BamInput {Rsamtools} | R Documentation

## Import, count, index, filter, sort, and merge ‘BAM’ (binary alignment) files.

### Description

Import binary ‘BAM’ files into a list structure, with facilities for selecting what fields and which records are imported, and other operations to manipulate BAM files.

### Usage

    scanBam(file, index=file, ..., param=ScanBamParam(what=scanBamWhat()))

    countBam(file, index=file, ..., param=ScanBamParam())

    idxstatsBam(file, index=file, ...)

    scanBamHeader(files, ...)
    ## S4 method for signature 'character'
    scanBamHeader(files, ...)

    asBam(file, destination=sub("\\.sam(\\.gz)?", "", file), ...)
    ## S4 method for signature 'character'
    asBam(file, destination=sub("\\.sam(\\.gz)?", "", file),
        ..., overwrite=FALSE, indexDestination=TRUE)

    asSam(file, destination=sub("\\.bam", "", file), ...)
    ## S4 method for signature 'character'
    asSam(file, destination=sub("\\.bam", "", file),
        ..., overwrite=FALSE)

    filterBam(file, destination, index=file, ...)
    ## S4 method for signature 'character'
    filterBam(file, destination, index=file, ...,
        filter=FilterRules(), indexDestination=TRUE,
        param=ScanBamParam(what=scanBamWhat()))

    sortBam(file, destination, ...)
    ## S4 method for signature 'character'
    sortBam(file, destination, ..., byQname=FALSE, maxMemory=512)

    indexBam(files, ...)
    ## S4 method for signature 'character'
    indexBam(files, ...)

    mergeBam(files, destination, ...)
    ## S4 method for signature 'character'
    mergeBam(files, destination, ..., region = GRanges(),
        overwrite = FALSE, header = character(), byQname = FALSE,
        addRG = FALSE, compressLevel1 = FALSE, indexDestination = FALSE)

### Arguments

`file` | The character(1) file name of the ‘BAM’ ('SAM' for `asBam`) file to be processed.
`files` | The character() file names of the ‘BAM’ file to be processed. For `mergeBam`, must satisfy `length(files) >= 2`.
`index` | The character(1) name of the index file of the 'BAM' file being processed; this is given without the '.bai' extension.
`destination` | The character(1) file name of the location where the sorted, filtered, or merged output file will be created. For `asBam` `asSam`, and `sortBam` this is without the “.bam” file suffix.
`region` | A GRanges() instance with `<= 1` elements, specifying the region of the BAM files to merged.
`...` | Additional arguments, passed to methods.
`overwrite` | A logical(1) indicating whether the destination can be over-written if it already exists.
`filter` | A `FilterRules` instance allowing users to filter BAM files based on arbitrary criteria, as described below.
`indexDestination` | A logical(1) indicating whether the created destination file should also be indexed.
`byQname` | A logical(1) indicating whether the sorted destination file should be sorted by Query-name (TRUE) or by mapping position (FALSE).
`header` | A character(1) file path for the header information to be used in the merged BAM file.
`addRG` | A logical(1) indicating whether the file name should be used as RG (read group) tag in the merged BAM file.
`compressLevel1` | A logical(1) indicating whether the merged BAM file should be compressed to zip level 1.
`maxMemory` | A numerical(1) indicating the maximal amount of memory (in MB) that the function is allowed to use.
`param` | An instance of `ScanBamParam`. This influences what fields and which records are imported.

### Details

The `scanBam` function parses binary BAM files; text SAM files can be parsed using R's `scan` function, especially with arguments `what` to control the fields that are parsed.

`countBam` returns a count of records consistent with `param`.

`idxstatsBam` visit the index in `index(file)`, and quickly returns the number of mapped and unmapped reads on each seqname.

`scanBamHeader` visits the header information in a BAM file, returning for each file a list containing elements `targets` and `text`, as described below. The SAM / BAM specification does not require that the content of the header be consistent with the content of the file, e.g., more targets may be present that are represented by reads in the file. An optional character vector argument containing one or two elements of `what=c("targets", "text")` can be used to specify which elements of the header are returned.

