
style <- switch(style,
default = 1,
mapped = 0,
sequence = 1,
readpos = 2,
stop(paste("specified unsupported style=", style)))
}

if (length(x) && length(alignments)) {
if (length(x) != length(alignments))
stop("'x' and 'alignments' must have the same length")
Expand All @@ -128,8 +156,8 @@ setMethod("mapFromAlignments", c("GenomicRanges", "GAlignments"),
FUN <- "ref_locs_to_query_locs"
seqname <- names(alignments)
}
s <- .Call(FUN, start(x), cigar(alignments), start(alignments), FALSE)
e <- .Call(FUN, end(x), cigar(alignments), start(alignments), TRUE)
s <- .Call(FUN, start(x), cigar(alignments), start(alignments), FALSE, style)
e <- .Call(FUN, end(x), cigar(alignments), start(alignments), TRUE, style)
e <- pmax(e, s - 1L)

## non-hits
Expand All @@ -146,20 +174,20 @@ setMethod("mapFromAlignments", c("GenomicRanges", "GAlignments"),

setMethod("pmapToAlignments", c("IntegerRanges", "GAlignments"),
function(x, alignments, ...)
ranges(.pmapAlignments(x, alignments, FALSE))
ranges(.pmapAlignments(x, alignments, FALSE, ...))
)

setMethod("pmapToAlignments", c("GenomicRanges", "GAlignments"),
function(x, alignments, ...)
.pmapAlignments(ranges(x), alignments, FALSE)
.pmapAlignments(ranges(x), alignments, FALSE, ...)
)

setMethod("pmapFromAlignments", c("IntegerRanges", "GAlignments"),
function(x, alignments, ...)
ranges(.pmapAlignments(x, alignments, TRUE))
ranges(.pmapAlignments(x, alignments, TRUE, ...))
)

setMethod("pmapFromAlignments", c("GenomicRanges", "GAlignments"),
function(x, alignments, ...)
.pmapAlignments(ranges(x), alignments, TRUE)
.pmapAlignments(ranges(x), alignments, TRUE, ...)
)
20 changes: 10 additions & 10 deletions inst/unitTests/test_coordinate-mapping-methods.R
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Original file line number Diff line number Diff line change
Expand Up @@ -109,17 +109,17 @@ test_ref_locs_to_query_locs <- function() {
ref <- 43425L + pos - 1L
query <- 238L
ans <- .Call("ref_locs_to_query_locs", ref, cigar, pos,
FALSE, PACKAGE="GenomicAlignments")
FALSE, 1, PACKAGE="GenomicAlignments")
checkIdentical(ans, query)

## out of bounds
ans_s <- .Call("ref_locs_to_query_locs",
start(x1[1]), cigar(align1[1]),
start(align1[1]), FALSE,
start(align1[1]), FALSE, 1,
PACKAGE="GenomicAlignments")
ans_e <- .Call("ref_locs_to_query_locs",
end(x1[1]), cigar(align1[1]),
start(align1[1]), TRUE,
start(align1[1]), TRUE, 1,
PACKAGE="GenomicAlignments")

checkIdentical(ans_s, NA_integer_)
Expand All @@ -130,11 +130,11 @@ test_query_locs_to_ref_locs <- function() {
## out of bounds
ans_s <- .Call("query_locs_to_ref_locs",
start(x1[4]), cigar(align1[1]),
start(align1[1]), FALSE,
start(align1[1]), FALSE, 1,
PACKAGE="GenomicAlignments")
ans_e <- .Call("query_locs_to_ref_locs",
end(x1[4]), cigar(align1[1]),
start(align1[1]), TRUE,
start(align1[1]), TRUE, 1,
PACKAGE="GenomicAlignments")

checkIdentical(ans_s, NA_integer_)
Expand All @@ -144,26 +144,26 @@ test_query_locs_to_ref_locs <- function() {
test_map_ref_locs_to_query_locs <- function() {
## hit
map <- .Call("map_ref_locs_to_query_locs",
12L, 16L, "11M", 10L)
12L, 16L, "11M", 10L, 1)
checkIdentical(unlist(map), c(3L, 7L, 1L, 1L))

## first record out of bounds
map <- .Call("map_ref_locs_to_query_locs",
c(5L, 12L), c(16L, 16L), "11M", 10L)
c(5L, 12L), c(16L, 16L), "11M", 10L, 1)
checkIdentical(unlist(map), c(3L, 7L, 2L, 1L))

## second record out of bounds
map <- .Call("map_ref_locs_to_query_locs",
c(12L, 5L), c(16L, 16L), "11M", 10L)
c(12L, 5L), c(16L, 16L), "11M", 10L, 1)
checkIdentical(unlist(map), c(3L, 7L, 1L, 1L))

## first alignment out of bounds
map <- .Call("map_ref_locs_to_query_locs",
12L, 16L, c("11M", "11M"), c(20L, 10L))
12L, 16L, c("11M", "11M"), c(20L, 10L), 1)
checkIdentical(unlist(map), c(3L, 7L, 1L, 2L))

## second alignment out of bounds
map <- .Call("map_ref_locs_to_query_locs",
12L, 16L, c("11M", "11M"), c(10L, 20L))
12L, 16L, c("11M", "11M"), c(10L, 20L), 1)
checkIdentical(unlist(map), c(3L, 7L, 1L, 1L))
}
12 changes: 8 additions & 4 deletions src/GenomicAlignments.h
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Expand Up @@ -66,28 +66,32 @@ SEXP map_query_locs_to_ref_locs(
SEXP start,
SEXP end,
SEXP cigar,
SEXP pos
SEXP pos,
SEXP style
);

SEXP map_ref_locs_to_query_locs(
SEXP start,
SEXP end,
SEXP cigar,
SEXP pos
SEXP pos,
SEXP style
);

SEXP ref_locs_to_query_locs(
SEXP ref_locs,
SEXP cigar,
SEXP pos,
SEXP narrow_left
SEXP narrow_left,
SEXP style
);

SEXP query_locs_to_ref_locs(
SEXP query_locs,
SEXP cigar,
SEXP pos,
SEXP narrow_left
SEXP narrow_left,
SEXP style
);


Expand Down
8 changes: 4 additions & 4 deletions src/R_init_GenomicAlignments.c
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Expand Up @@ -19,10 +19,10 @@ static const R_CallMethodDef callMethods[] = {
CALLMETHOD_DEF(cigar_qnarrow, 3),

/* mapping_methods.c */
CALLMETHOD_DEF(map_query_locs_to_ref_locs, 4),
CALLMETHOD_DEF(map_ref_locs_to_query_locs, 4),
CALLMETHOD_DEF(ref_locs_to_query_locs, 4),
CALLMETHOD_DEF(query_locs_to_ref_locs, 4),
CALLMETHOD_DEF(map_query_locs_to_ref_locs, 5),
CALLMETHOD_DEF(map_ref_locs_to_query_locs, 5),
CALLMETHOD_DEF(ref_locs_to_query_locs, 5),
CALLMETHOD_DEF(query_locs_to_ref_locs, 5),

/* encodeOverlaps_methods.c */
CALLMETHOD_DEF(encode_overlaps1, 10),
Expand Down
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