CHANGES.md

Change logs

[v0.2.5] - 2025-01-26

Enhancement

• rename, use g1, g2, g3 ... to rename duplicates chromosomes, when --unphased specified.

[v0.2.4] - 2025-01-25

Enhancement

• pairs2depth, speed up by pipeline
• alleles, add --trim-length to trim the both end of contigs to remove the effect of overlapping from hifiasm assembly graph.
• pipeline
  • --preset precision: Optimize parameters to improve accuracy at the expense of anchor rate
  • --preset sensitive: Using in some complex genome, which contain many fragmented contigs and low signals contigs

Bug fixes

• activate_cphasing, fixed bug that exit shell window when pixi failed to install
• pipeline
  • fixed bug that program can not exit when error occurred
  • fixed bug that alleles parameters cannot affect in phasing mode
  • fixed bug that reported in issue #14, which --chimeric-correct mode cannot use correct fasta in 3.hyperpartition
• plot, fixed bug that program can not coarsen adjusted matrix to plot another binsize matrix

[v0.2.3] - 2025-01-14

Enhancement

• pipeline, report peak memory usage
• hyperpartition
  • add --min-cis-weight=5.0 to remove low contacts contigs
  • increase --min-contacts to 25.0 to remove low contacts contigs

Bug fixes

• pairs2cool, fixed bug that "bin1_id > bin2_id" in some cases

[v0.2.2] - 2025-01-10

Enhancement

• pipeline, When mode=phasing, pipeline integrating 1.alleles into 3.hyperpartition to speed up

Bug fixes

• prepare, fixed bug of "got unexpected keyword argument has_header'

[v0.2.1] - 2025-01-07

Enhancement

• hypergraph, add hcr_bed filter step.
• hyperpartition, speed up the phasing mode
• activate_cphasing, use pixi to activate the environment of CPhasing
• pairs2cool, speed up it at the expense of memory consumption
• plot, speed up it

Bug fixes

• alleles, a cheat method to fix bug of partig can not parse contig > 130 Mb
• rename, bug of read agp
• pipeline
  • input hic with _1 or _2 suffix can not load successful
  • input hic can not find fastq path in output dir

[v0.2.0] - 2024-10-1

Enhancement

• pipeline
  • change the normalization method of the hic pipeline
  • change pipeline output directories
• hyperpartition, improve the performance of cluster merge

Bug fixes

• plot, fixed bug of split contigs

[v0.1.9] - 2024-07-09

New features

• collapsed-rescue, init a collapsed contigs rescue function

Enhancement

• higig
  • support for hifi data. Moreover, support for junk and collapsed identification
  • correct-alignments, increase performance by filtering low quality LIS
• pairs2cool, add min_mapq filtering
• plot, add triangle plot
• scaffolding, speed up split clm by cphasing-rs splitclm
• alleles, speed up

Bug fixes

• pipeline
  • fixed bug of contacts generating
  • fixed bug of the corrected.agp not output when chimeric correct mode
• scaffolding, fixed bug of countre extract not found contigs
• hcr_from_contacts, find error peak in low coverage regions

[v0.1.8] - 2024-05-15

Enhancement

• hypergraph, Extractor, add mapq to hypergraph
• remove_misassembly, add remove_misassembly of error between homologous chromosome

Bug fixes

• plot, fixed bug of resolution not in filename

[v0.1.7] - 2024-05-11

Enhancement

• hypergraph, speed up data loading
• scaffolding, speed up clm loadding

[v0.1.6] - 2024-05-07

Enhancement

• hcr_by_contacts, remove whole collapsed contigs
• stat_porec_table, reduce memory usage

Bug fixes

• scaffolding, length db not load contig that RE count < 3
• simulate_collapse, fixed bug of contig position in collapsed contigs

[v0.1.5] - 2024-04-29

Enhancement

• environment, add pigz
• hic mapper, add "remove pcr duplicates" as default parameters

[v0.1.4] - 2024-04-23

Enhancement

• colorful the help text
• hcr, use kde peaks
• pipeline, use

[v0.1.3] - 2024-04-22

New features

• _chromap, add a modified chromap

Enhancement

• hypergraph, reduce memory usage

[v0.1.2] - 2024-04-18

Enhancement

• scaffolding, optimized
• cphasing-rs pairs2clm, speed up

[v0.1.1] - 2024-04-11

New features

• hitig
  • scaffolding, which enable to scaffolding by ultra-long reads.

