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b55908f
docs(design): add design document for graph merge command
mmolari Aug 10, 2026
57decee
fix(build): support building a graph from a single input sequence
mmolari Aug 10, 2026
bb7187a
Merge pull request #191 from neherlab/feat/merge-single-seq-build
mmolari Aug 10, 2026
59b48b1
feat(merge): add command to merge two pangenome graphs
mmolari Aug 10, 2026
82d126e
feat(build): reject duplicate genome names, shared with merge
mmolari Aug 10, 2026
2a599b1
refactor(merge): drop unreachable relabeling retry loop
mmolari Aug 10, 2026
5c9645f
refactor(pangraph): relabel graphs by value instead of in place
mmolari Aug 10, 2026
25b7ca1
refactor(pangraph): move sequence reconstruction into the graph module
mmolari Aug 10, 2026
844db45
feat(pangraph): add name-keyed sequence verification
mmolari Aug 10, 2026
8627366
fix(build): verify reconstructed sequences by genome name, not by index
mmolari Aug 10, 2026
db167ce
fix(reconstruct): match verification sequences by name
mmolari Aug 10, 2026
eea2d66
test: cover build --verify and name-keyed reconstruct verification
mmolari Aug 10, 2026
47e17de
docs(tutorial): add page on merging two graphs
mmolari Aug 14, 2026
92e3b89
docs: add changelog entries for the merge command
mmolari Aug 14, 2026
dc44757
docs(design): mark merge roadmap as complete
mmolari Aug 14, 2026
5b40fdd
docs: add PR references to changelog
mmolari Aug 14, 2026
1f9e8de
docs: remove merge design document
mmolari Aug 14, 2026
755acf7
test(merge): drop redundant sanity checks from the integration tests
mmolari Aug 14, 2026
cb83e23
fix(merge): vary the relabeling salt so repeated merges do not collide
mmolari Aug 14, 2026
2d77cce
fix(cli): keep non-alignment options out of the Alignment help section
mmolari Aug 14, 2026
e6bb9e9
refactor(merge): verify merged genomes one at a time
mmolari Aug 14, 2026
bad3c2b
docs: simplify changelog
mmolari Aug 14, 2026
cc30583
Merge pull request #196 from neherlab/feat/merge-fixes
mmolari Aug 14, 2026
4d51586
fix(pangraph): reject unnamed and duplicate genome names in merge and…
mmolari Aug 14, 2026
f03429c
perf(reconstruct): drop redundant re-sort of an already-ordered path map
mmolari Aug 14, 2026
0c79a24
refactor(reconstruct): drop redundant record reset before reading
mmolari Aug 14, 2026
daa927c
fix(reconstruct): elide long genome name lists in the verification error
mmolari Aug 14, 2026
81f79c8
fix(cli): make the Default impl agree with the clap default for outpu…
mmolari Aug 14, 2026
166ab57
fix(pangraph): report malformed graph ids instead of panicking during…
mmolari Aug 14, 2026
c654879
fix(cli): keep --jobs out of the Verbosity help section
mmolari Aug 14, 2026
774a08c
test(cli): pin the help section of every argument
mmolari Aug 14, 2026
e1f6dbc
docs: update changelog for merge and stricter genome id checks
mmolari Aug 14, 2026
8f5d2f8
fix(pangraph): reject empty genome and sequence names
mmolari Aug 14, 2026
348e51d
refactor(pangraph): derive block and node ids from genome names
mmolari Aug 17, 2026
e2a2622
docs(cli): simplify the help text of the merge input arguments
mmolari Aug 17, 2026
a1705ec
docs: fix broken documentation link in pangraph --help
mmolari Aug 18, 2026
2cfcc85
fix(pangraph): report malformed graphs on load instead of panicking
mmolari Aug 18, 2026
1924759
Merge branch 'feat/merge' into refactor/name-derived-ids
mmolari Aug 18, 2026
ea1f9fa
refactor(pangraph): require an explicit id in the node constructor
mmolari Aug 18, 2026
3c64030
docs: improve error message for identifier collisions in input graphs
mmolari Aug 18, 2026
7c6a770
fix(pangraph): reject genome names with leading or trailing whitespace
mmolari Aug 18, 2026
fa876df
style: use plain ascii punctuation in comments and docs
mmolari Aug 18, 2026
d00bf69
Merge pull request #199 from neherlab/refactor/name-derived-ids
mmolari Aug 18, 2026
51f99d7
refactor(pangraph): require an explicit id in the path constructor
mmolari Aug 18, 2026
330316d
refactor(pangraph): derive the genome seed in a single place
mmolari Aug 18, 2026
8dfb00f
perf(pangraph): renumber path ids without rebuilding the node map
mmolari Aug 18, 2026
c2ea5b5
refactor(pangraph): share the whitespace check between the name valid…
mmolari Aug 18, 2026
a201dc5
refactor(reconstruct): flatten path reconstruction with a let-else guard
mmolari Aug 18, 2026
5bce759
perf(pangraph): avoid cloning genome names for an error message
mmolari Aug 18, 2026
e12359b
test(pangraph): build the single-genome fixture with Pangraph::singleton
mmolari Aug 18, 2026
e4d98b7
perf(merge): drop the duplicate sanity check of the merged graph
mmolari Aug 18, 2026
04bd3c1
perf(align): align sequence pairs without materializing them first
mmolari Aug 18, 2026
a46fa46
test(merge): define read_and_split in terms of read_records
mmolari Aug 18, 2026
84e6f9f
docs: update changelog
mmolari Aug 19, 2026
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9 changes: 9 additions & 0 deletions CHANGELOG.md
Original file line number Diff line number Diff line change
@@ -1,3 +1,12 @@
## Unreleased

- added `pangraph merge` command, to combine two existing pangenome graphs into a single one, see #197.
- `pangraph build` now accepts a single input sequence.
- more strict checks on input sequence ids: duplicated or empty ids are now rejected. The `--verify` options compare the input sequences by id and not by order.
- more strict graph validation at loading.
- block and node identifiers are now derived from genome names instead of the order the input sequences are read in, enforcing order-independence.
- fixed a race condition in `pangraph build` that could produce slightly different graphs on repeated runs over the same input.

## 1.3.0

- added `--guide-tree` option to `pangraph build` command to allow users to provide a custom guide tree in Newick format, see #180.
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234 changes: 234 additions & 0 deletions docs/docs/assets/svgs/merge.svg
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