From a1d9948d104e3bec2801066b8169114c8d713295 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bertrand=20N=C3=A9ron?= Date: Fri, 15 Dec 2023 13:11:20 +0100 Subject: [PATCH] :pencil2: improve what's new documentation --- doc/source/user_guide/new_v2.rst | 22 +++++++++++++++++++--- 1 file changed, 19 insertions(+), 3 deletions(-) diff --git a/doc/source/user_guide/new_v2.rst b/doc/source/user_guide/new_v2.rst index 18936f96..a6b1e2cd 100644 --- a/doc/source/user_guide/new_v2.rst +++ b/doc/source/user_guide/new_v2.rst @@ -12,20 +12,36 @@ What's new in MacSyFinder v2? ***************************** -======= -V 2.1.2 -======= +====== +master +====== + +Features +======== +Support of *gziped* files +------------------------- + +MSF can also read *.gz* compressed files both for hmm profiles and sequences in fasta. +It will uncompress them on the fly. +The compressed files must end with the *.gz* extension. +For the `hmmsearch` step You need to have `gunzip` installed on your system for this to work. + +search engine +------------- A group of hits that respect the distance constraints but each hit represent the same gene on the model, is **not** considered as a *cluster*. A group of hits that respect the distance constraints but all hits represent a Neutral gene in model, is **not** considered as a *cluster*. +timeout improvement +------------------- If a replicon is skipped due to timeout during best_solution phase. The results corresponding to this replicon are not produced, but a warning indicating that msf skip this replicon appear in outputs. + ======= V 2.1.1 =======