Enhancement

• plot, speed up
• alleles, remove filter function
• hypergraph, speed up by porec table load.

[v0.1.0] - 2024-04-07

New features

• alleles2, a method for allelic contig identification by self mapping
• cphasing-rs prune, a method to prune by raw allele table (ALLHiC allele table)

Enhancement

• scaffolding, increase the performance of long contigs

Bug fixes

• plot, fixed bug that it can not be used in pandas v2.0

[v0.0.64] - 2024-03-11

Bug fixes

• hyperpartition, fixed the inconsistent of phasing results, when specified alleletable and prunetable
• alleles, filterring by valid kmer length of contigs

[v0.0.62] - 2024-02-18

New features

• cphasing-rs kprune, increase the recall of cross-allelic

[v0.0.61] - 2024-01-19

New features

• plot_high_order_distribution.py, plot the contact order distribution of pore-c alignments

Enhancement

• scaffolding, adopt the HapHiC_sort to scaffolding, and add HaplotypeAlign
• partig, change d to 0.1
• AlleleTable, add strand column to the format of allele2
• Tour, add to_dict, backup, save

[v0.0.60]

Enhancement

• hyperpartition, add prune based on hypergraph
• hyperpartition, add different n setting
• pipeline, remove single kprune, change it to hypergraph prune

[v0.0.59]

Enhancement

• hyperpartition, add automatic search resolution
• kprune, update the formulate of normalization

[v0.0.58]

Enhancement

• mapper, add restriction site filter and realign
• hyperpartition, new mode by phasing
• hyperpartition, support import pore-c table or pairs
• HyperEdges, add contigsizes, mapq

[v0.0.57]

Enhancement

• pipeline, add hcr
• hcr, optimized

[v0.0.56]

Enhancement

• cphasing-rs, update pairs-intersect and porec-intersect
• kprune, remove count_re argument

[v0.0.55]

New features

• hcr_from_contacts, add new function of hcr
• plot_lines, plot lines of evaluation

[v0.0.54]

Bug fixes

• pipeline, fixed bugs

[v0.0.53]

New features

• pipeline, add a pipeline of C-Phasing

Enhancement

• prepare, restruct
• pairs2cool, move to second command

[v0.0.52]

Enhancement

• kprune, load data into tempfile to decrease the memory usage.

##[v0.0.51]

• 2023-11-11

New features

• agp, add pseudo-agp, create a pseudo agp from simulation contigs

Bug fixed

• hyperpartition, add cross_allelic_factor

##[v0.0.50]

• 2023-11-10

Enhancement

• kprune, add multiprocessing

##[v0.0.49]

• 2023-11-10

Enhancement

• cphasing-rs, update it into v0.0.10

New features

• porec2csv, import porec table into pao csv
• PoreCTable.binnify, binnify the contig by binsize
• PoreCTable.divide_contig_by_nparts, divide contig by the number of parts

Bug fixed

• hyperpartition, fixed bug that phasing mode report error when the prune table not apply

[v0.0.48]

• 2023-11-05

Enhancement

• kprune, advanced it to identity more cross-allelic

New features

• evaluate_prune.py, evaluate the result of kprune
• methalign/pipe, init the pipeline of methalign

[v0.0.47]

• 2023-10-15

Enhancement

• higig, mv ontig to hitig.

[v0.0.46]

Enhancement

• hcr, add break_pos to correct hcr by break positions

Bug fixed

• mapper, fixed min_quality can not be adopt

[v0.0.45]

Enhancement

• hcr, intergated bed2depth into hcr

Bug fixed

• bed2depth, fixed bug

[v0.0.44]

Enhancement

• ontig, restruct the framework and add split-reads, find-chimeric, hcr three functions.

[v0.0.43] - 2023-09-24

New features

• methalign, init

Enhancement

• rename ultra_long to ontig

[v0.0.42] - 2023-09-22

Enhancement

• ultra_long, expose ultra_long tutorial to C-Phasing README.md

[v0.0.41] - 2023-08-25

Bug fixed

• scaffolding, fixed cp groups.agp error when change the name of agp

[v0.0.40]

• 2023-08-19

Enhancement

• add pyproject.toml

Bug fixed

• setup.py, fixed the setup_helper error.

