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| Description |
This module provides a data type to represent an alignment
produced by the Bowtie short-read alignment tool (see
http://bowtie-bio.sourceforge.net/index.shtml).
The simple accessors recapitulate the details of the Bowtie alignment
output. The position of the alignment is given by the "0-based offset
into the reference sequence where leftmost character of the alignment
occurs". Thus, for forward-strand alignments this is the 5' end of
the query sequence while for reverse-complement alignments this is the
3' end of the query sequence. Similarly, the query sequence and query
quality are shown in reference forward strand orientation, and thus
may be reverse complemented.
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| Synopsis |
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| Data type and basic accessors
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| Constructors | | Align | | | name :: !SeqName | Name of the query sequence
| | strand :: !Strand | Strand of the alignment on the reference sequence
| | refname :: !SeqName | Name of the reference sequence
| | leftoffset :: !Offset | Zero-based offset of the left-most aligned position in the reference
| | sequ :: !SeqData | Query sequence, in the reference forward strand orientation
| | qual :: !QualData | Query quality, in the reference forward strand orientation
| | mismatches :: ![Mismatch] | Mismatches
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|  Instances | |
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| Representation of a single mismatch in a bowtie alignment
| | Constructors | | Mismatch | | | mmoffset :: !Offset | Offset of the mismatch site from the 5' end of the query
| | refbase :: !Char | Reference nucleotide
| | readbase :: !Char | Query nucleotide
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| | Instances | |
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| Returns the length of the query sequence
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| Returns the number of mismatches in the alignment
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| Query sequence as given in the query file
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| Query quality as given in the query file
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| Sequence positions of alignments
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| As refCSeqLoc but without the reference sequence name.
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| Returns the sequence location covered by the query in
the alignment. This will be a sequence location on the reference
sequence and may run on the forward or the reverse complement
strand.
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| Returns the sequence location covered by the query, as
refCSeqLoc, as a SeqLoc location.
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| Returns the sequence position of the start of the query sequence
alignment. This will include the strand of the alignment and will
not be the same as the position computed from leftoffset when the
alignment is on the reverse complement strand.
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| Sequence position of a mismatch on the reference sequence.
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| Parsing Bowtie output
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| Parses a line of Bowtie output to produce a Align
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| Other utilities
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Returns true when two alignments were derived from the same
sequencing read. As Bowtie writes alignments of query sequences in
their order in the query file, all alignments of a given read are
grouped together and the lists of all alignments for each read can
be gathered with
groupBy sameRead
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| Produced by Haddock version 2.6.1 |
