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docs(derive/junction_annotation): be more clear in results docs
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a-frantz committed Dec 27, 2023
1 parent 390dc1f commit 3a7051f
Showing 1 changed file with 22 additions and 9 deletions.
31 changes: 22 additions & 9 deletions src/derive/junction_annotation/results.rs
Original file line number Diff line number Diff line change
Expand Up @@ -101,7 +101,10 @@ pub struct SummaryResults {
/// The total number of junctions observed in the file.
pub total_junctions: usize,

/// The total number of spliced reads observed in the file.
/// The total number of splices detected observed in the file.
/// More than one splice can be observed per read, especially
/// with long read data, so this number is not necessarily equal
/// to the number of spliced reads. It may be greater.
pub total_junctions_read_support: usize,

/// The average number of spliced reads supporting a junction.
Expand All @@ -120,17 +123,27 @@ pub struct SummaryResults {
/// annotations were not found.
pub unannotated_reference_junctions: usize,

/// The total number of known spliced reads observed in the file.
/// The number of reads supporting known junctions.
/// If a read supports more than one known junction, it is counted more than once.
/// A read with more one junction may also contribute to the support of
/// partially novel or completely novel junctions.
pub known_junctions_read_support: usize,

/// The total number of partially novel spliced reads observed in the file.
/// The number of reads supporting partially novel junctions.
/// If a read supports more than one partially novel junction, it is counted more than once.
/// A read with more one junction may also contribute to the support of
/// known or completely novel junctions.
pub partial_novel_junctions_read_support: usize,

/// The total number of complete novel spliced reads observed in the file.
/// The number of reads supporting completely novel junctions.
/// If a read supports more than one completely novel junction, it is counted more than once.
/// A read with more one junction may also contribute to the support of
/// known or partially novel junctions.
pub complete_novel_junctions_read_support: usize,

/// The total number of spliced reads on reference sequences for which
/// The number of reads supporting junctions on reference sequences for which
/// junction annotations were not found.
/// If a read supports more than one junction, it is counted more than once.
pub unannotated_reference_junctions_read_support: usize,

/// The percentage of junctions that are known.
Expand Down Expand Up @@ -160,17 +173,17 @@ pub struct SummaryResults {
/// The total number of junctions that have been rejected because
/// they failed the min_read_support or the min_intron_length filter.
/// A junction can be rejected for both reasons, so do not expect this
/// number to be equal to the sum of `junctions_with_not_enough_read_support`
/// and `intron_too_short`.
/// number to be equal to the sum of junctions_with_not_enough_read_support
/// and intron_too_short.
pub total_rejected_junctions: usize,

/// The total number of junctions which were discarded due to lack of
/// read support. This is not mutually exclusive with `intron_too_short`.
/// read support. This is not mutually exclusive with intron_too_short.
pub junctions_with_not_enough_read_support: usize,

/// The number of junctions that have been ignored because
/// they failed the min_intron_length filter.
/// This is not mutually exclusive with `junctions_with_not_enough_read_support`.
/// This is not mutually exclusive with junctions_with_not_enough_read_support.
pub intron_too_short: usize,
}

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