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…odles Coordinate-math correctness pass driven by a differential test against bladerunner, aimed at letting bladerunner link bedpull as a library. - Fix boundary-coincidence bug in get_read_cuts: a read whose alignment began/ended exactly at a region boundary was mis-sliced or silently dropped (BAM/CRAM path). Replace the `start > 0` sentinel with an explicit found_start flag + op-entry guard; the op-level `== ref_end` shortcut no longer skips a mid-op ref_start crossing. - get_read_cuts now takes align_end (exclusive) and clamps its fire-on boundaries to the alignment span internally, so partial reads return a real slice instead of a read_end == 0 sentinel. - ReadCuts gains softclip_lead_start / softclip_trail_end, making its layout field-identical to bladerunner's ReadCuts. - Simplify resolve_cuts: spanning is decided by align coverage, not by un-swapping sentinel fields. Real-data BAM/CRAM tests unchanged (40 spanning / 44 partial). - Bump noodles 0.110 -> 0.111 to match bladerunner across the boundary. - Add regression battery for the boundary cases and soft-clip fields; update CHANGELOG and version.
…odles Coordinate-math correctness pass driven by a differential test against bladerunner, aimed at letting bladerunner link bedpull as a library. - Fix boundary-coincidence bug in get_read_cuts: a read whose alignment began/ended exactly at a region boundary was mis-sliced or silently dropped (BAM/CRAM path). Replace the `start > 0` sentinel with an explicit found_start flag + op-entry guard; the op-level `== ref_end` shortcut no longer skips a mid-op ref_start crossing. - get_read_cuts now takes align_end (exclusive) and clamps its fire-on boundaries to the alignment span internally, so partial reads return a real slice instead of a read_end == 0 sentinel. - ReadCuts gains softclip_lead_start / softclip_trail_end, making its layout field-identical to bladerunner's ReadCuts. - Simplify resolve_cuts: spanning is decided by align coverage, not by un-swapping sentinel fields. Real-data BAM/CRAM tests unchanged (40 spanning / 44 partial). - Bump noodles 0.110 -> 0.111 to match bladerunner across the boundary. - Add regression battery for the boundary cases and soft-clip fields; update CHANGELOG and version.
get_bam_reads/get_cram_reads returned ref_start/ref_end in the 1-based CIGAR-walk frame, but the |missing_left/right header suffix compares them against 0-based BED coordinates — so every fully-spanning read was mislabelled missing_left=1bp. Normalise the returned coordinates to 0-based at the reads-layer boundary (lengths unchanged, so the partial coverage check is unaffected). Pre-existing since v0.2.0; only the header text was wrong, never the extracted sequence. Add an end-to-end regression test via the read_bed (+1-shifted) path.
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[0.3.0] — 2026-07-21
Coordinate-math correctness pass, driven by a differential test against
bladerunner and aimed at letting bladerunner link
bedpullas a library.Fixed
Boundary-coincidence bug in
get_read_cuts— a read whose alignment began (or ended)exactly at a region boundary was mis-sliced or silently dropped. The
start > 0sentinelconflated "start not found yet" with "start found at read offset 0". Replaced with an explicit
found_startflag plus an op-entry guard, and the op-level== ref_endshortcut no longerskips a mid-op
ref_startcrossing. This affected BAM/CRAM extraction (the PAF path alreadyrouted around it via
read_pos_at_ref).Spurious
missing_left=1bpon fully-spanning BAM/CRAM reads —get_bam_reads/get_cram_readsreturnedref_start/ref_endin the 1-based CIGAR-walk frame while theheader suffix compared them against 0-based BED coordinates, so every spanning read was
mislabelled as missing 1bp on the left. The returned coordinates are now normalised to
0-based (a pre-existing bug, also present in v0.2.0; extraction/sequences were never affected).
Changed
get_read_cutssignature is nowget_read_cuts(cigar_ops, align_start, align_end, region_start, region_end). It takes thealignment end and clamps its fire-on boundaries to the alignment span internally
(
ref_start = max(region_start, align_start),ref_end = min(region_end, align_end)), so apartially-overlapping read yields a real slice instead of a
read_end == 0sentinel.region_start/region_endare the desired (flank-expanded) window; the caller no longerpre-clamps.
align_endis exclusive (one past the last reference base) — callers usingnoodles' inclusive
alignment_end()must add 1.ReadCutsgainssoftclip_lead_startandsoftclip_trail_end(read offsets of theleading/trailing soft-clip runs; equal to
read_start/read_endwhen no extension isavailable). Layout is now field-identical to bladerunner's
ReadCuts.0.110→0.111to match bladerunner across the crate boundary.Added