[v0.0.39]

Enhancement

• before this version cphasing-rs can not found

[v0.0.38]

• 2023-08-18

Bug fixed

• build, fixed bug that can not specify the output of agp
• scaffolding, fixed bug that can not specify the output of agp

[v0.0.37]

• 2023-08-16

Enhancement

• README.md, add detail describtions
• scaffolding, directly output groups.agp

Bug fixed

• fixed bug that resulted some misassembly from v0.0.17

[v0.0.36]

• 2023-08-14

Bug fixed

• hyperpartition
  • fixed bug from v0.0.35 that default run ultra-complex mode
  • fixed bug that whitelist can not used in single partition
• recluster
  • fixed bug of KeyError

[v0.0.35]

• 2023-08-12

Enhancement

• pairs2cool, add --fofn parameter
• hyperpartition, mask ultra-complex parameter

[v0.0.34]

• 2023-08-11

Enhancement

• mapper, compress hic mapper result
• hyperpartition, add contig filter when import first cluster result
• 2023-08-04

Bug fixed

• hypergraph, fixed the column index error

[v0.0.32]

• 2023-08-04

Bug fixed

• hypergraph, fixed it can not parse single porec table

[v0.0.31]

• 2023-08-02

New features

• ultra_long, add v1 pipeline

[v0.0.30]

• 2023-08-02

Enhancement

• hypergraph, speed up

Bug fixed

• porec-intersection, fixed it can not output result

[v0.0.29]

• 2023-07-31

Bug fixed

• hyperpartition, fixed key word of edges not yet change to hypergraph

[v0.0.28]

• 2023-07-29

New features

• collapse, create a collapse rescued contact matrix

Enhancement

• update environment.yml
• update cphasing-rs, which reduce the size of binary and update to v0.0.4

Bug fixed

• scaffolding, fixed path error

[v0.0.27]

• 2023-07-14

Enhancement

• remove check_allhic_version

[v0.0.26]

• 2023-07-12

New features

• statcluster, stat the clustertable
• plot_hist, plot the distribution of somethings

Enhancement

• hypergraph, add prune allelic hyperedges
• statagp, change agpstat to statagp
• change extract to hypergraph
• change optimize to scaffolding
• hyperpartition, out "Chr??g?" as chromosome name

Bug fixed

• hyprpartition, not add -pt or at, the -inc not work

[v0.0.25]

• 2023-07-05

New features

• evalutate_known_assembly.py, evalutate the simulated human genome
• cis_trans_by_contigs.py, calculate the cis and trans contacts by pairs
• logo, add logo

Enhancement

• hyperpartition, automatic using the exists first clusters results

[v0.0.24]

• 2023-06-20

New features

• ultra_long, init ultra_long method

Enhancement

• mapper, add outprefix prameter

[v0.0.23]

• 2023-06-17

New features

• pictures, add the heatmap of M1

Enhancement

• hyperpartition, expose --min-allelic-overlap
• kprune, add sort and normalize function

[v0.0.22]

• 2023-06-16

New features

• tmpoptimze, a temp function for order and orientation
• PoreCMapper, based on minimap2 and cphasing-rs

Enhancement

• plot, add --no-ticks to remove ticks from picture

[v0.0.21]

• 2023-06-12

Enhancement

• hyperpartition
  • change zero-allelic to allelic-factor
  • add merge_cluster
  • init ultra_complex

Bug fixed

• plot, enable factor can set to 1

[v0.0.20]

• 2023-06-07

Enhancement

• AlleleTable, load info
• PartigRecord, output allele table with additional information

New features

• AlleleInfo, object function of allele table information

Bug fixed

• HyperPartition, fixed bug of prunt -> prunetable

[v0.0.19]

• 2023-06-06

Enhancement

• KPruneHyperGraph, speed up
• HyperPartition, add the get_prunetable_KPrune

[v0.0.18]

• 2023-06-06

Enhancement

• hyperpartition
  • min_weight, add a parameter of the graph minimum weight
• IRMM, add a function of the graph filter by minimum weight

New features

• KPruneHyperGraph, add a function that implement pruning on hypergraph

[v0.0.17]

• 2023-06-01

Enhancement

• environment.yml, update
• hyperpartition
  • add --first-cluster to load exists first cluster results
  • expose --zero-allelic parameter
  • expose --allelic-similarity parameter
• PoreCTable, change to cphasing-rs porec table

New features

• docs, add docs
• utils
  • extract_matrix, extract matrix by th contig list
  • prune_matrix, prune matrix by prune table

Bug fixes

• merge-matrix, fixed the empty contact in result

[v0.0.16]

• 2023-05-05

Enhancement

• hyperpartition, add mutual exclusion merge

Bug fixes

• hyperpartition, fixed the bug that incorrect scaffold length in_incremental_partition

[v0.0.15]

• 2023-05-01

New features

• PruneTable, Object for prune table.

