diff --git a/src/ChangeLog b/src/ChangeLog index e7e8acea..056b61bc 100644 --- a/src/ChangeLog +++ b/src/ChangeLog @@ -6,6 +6,7 @@ - Added option `--culling-overlap` to set the minimum overlap with a higher scoring hit for a hit to be deleted and changed the default value from 90% to 50%. - Added command `diamond test` to run a series of regression tests. +- Fixed an off-by-one error of the query end position in the XML output format. [0.9.30] - Added support for output field `cigar` to the tabular format. diff --git a/src/align/align.h b/src/align/align.h index aa26d7b8..5f26d8a2 100644 --- a/src/align/align.h +++ b/src/align/align.h @@ -67,18 +67,6 @@ struct Ring_buffer_sink void align_queries(Trace_pt_buffer &trace_pts, Consumer* output_file, const Parameters ¶ms, const Metadata &metadata); namespace ExtensionPipeline { - namespace Greedy { - struct Target; - struct Pipeline : public QueryMapper - { - Pipeline(const Parameters ¶ms, size_t query_id, Trace_pt_list::iterator begin, Trace_pt_list::iterator end, const Metadata &metadata) : - QueryMapper(params, query_id, begin, end, metadata) - {} - Target& target(size_t i); - virtual void run(Statistics &stat, const sequence *subjects = nullptr, size_t subject_count = 0); - virtual ~Pipeline() {} - }; - } namespace Swipe { struct Pipeline : public QueryMapper {