`asBam` converts 'SAM' files to 'BAM' files, equivalent to `samtools view -Sb file > destination`. The 'BAM' file is sorted and an index created on the destination (with extension '.bai') when `indexDestination=TRUE`.

`asSam` converts 'BAM' files to 'SAM' files, equivalent to `samtools view file > destination`.

`filterBam` parses records in `file`. Records satisfying the `bamWhich` `bamFlag` and `bamSimpleCigar` criteria of `param` are accumulated to a default of `yieldSize = 1000000` records (change this by specifying `yieldSize` when creating a `BamFile` instance; see `BamFile-class`). These records are then parsed to a `DataFrame` and made available for further filtering by user-supplied `FilterRules`. Functions in the `FilterRules` instance should expect a single `DataFrame` argument representing all information specified by `param`. Each function must return a `logical` vector equal to the number of rows of the `DataFrame`. Return values are used to include (when `TRUE`) corresponding records in the filtered BAM file. The BAM file is created at `destination`. An index file is created on the destination when `indexDestination=TRUE`. It is more space- and time-efficient to filter using `bamWhich`, `bamFlag`, and `bamSimpleCigar`, if appropriate, than to supply `FilterRules`. `filter` may be a list of `FilterRules` instances, in which case `destination` must be a character vector of equal length. The original `file` is then separately filtered into `destination[[i]]`, using `filter[[i]]` as the filter criterion.

`sortBam` sorts the BAM file given as its first argument, analogous to the “samtools sort” function.

`indexBam` creates an index for each BAM file specified, analogous to the ‘samtools index’ function.

`mergeBam` merges 2 or more sorted BAM files. As with samtools, the RG (read group) dictionary in the header of the BAM files is not reconstructed.

Details of the `ScanBamParam` class are provide on its help page; several salient points are reiterated here. `ScanBamParam` can contain a field `what`, specifying the components of the BAM records to be returned. Valid values of `what` are available with `scanBamWhat`. `ScanBamParam` can contain an argument `which` that specifies a subset of reads to return. This requires that the BAM file be indexed, and that the file be named following samtools convention as `<bam_filename>.bai`. `ScanBamParam` can contain an argument `tag` to specify which tags will be extracted.

### Value

The `scanBam,character-method` returns a list of lists. The outer list groups results from each `IntegerRanges` list of `bamWhich(param)`; the outer list is of length one when `bamWhich(param)` has length 0. Each inner list contains elements named after `scanBamWhat()`; elements omitted from `bamWhat(param)` are removed. The content of non-null elements are as follows, taken from the description in the samtools API documentation:

- qname: This is the QNAME field in SAM Spec v1.4. The query name, i.e., identifier, associated with the read.

- flag: This is the FLAG field in SAM Spec v1.4. A numeric value summarizing details of the read. See `ScanBamParam` and the `flag` argument, and `scanBamFlag()`.

- rname: This is the RNAME field in SAM Spec v1.4. The name of the reference to which the read is aligned.

- strand: The strand to which the read is aligned.

- pos: This is the POS field in SAM Spec v1.4. The genomic coordinate at the start of the alignment. Coordinates are ‘left-most’, i.e., at the 3' end of a read on the '-' strand, and 1-based. The position excludes clipped nucleotides, even though soft-clipped nucleotides are included in `seq`.

- qwidth: The width of the query, as calculated from the `cigar` encoding; normally equal to the width of the query returned in `seq`.

- mapq: This is the MAPQ field in SAM Spec v1.4. The MAPping Quality.

- cigar: This is the CIGAR field in SAM Spec v1.4. The CIGAR string.

- mrnm: This is the RNEXT field in SAM Spec v1.4. The reference to which the mate (of a paired end or mate pair read) aligns.

- mpos: This is the PNEXT field in SAM Spec v1.4. The position to which the mate aligns.

- isize: This is the TLEN field in SAM Spec v1.4. Inferred insert size for paired end alignments.

- seq: This is the SEQ field in SAM Spec v1.4. The query sequence, in the 5' to 3' orientation. If aligned to the minus strand, it is the reverse complement of the original sequence.

- qual: This is the QUAL field in SAM Spec v1.4. Phred-encoded, phred-scaled base quality score, oriented as `seq`.

