Annotate bed overlaps to fix #1806#1808
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adamnovak merged 6 commits intovgteam:masterfrom Aug 3, 2018
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Jenkins vg tests never ran (Check the logs for setup or build errors) for PR 1808. View the full report here. |
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Jenkins vg tests never ran (Check the logs for setup or build errors) for PR 1808. View the full report here. |
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Jenkins vg tests complete for PR 1808. View the full report here. 19 tests passed, 0 tests failed and 10 tests skipped in 20025 seconds Tests produced 2790 warnings. 2790 were for lower-than-expected alignment scores |
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This should fix #1806 by allowing you to use
vg annotate -x graph.xg -b features.bed -g reads.gamto annotate reads with the BED feature names that they overlap. The annotation is "features", accessible with jq as.annotation.features, and is string-vector-valued. BED records with no name get the empty string as their feature name. Multiple BED records with the same name appear only once in the annotation.This is designed for large-ish, sparse-ish features spanning many nodes; it won't perform well with many small features on a single node, because within a node I am using a linear scan to find overlaps.