Enhancement

• kprune, output prune table
• hyperpartition
  • add k parameter to output the specified number groups

[v0.0.14]

• 2023-03-22

New features

• plot_heatmap, custom function to plot heatmap

Enhancement

• HyperPartition
  • add post check to increase the accuracy of partition
  • add min-contacts parameters to remove low contact contig pairs
  • add negative allelic algorithm
  • change multi to incremental
  • add whitelist and blacklist parameters

Bug fixes

• KPrune, dropna in pixels which will let igraph fall into loops

[v0.0.13]

• 2023-03-15

New features

• KPruner, prune contig contacts according similarity allele table

Enhancement

• extract_incidence_matrix, restruct to speed up
• extract, hyperpartition, import contig sizes instead of fasta
• HyperPartition, add filter function of minimum scaffolding length
• build, add only-agp option

Bug fixes

• HyperExtractor, fixed the problem of read index for multi dataframe concat

[v0.0.12]

• 2023-03-11

New features

• HyperGraph, instead of hypernetx to speed up
• prepare, a cli function for some preparation for C-Phasing
• optimize.cpp, optimize algorithm v1

Enhancement

• HyperEdges, restruct to {idx, row, col}
• Extractor and HyperExtractor, change to export HyperEdges
• process_pore_c_table, speed up
• HyperPartition, use custom HyperGraph to speed up
• merge_matrix, merge binning matrix into whole contigs
• optimize, cli for optimize score cacluation

Bug fixes

• alleles, fix the bug of empty allele table

[v0.0.11]

• 2023-03-08

Enhancement

• Extractor and HyperExtractor, change to export dict to list
• HyperPartition, add parallel in hypergraph generation

[v0.0.10]

• 2023-03-08

New features

• Extractor, extract edges from pairs file
• HyperExtractor, extract hyperedges from pore-c table
• HyperEdges, msgspec Struct for hyperedges serialization

Enhancement

• HyperPartition, divesting edges extract function to improve usability

[v0.0.9]

• 2023-01-06 refactor the frame of cphasing that seperating the hic and pore-c pipelines

New features

• agp2assembly, convert agp to assembly file
• pairs2mnd, convert pairs to mnd file
• paf2table, convert paf to table
• pore_c_cchrom2contig, convert chromosome-level to contig-level
• pairs_chrom2contig, convert chromosome-level to contig-level
• optimzie, init add optimize

Enhancement

• PAFTable, speed up
• PoreCTable, speed up and add chrom2contig
• HyperPartition, speed up the pore-c reads process
• paf2pairs, speed up

Bug fixes

• plot, to humanized

[v0.0.8]

• 2022-11-17

New features

• hypergraph, contain a hypergraph cluster algorithms
• HyperPartition, partition contigs in diploid or allopolyploid
• PartigAllele, enable using sequences similarity to generate allele table
• PAFTable, filter alignment
• PoreCTable, stat alignment information

Enhancement

• agp2fasta, build, using dictory instead of faidx to speed up

Bug fixes

• PairHeader, save header without "\n".
• rescue, fix CountRE only default load >=3.
• plot, fix bug of hicexplorer outputFilename error.

[v0.0.7]

• 2022-10-31

New features

• plot, provide adjust matrix and plot matrix function.
• AdapativePartition, partition by adapative pipeline for find best results
• PoreCMapper, Pore-C reads mapping pipeline.
• PAFTable, a function for processing paf file. (include to_pairs)

Enhancement

• correct, increase recall and precision to 70%
• pairs, add chrom2contig to convert a chrom-level pairs to contig-level

[v0.0.6]

• 2022-10-07

New features

• Change packages name to CPhasing.
• New function of
  • correct
  • alleles
  • rescue
  • partition
• New API of Pairs in core.

Bug fixes

• Using normalized signal in prune.