From 5c4be5cffbddead9fbdd723b7142877ba3cecad2 Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Mon, 11 May 2020 11:56:07 +0200
Subject: [PATCH] set neff value when generating sub-profile
---
modules/seq/base/doc/seq.rst | 3 ++-
modules/seq/base/src/profile_handle.cc | 1 +
2 files changed, 3 insertions(+), 1 deletion(-)
diff --git a/modules/seq/base/doc/seq.rst b/modules/seq/base/doc/seq.rst
index dec35ea21..e210687d1 100644
--- a/modules/seq/base/doc/seq.rst
+++ b/modules/seq/base/doc/seq.rst
@@ -755,7 +755,8 @@ probabilities between Match, Insertion or Deletion states or neff values
:type to: :class:`int`
:returns: sub-profile as defined by given indices
- (:attr:`null_model` is copied)
+ (:attr:`null_model` and :attr:`neff` are copied,
+ you might want to manually reset neff)
:rtype: :class:`ProfileHandle`
:raises: :exc:`~exceptions.Error` if *to* <= *from* or
diff --git a/modules/seq/base/src/profile_handle.cc b/modules/seq/base/src/profile_handle.cc
index 8a4582620..80b456583 100644
--- a/modules/seq/base/src/profile_handle.cc
+++ b/modules/seq/base/src/profile_handle.cc
@@ -149,6 +149,7 @@ ProfileHandlePtr ProfileHandle::Extract(uint from, uint to) const {
// get subset to return
ProfileHandlePtr return_prof(new ProfileHandle);
return_prof->SetNullModel(null_model_);
+ return_prof->SetNeff(neff_);
for (uint i = from; i < to; ++i) {
return_prof->AddColumn(columns_[i], seq_[i]);
}
--
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