diff --git a/docs/fasten_repair/index.html b/docs/fasten_repair/index.html index 48fac48c..99404126 100644 --- a/docs/fasten_repair/index.html +++ b/docs/fasten_repair/index.html @@ -18,22 +18,21 @@

Usage

Methods of repair

+ panic when the first issue comes up. Default:repair

Methods of repair

Repair mode

If you choose --mode repair, then this is the expected behavior

-

Panic

-

If the sequences are not repaired but there is still an issue, the program might still panic:

+

Panic mode

Functions

main
repair_one_read

Repair exactly one read

diff --git a/docs/settings.html b/docs/settings.html index 3b331eb3..a6263ec3 100644 --- a/docs/settings.html +++ b/docs/settings.html @@ -1,5 +1,5 @@ Rustdoc settings -

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Use system theme
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\ No newline at end of file diff --git a/docs/src/fasten_repair/fasten_repair.rs.html b/docs/src/fasten_repair/fasten_repair.rs.html index 4ded83c9..8d2da6df 100644 --- a/docs/src/fasten_repair/fasten_repair.rs.html +++ b/docs/src/fasten_repair/fasten_repair.rs.html @@ -347,22 +347,22 @@ //! //! # Methods of repair //! +//! # Repair mode +//! //! If you choose `--mode repair`, then this is the expected behavior //! //! * Mismatched seq and qual lengths: seq or qual length will be truncated //! * R1 or R2 not passing: then the other (R1 or R2) will also not pass and they will not be //! printed. //! -//! # Panic -//! -//! If the sequences are not repaired but there is still an issue, the program might still panic: +//! # Panic mode //! -//! * seq length < min length (TODO when implementing PE reads) -//! * avg qual < min qual (TODO when implementing PE reads) -//! * invalid characters in seq (TODO when implementing PE reads) -//! * invalid characters in qual (TODO when implementing PE reads) -//! * `@` not present in first character of the entry (TODO when implementing PE reads) -//! * `+` not present in the first character of the third line (TODO when implementing PE reads) +//! * seq length < min length +//! * avg qual < min qual +//! * invalid characters in seq +//! * invalid characters in qual +//! * `@` not present in first character of the entry +//! * `+` not present in the first character of the third line //! extern crate getopts;