v0.3.3

What's Changed

• Enable building impg with GNU Guix by @fredmanglis in #114
• Recover/msa work by @maxgmarin in #115
• Add impg refine command by @AndreaGuarracino in #117
• Fix bgzip-compressed PAF files without their indexes by @AndreaGuarracino in #118
• Support more alignment files in input by @AndreaGuarracino in #119

New Contributors

• @fredmanglis made their first contribution in #114
• @maxgmarin made their first contribution in #115

Full Changelog: v0.3.2...v0.3.3

v0.3.2

What's Changed

• impg lace: support both GFA and VCF lacing by @AndreaGuarracino in #100
• impg lace: faster path range length validation while lacing GFA files by @AndreaGuarracino in #101
• Refactor a bit the interface by @AndreaGuarracino in #102
• Stop early if gzi indexes are missing for bgzip-compressed PAF files by @AndreaGuarracino in #103
• Progress bar during PCA by @AndreaGuarracino in #104
• Better input/output compressed formats support by @AndreaGuarracino in #105
• Include gap-compressed and block identities to BEDPE output by @AndreaGuarracino in #106
• Add progress bar for GFA writing in impg lace by @AndreaGuarracino in #107
• Initialize threads ASAP to avoid ThreadPoolBuildError { kind: GlobalPoolAlreadyInitialized } by @AndreaGuarracino in #109
• impq query/similarity --subset-sequence-list by @AndreaGuarracino in #110
• Add help headings to command-line arguments by @AndreaGuarracino in #111
• Make GZI files optional when the input PAF file is bgzip-compressed by @AndreaGuarracino in #112
• Add fasta+paf output format and -O output basename option to impg query by @adamnovak in #113

New Contributors

• @adamnovak made their first contribution in #113

Full Changelog: v0.3.1...v0.3.2

v0.3.1

What's Changed

• More logging during partition writing by @AndreaGuarracino in #93
• Sort sequences by length before POA by @AndreaGuarracino in #94
• feat: add merge distance validation in region size check by @AndreaGuarracino in #95
• impq query: add --original-sequence-coordinates flag to get coordinates w.r.t. the original sequences by @AndreaGuarracino in #96
• Manage sequence length in PAF output when --original-sequence-coordinates are requested by @AndreaGuarracino in #97
• impg partition: emit a single BED file by default by @AndreaGuarracino in #98
• Add impg lace command by @AndreaGuarracino in #99

Full Changelog: v0.3.0...v0.3.1

v0.3.0

What's Changed

• impg query: Add merge logic for all output formats by @AndreaGuarracino in #63
• Merge same consecutive CIGAR operations while merging intervals by @AndreaGuarracino in #68
• impg query and impg partition: filter by (gap-compressed) identity by @AndreaGuarracino in #69
• impq query: reduce memory usage with BED format output by @AndreaGuarracino in #70
• Deterministic IMPG index by @AndreaGuarracino in #72
• Add the impg index command by @AndreaGuarracino in #73
• Update dependencies, including noodles and bincode by @AndreaGuarracino in #75
• impg partition: add option to make BFS transitive queries by @AndreaGuarracino in #76
• Breadth-First Search transitive queries by default by @AndreaGuarracino in #77
• impq query and impg partition: Add GFA (v1.0) and MAF formats by @AndreaGuarracino in #71
• Add impg similarity by @AndreaGuarracino in #78
• impg similarity --pca: TSV output by @AndreaGuarracino in #79
• impg similarity: polarize pca by @AndreaGuarracino in #80
• add error handling for missing FASTA files in GFA/MAF output format by @AndreaGuarracino in #81
• impg query and impg partition: add support for FASTA output format by @AndreaGuarracino in #82
• A little bit smaller and simpler impg index and better error handling by @AndreaGuarracino in #83
• Avoid problems with substitution pipe -b <(grep patter x.bed) by @AndreaGuarracino in #84
• Fix IMPG index regression by @AndreaGuarracino in #85
• Avoid panic! during PCA computation and cleaning by @AndreaGuarracino in #86
• impg partition: add --output-folder option by @AndreaGuarracino in #87
• impg similarity: emit 1/0 similarity/distance with perfect matches by @AndreaGuarracino in #88
• Emit the range as the output name if the name is missing from the input range by @AndreaGuarracino in #89
• Add a forest map to enable lazy tree loading by @AndreaGuarracino in #90
• Reduce code for maintainability and input range validation by @AndreaGuarracino in #92
• agc integration by @ekg in #91

