Commit 57be3d55 authored by Mathieu Giraud's avatar Mathieu Giraud

core/segment.cpp: comments 'align_against_collection'

parent bfc3aac3
......@@ -580,6 +580,23 @@ bool comp_pair (pair<int,int> i,pair<int,int> j)
return ( i.first > j.first);
* 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_both: if true, reverse both the read and the reference sequences (J segment)
* @param local: if true, Local alignment (D segment), otherwise LocalEndWithSomeDeletions (V and J segments)
* @param segment_cost: the cost used by the dynamic programing
* @return score: the maximized score, together with the following values:
* @return tag: - the name of the sequence
* @return del: - the number of deletions at the end of the reference sequence (or at the start if 'reverse_both')
* @return del2: - the number of deletions at the start of the reference sequence (used with 'local')
* @return begin: - the start position of the aligned segment in the read
* @return length: - the length of the alignmed segment in the read
* @return best_best_i: ?
int align_against_collection(string &read, Fasta &rep, bool reverse_both, bool local, int *tag,
int *del, int *del2, int *begin, int *length, vector<pair<int, int> > *score
, Cost segment_cost)
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