- groupid: This is an integer vector of unique group ids returned when `asMates=TRUE` in a BamFile object. `groupid` values are used to create the partitioning for a `GAlignmentsList` object.

- mate_status: Returned (always) when `asMates=TRUE` in a BamFile object. This is a factor indicating status (`mated`, `ambiguous`, `unmated`) of each record.

`idxstatsBam` returns a `data.frame` with columns `seqnames`, `seqlength`, `mapped` (number of mapped reads on `seqnames`) and `unmapped` (number of unmapped reads).

`scanBamHeader` returns a list, with one element for each file named in `files`. The list contains two element. The `targets` element contains target (reference) sequence lengths. The `text` element is itself a list with each element a list corresponding to tags (e.g., ‘@SQ’) found in the header, and the associated tag values.

`asBam`, `asSam` return the file name of the destination file.

`sortBam` returns the file name of the sorted file.

`indexBam` returns the file name of the index file created.

`filterBam` returns the file name of the destination file created.

### Author(s)

Martin Morgan <mtmorgan@fhcrc.org>. Thomas Unterhiner <thomas.unterthiner@students.jku.at> (`sortBam`).

### References

http://samtools.sourceforge.net/

### See Also

`ScanBamParam`, `scanBamWhat`, `scanBamFlag`

### Examples

    fl <- system.file("extdata", "ex1.bam", package="Rsamtools",
                      mustWork=TRUE)

    ##
    ## scanBam
    ##

    res0 <- scanBam(fl)[[1]] # always list-of-lists
    names(res0)
    length(res0[["qname"]])
    lapply(res0, head, 3)
    table(width(res0[["seq"]])) # query widths
    table(res0[["qwidth"]], useNA="always") # query widths derived from cigar
    table(res0[["cigar"]], useNA="always")
    table(res0[["strand"]], useNA="always")
    table(res0[["flag"]], useNA="always")

    which <- IRangesList(seq1=IRanges(1000, 2000),
                         seq2=IRanges(c(100, 1000), c(1000, 2000)))
    p1 <- ScanBamParam(which=which, what=scanBamWhat())
    res1 <- scanBam(fl, param=p1)
    names(res1)
    names(res1[[2]])

    p2 <- ScanBamParam(what=c("rname", "strand", "pos", "qwidth"))
    res2 <- scanBam(fl, param=p2)

    p3 <- ScanBamParam(
        what="flag",           # information to query from BAM file
        flag=scanBamFlag(isMinusStrand=FALSE))
    length(scanBam(fl, param=p3)[[1]]$flag)

    ##
    ## idxstatsBam
    ##

    idxstatsBam(fl)

    ##
    ## filterBam
    ##

    param <- ScanBamParam(
       flag=scanBamFlag(isUnmappedQuery=FALSE),
       what="seq")
    dest <- filterBam(fl, tempfile(), param=param)
    countBam(dest)  ## 3271 records

    ## filter to a single file
    filter <- FilterRules(list(MinWidth = function(x) width(x$seq) > 35))
    dest <- filterBam(fl, tempfile(), param=param, filter=filter)
    countBam(dest)  ## 398 records
    res3 <- scanBam(dest, param=ScanBamParam(what="seq"))[[1]]
    table(width(res3$seq))

    ## filter 1 file to 2 destinations
    filters <- list(
        FilterRules(list(long=function(x) width(x$seq) > 35)),
        FilterRules(list(short=function(x) width(x$seq) <= 35))
    )
    destinations <- replicate(2, tempfile())
    dest <- filterBam(fl, destinations, param=param, filter=filters)
    lapply(dest, countBam)

    ##
    ## sortBam
    ##

    sorted <- sortBam(fl, tempfile())

    ##
    ## scanBamParam re-orders 'which'; recover original order
    ##

    gwhich <- as(which, "GRanges")[c(2, 1, 3)]    # example data
    cnt <- countBam(fl, param=ScanBamParam(which=gwhich))
    reorderIdx <- unlist(split(seq_along(gwhich), seqnames(gwhich)))
    cnt
    cnt[reorderIdx,]

[Package Rsamtools version 2.2.3 Index]