Support outputting alignments in GAF format #384
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karasikov
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Feb 7, 2022
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karasikov
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Please add integration / unit tests.
| md_string += std::to_string(match_count); | ||
| match_count = 0; | ||
| } | ||
| md_string += std::string(ref_it, ref_it + num); |
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string_view would be enough. Why do you create a new string?
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| for (size_t i = 0; i < paths.size(); ++i) { | ||
| const auto &path = paths[i]; |
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| for (size_t i = 0; i < paths.size(); ++i) { | |
| const auto &path = paths[i]; | |
| for (const auto &path : paths) { |
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I had it set up this way because a bug in GCC-8 was causing the compilation to crash because of this kind of for-loop. Let's see if it happens this time.
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This format reports the node IDs of alignment paths.
See "The Graph Alignment Format (GAF)" and "Sequence Alignment/Map Optional Fields Specification"