[cudamapper] Add anchor chain output functions to chainer_utils.cuh. #590
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Adds two functions required for retrieving the anchors within an overlap.
…t calculation to output_overlap_chains_by_backtrace.
edawson
requested review from
tijyojwad and
mimaric
and removed request for
tijyojwad
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This adds the functions needed to generate the anchor chains from a list of overlaps, assuming the overlap list has not been previously filtered (though masking using the select_mask is permissible). |
… However, tests fail because the allocator used in testing can't actually allocate memory.
cudamapper/src/chainer_utils.cuh
Outdated
| /// \param start The first anchor in the chain. | ||
| /// \param end The last anchor in the chain. | ||
| /// \param num_anchors The total number of anchors in the chain. | ||
| __host__ __device__ Overlap create_simple_overlap(const Anchor& start, |
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This function is only called by backtrace_anchors_to_overlaps(). I understand that it cannot be in an anonymous namespace in order be able to call it form unittest, but it could be moved to details namespace in order to signal the users that they do not have to think about it
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I think creating an overlap from two anchors and a number of residues is useful and could be a user-facing API function, but the function could be better named.
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I agree. That's why I was suggesting moving it closed to Overlap's definition: #590 (comment)
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I see. I've renamed it to create_overlap in c72e5c9.
…meworks into anchor-backtrace-io
…e) and fix docs issues brought up in review.
… when instantiating device arrays.
… to process backtraced overlaps.
- Use thrust transform_reduce and transform_exclusive_scan (rather than make_transform iterator) whe> - Constify pointers where possible. - Remove unnecessary includes. - Tweak docs for backtrace_anchors_to_overlap
Primarily, this adds a number of tests for output_overlap_chains_by_RLE, output_overlap_chains_by_backtrace, and backtrace_anchors_to_overlaps. It also fixes a bug where the last anchor position in a chain was not returned from backtrace_anchors_to_overlaps, causing faulty output when later extracting anchor chains.
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rerun tests |
| /// \param unrolled_anchor_chains An array of int32_t. Will be resided on return. | ||
| /// \param anchor_chain_starts An array holding the index in the anchors array of the first | ||
| /// anchor in an overlap. | ||
| /// \param num_overlaps The number of overlaps in the overlaps array. |
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num_overlaps does not exist anymore
| ASSERT_EQ(overlaps_d.size(), 3); | ||
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| ASSERT_EQ(overlaps[0].num_residues_, 1); | ||
| ASSERT_EQ(overlaps[0].target_read_id_, UINT32_MAX); |
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Better use std::numeric_limits<decltype(overlaps[0].target_read_id_)>::max()
https://en.cppreference.com/w/cpp/types/numeric_limits
| #include <algorithm> | ||
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| #ifndef NDEBUG |
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Why is algorithm needed in release mode as well?
| /// Launch configuration: any number of blocks/threads, no dynamic shared memory, cuda_stream must be the same in which anchors/overlaps/scores/mask/predecessors/chains/starts were allocated. | ||
| /// example: backtrace_anchors_to_overlaps<<<2048, 32, 0, cuda_stream>>>(...) |
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Further descriptions should be placed between \brief and \param
| void allocate_anchor_chains(const device_buffer<Overlap>& overlaps, | ||
| device_buffer<int32_t>& unrolled_anchor_chains, | ||
| device_buffer<int32_t>& anchor_chain_starts, | ||
| int64_t& num_total_anchors, |
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Is this necessary? I see it's used to set the size of unrolled_anchor_chains
…meworks into anchor-backtrace-io
Adds the necessary functions for outputting the chains of anchors that represent an overlap.