From 3a7051fddb8a6b5cb0a50ab59233e451b7d46136 Mon Sep 17 00:00:00 2001 From: Andrew Frantz Date: Wed, 27 Dec 2023 10:09:53 -0500 Subject: [PATCH] docs(derive/junction_annotation): be more clear in results docs --- src/derive/junction_annotation/results.rs | 31 ++++++++++++++++------- 1 file changed, 22 insertions(+), 9 deletions(-) diff --git a/src/derive/junction_annotation/results.rs b/src/derive/junction_annotation/results.rs index 6f7330b..b426d3b 100644 --- a/src/derive/junction_annotation/results.rs +++ b/src/derive/junction_annotation/results.rs @@ -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. @@ -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. @@ -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, }