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feat: enable index resumption and enforce directory creation

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The command now supports reopening existing indexes instead of failing when the output file exists. Control flow branches between opening an existing index and constructing a new one, moving configuration setup exclusively to the creation path. Directory existence is enforced upfront with proper I/O error propagation. The --force flag retains its original semantics by removing the target directory before proceeding with a fresh build.
This commit is contained in:
Eric Coissac
2026-08-21 05:06:38 +02:00
parent abc51c2add
commit 5c1584967f
161 changed files with 5274 additions and 845 deletions
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DevDocMD/implementation/filtering.md
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@@ -303,7 +303,7 @@ This parameter has no effect on presence/absence indexes (where values are alrea
## Implementation
- **`obikpartition::filter::GroupQuorumFilter`** — implements `KmerFilter`
- **`obikindex::partition::filter::GroupQuorumFilter`** — implements `KmerFilter`
using pre-computed ingroup and outgroup index vectors. The heavy logic
(predicate parsing, three-value evaluation, genome classification) happens
once before any iteration; each k-mer row evaluation is a simple index
@@ -314,7 +314,7 @@ This parameter has no effect on presence/absence indexes (where values are alrea
`UnitigArgs`. `FilterArgs::build_filters()` returns a ready-to-use filter
list.
- **`obikpartition::KmerPartition::iter_partition_kmers`** — accepts
- **`obikindex::partition::KmerPartition::iter_partition_kmers`** — accepts
`filters: &[Box<dyn KmerFilter>]` and applies them per-kmer before invoking
the callback. `filter`, `dump`, and `unitig` all go through this single
entry point.