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Fetch out edit
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adamnovak committed Aug 29, 2024
1 parent ad62378 commit 3bf557e
Showing 1 changed file with 1 addition and 0 deletions.
1 change: 1 addition & 0 deletions src/alignment.cpp
Original file line number Diff line number Diff line change
Expand Up @@ -2761,6 +2761,7 @@ Alignment target_alignment(const PathPositionHandleGraph* graph, const path_hand
size_t node_pos = pos1 - graph->get_position_of_step(step);
while (edit_idx < cigar_mapping.edit_size()) {
if (step == graph->path_end(path)) {
const auto& edit = cigar_mapping.edit(edit_idx);
if (edit.from_length() == 0 && aln.path().mapping_size() != 0) {
// This is a softclip off the end of the contig.
// We can add it to the last mapping as an edit
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vg CI tests complete for branch lr-giraffe. View the full report here.

0 tests passed, 16 tests failed and 0 tests skipped in 54 seconds

Failed tests:

  • test_sim_chr21_snp1kg (0 seconds)
  • test_full_brca2_cactus (4 seconds)
  • test_full_brca2_primary (3 seconds)
  • test_full_brca2_snp1kg (3 seconds)
  • test_map_brca1_cactus (3 seconds)
  • test_map_brca1_primary (3 seconds)
  • test_map_brca1_snp1kg (3 seconds)
  • test_map_brca1_snp1kg_mpmap (3 seconds)
  • test_map_mhc_primary (3 seconds)
  • test_map_mhc_snp1kg (3 seconds)
  • test_sim_mhc_cactus (0 seconds)
  • test_sim_mhc_snp1kg (0 seconds)
  • test_sim_mhc_snp1kg_mpmap (0 seconds)
  • test_call_chr21_snp1kg (4 seconds)
  • test_sim_chr21_snp1kg_trained (0 seconds)
  • test_sim_yeast_cactus (0 seconds)

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