Commit f06cd9cc authored by Mathieu Giraud's avatar Mathieu Giraud

core/segment.{h,cpp}: gather comments in one place and be more explicit about 'evalue_threshold'

parent 535e4796
Pipeline #32762 canceled with stages
...@@ -830,19 +830,6 @@ bool comp_pair (pair<int,int> i,pair<int,int> j) ...@@ -830,19 +830,6 @@ bool comp_pair (pair<int,int> i,pair<int,int> j)
} }
/**
* Align a read against a collection of sequences, maximizing the alignment 'score'
* @param read: the read
* @param rep: a collection of reference sequences
* @param reverse_ref: if true, reverse the reference sequences (VkVk)
* @param reverse_both: if true, reverse both the read and the reference sequences (J segment)
* @param local: if true, Local alignment (D segment), otherwise LocalEndWithSomeDeletions and onlyBottomTriangle (V and J segments)
* @param box: the AligBox to fill
* @param segment_cost: the cost used by the dynamic programing
* @param banded_dp: should we perform a banded DP?
* @post box is filled
*/
void align_against_collection(string &read, BioReader &rep, int forbidden_rep_id, void align_against_collection(string &read, BioReader &rep, int forbidden_rep_id,
bool reverse_ref, bool reverse_both, bool local, bool reverse_ref, bool reverse_both, bool local,
AlignBox *box, Cost segment_cost, bool banded_dp, AlignBox *box, Cost segment_cost, bool banded_dp,
......
...@@ -395,10 +395,20 @@ class FineSegmenter : public Segmenter ...@@ -395,10 +395,20 @@ class FineSegmenter : public Segmenter
}; };
/** /**
* @param segment_cost: cost used * Align a read against a collection of sequences, maximizing the alignment 'score'
* @param read: the read
* @param rep: a collection of reference sequences
* @param reverse_ref: if true, reverse the reference sequences (VkVk)
* @param reverse_both: if true, reverse both the read and the reference sequences (J segment)
* @param local: if true, Local alignment (D segment), otherwise LocalEndWithSomeDeletions and onlyBottomTriangle (V and J segments)
* @param box: the AligBox to fill
* @param segment_cost: the cost used by the dynamic programing
* @param banded_dp: Should we use banded dynamic programming? * @param banded_dp: Should we use banded dynamic programming?
* @param evalue_threshold: threshold for randomly expected segmentation (evalue) * @param evalue_threshold: threshold for randomly expected segmentation (evalue) to relaunch a full DP without banded_dp
* @post box is filled
*/ */
void align_against_collection(string &read, BioReader &rep, int forbidden_rep_id, void align_against_collection(string &read, BioReader &rep, int forbidden_rep_id,
bool reverse_ref, bool reverse_both, bool local, bool reverse_ref, bool reverse_both, bool local,
......
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