object FindSwitchbackReads

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  1. case class ReadBasedHit(offset: Int, length: Int, read: Option[SamRecord] = None) extends SwitchHit with Product with Serializable

    Information about a switchback found by looking at soft-clipped complementary sequence within a single read.

    Information about a switchback found by looking at soft-clipped complementary sequence within a single read.

    offset

    the offset between the reference position at the last base read on the original strand and the first base read on the opposite strand.

    length

    the length of the post-switch sequence within the read

    read

    optionally the read in which the hit was found (generally filled in later)

  2. sealed trait SwitchHit extends AnyRef

    Parent trait for the different kinds of hits we can find.

  3. case class SwitchMetric(sample: String, library: String, templates: Count, aligned_templates: Count, switchback_templates: Count, fraction_switchbacks: Proportion, read_based_switchbacks: Count, mean_length: Double, mean_offset: Double, tandem_based_switchbacks: Count, mean_gap: Double) extends Metric with Product with Serializable

    Summary metrics regarding switchback reads found.

    Summary metrics regarding switchback reads found.

    sample

    the name of the sample sequenced.

    library

    the name of the library sequenced.

    templates

    the total number of templates (i.e. inserts, unique read names) seen in the input.

    aligned_templates

    the number of templates that had at least one aligned read.

    switchback_templates

    the number of templates identified as having a switchback event.

    fraction_switchbacks

    the fraction of all templates that appear to have switchbacks in them.

    read_based_switchbacks

    the count of switchback_templates that were identified by looking for soft-clipped reverse complementary sequence at the ends of reads.

    mean_length

    the mean length of the reverse complementary sequence in the read_based_switchbacks.

    mean_offset

    the mean offset of the read_based_switchbacks.

    tandem_based_switchbacks

    the count of switchback_templates that were identified because they had paired reads mapped in FF or RR orientations within the designated gap size range.

    mean_gap

    the mean gap size for tandem_based_switchbacks

  4. case class TandemBasedHit(gap: Int) extends SwitchHit with Product with Serializable

    Information about a switchback found by examining a template with a tandem (i.e.

    Information about a switchback found by examining a template with a tandem (i.e. FF or RR) pair orientation. The offset in this case is the distance between the end of one read and the beginning of the next. E.g.

    01234567890123456789 -----> -----> gap = 2 <----- <----- gap = 1 -----> ------> gap = -2

    gap

    the unsequenced gap between the the 3' end of the "earlier" read and the 5' end of the "later" read.

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  4. val SwitchTag: String

    The name of the BAM extended attribute tag used to store switchback information.

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  10. def find(query: String, target: String, maxErrorRate: Double, preferLaterMatches: Boolean): Option[ReadBasedHit]

    Attempts to find the first ungapped match of the query sequence within the target sequence.

    Attempts to find the first ungapped match of the query sequence within the target sequence. "First" is either from the start of the target sequence, or if preferLaterMatches is true, from the end of the target sequence.

    query

    the query sequence to be found

    target

    the target sequence in which the query sequence is to be located

    maxErrorRate

    the maximum rate of mismatches allowed when matching the sequences

    preferLaterMatches

    if true prefer matches closer to the end of targetSequence, else prefer matches closer to the start

    returns

    a ReadBasedHit if a match is found, otherwise None.

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