New Contributors

• @ekg made their first contribution in #91

Full Changelog: v0.2.4...v0.3.0

v0.2.4

What's Changed

• Performance tweaks in coordinate projection by @AndreaGuarracino in #39
• Add max_depth parameter to impg query and impg partition to limit recursion depth by @AndreaGuarracino in #40
• impg query/partition: Add min_interval_size parameter for transitive queries by @AndreaGuarracino in #41
• impg query/partition: Add min_distance_between_ranges parameter for transitive queries by @AndreaGuarracino in #42
• impg partition: avoid too short chunks by @AndreaGuarracino in #43
• max_depth as u16 to reduce memory usage by @AndreaGuarracino in #44
• Do not store CIGAR strings during partitioning by @AndreaGuarracino in #45
• fix visited_range initialization by @AndreaGuarracino in #46
• Cigar parsing speedup by @bkille in #47
• Avoids the overhead of the .then() closure by @AndreaGuarracino in #49
• impg partition: reduce fragmentation and fix missing sequences by @AndreaGuarracino in #50
• impg stats: emit more statistics by @AndreaGuarracino in #51
• impg partition: fix duplicated sequences, no padding by default, fix tail-window merging, reduce fragmentaton by @AndreaGuarracino in #52
• impg partition: Conditional scientific notation in the log by @AndreaGuarracino in #53
• impg partition: Filter input range too in query_transitive by @AndreaGuarracino in #54
• Faster impg partition by @AndreaGuarracino in #55
• impg partition: fix --selection-mode haplotype/sample by @AndreaGuarracino in #56
• Parallel query_transitive and little impg partition optimizations by @AndreaGuarracino in #57
• fmt and update by @AndreaGuarracino in #58
• Multiple PAF files as input + -o/--output-format + Reduce index size by @AndreaGuarracino in #59
• Lower memory usage during IMPG index creation by @AndreaGuarracino in #60
• Parallelization and a bit less memory usage by @AndreaGuarracino in #61
• impg query: Add merge logic for BED output by @AndreaGuarracino in #62
• Lower memory usage during IMPG index creationg by @AndreaGuarracino in #64
• impg query: Consider orientation while BED merging by @AndreaGuarracino in #65

Full Changelog: v0.2.3...v0.2.4

v0.2.3

What's Changed

• Do not manage strandness in bedtools operations for pangenome partitioning by @AndreaGuarracino in #31
• Avoid too short intervals in the partitions by @AndreaGuarracino in #32
• Introduce commands (impg query and impg stats) by @AndreaGuarracino in #33
• fix query transitive: correct range insertion by handling start and end values by @AndreaGuarracino in #35
• Add impg partition command by @AndreaGuarracino in #34
• Fix target id in PAF and BEDPE outputs by @AndreaGuarracino in #36
• Fix empty target ranges, refactoring and performance tweaks by @AndreaGuarracino in #37
• Merge overlapping/contiguous ranges to visit in query_transitive to strongly improve performance by @AndreaGuarracino in #38

Full Changelog: v0.2.2...v0.2.3

v0.2.2

What's Changed

• Fix condition for query_transitive by @AndreaGuarracino in #25
• avoid duplicates in query_transitive by @AndreaGuarracino in #26
• Fix BED format strandness by @AndreaGuarracino in #27
• do not explore the same ranges multiple times in query_transitive by @AndreaGuarracino in #28
• Pangenome partitioning by @AndreaGuarracino in #29
• Fix query_range length calculation so that it works for reversed queries too by @AndreaGuarracino in #30

Full Changelog: v0.2.1...v0.2.2

v0.2.1

What's Changed

• add bioconda badge by @AndreaGuarracino in #8
• Manage ranges in extracted sequences (subsequences) by @AndreaGuarracino in #13
• Ensure that target end <= target length by @AndreaGuarracino in #14
• Compare paf index timestamps by @bkille in #16
• Fix seq_index by @AndreaGuarracino in #20
• Add (updated) gap-compressed-identity and block-identity to PAF output by @AndreaGuarracino in #21
• Drop self range in PAF/BEDPE output by @AndreaGuarracino in #22
• Fix invalid results in output by @AndreaGuarracino in #23
• do not push wrong ranges in the stack by @AndreaGuarracino in #24

Full Changelog: v0.2.0...v0.2.1

v0.2.0

What's Changed

• Store cigar offsets in lightweight index by @bkille in #1
• Add bed input, bedpe output, and paf output by @AndreaGuarracino in #3
• manage 'NAME' column in BED, BEDPE and PAF, 'M' CIGAR operation, GitHub workflow, strandness by @AndreaGuarracino in #4
• Remove path from index by @bkille in #7
• Adjust also target ranges and make valid outputs by @AndreaGuarracino in #6

New Contributors

• @bkille made their first contribution in #1
• @AndreaGuarracino made their first contribution in #3

Full Changelog: https://github.com/pangenome/impg/commits/v0.2.0