R: bamAlign

bamAlign {rbamtools} | R Documentation

## bamAlign

### Description

The function takes data stored in aling-fields and creates a `bamAlign` object, which can be stored in a BAM file via bamWriter.

### Usage

    bamAlign(qname,qseq,qqual,cigar,refid,position,flag=272L,alqual=10L,
                       mrefid=(-1L),mpos=(-1L),insertsize=0L)

### Arguments

`qname` | Query name, e.g. "HWUSI..." for Illumina sequences.

`qseq` | Query sequence (DNA-sequence)

`qqual` | Query quality (ASCII coded quality values). Must contain same number of characters as qseq

`cigar` | CIGAR string. Must be in valid format, e.g. 45M100N56N. Sequence length must match encoded items in CIGAR string.

`refid` | Integer. 0-based index which must have a counterpart in Reference Sequence Dictionary (otherwise samtools crashed when creating a BAM-index file).

`position` | `integer`: Genomic start position of alignment.

`flag` | `integer`: Contains information about binary stored flags in align.

`alqual` | `integer`: Alignment quality.

`mrefid` | `integer`: Mate refid. Used for paired end reads.

`mpos` | `integer`: Mate position. Used for paired end reads.

`insertsize` | `integer`.

### Value

bamGapList

### Author(s)

Wolfgang Kaisers

### Examples

    # Create alignment object from scratch
    align<-bamAlign("HWUSI-0001", "ATGTACGTCG", "Qual/Strng", "4M10N6M",
                refid=0, position=100)

    # Print and access data
    align
    name(align)
    alignSeq(align)
    alignQual(align)
    cigarData(align)
    refID(align)
    position(align)

[Package rbamtools version 2.16.17 Index]