Skip to content

CHANGES

[v0.2.7] - 2025-07-08#

Bug fixes#

  • methalign, fixed bug that input bam contain 5hmC

[v0.2.6] - 2025-03-27#

New features#

  • collapse, rescue the collapsed contigs

Enhancement#

  • Parameter optimization.
  • Supported pairs.pqs processing.
  • chimeric, improve the performance that avoids too high of false correct
  • pipeline, if input pairs or pairs.gz, it will first convert it to pairs.pqs to speed up subsequence pairs data load. About a 15 percent increase in speed.
  • plot, enable plot the border or haplotypes (--add-hap-border)

Bug fixes#

  • pipeline, fixed bug that when user input uncommon suffix of Hi-C data (e.g. "_R1.f.fastq.gz") the pairs file could not be found. #issue17
  • hypergraph
    - fixed bug that cphasing-rs pairs-intersect can not filter contacts by mapq
    - fixed bug that report error when edge_length set to 0
  • pairs2cool, fixed bug that loss contacts when the chromsizes in pairs.gz is unsorted.
  • rename - fixed bug that when the chromname in agp is named group??, the rename cannot be executed - generate the unrenamed chromosome, #issue16

[v0.2.5] - 2025-02-07#

New features#

  • PQS, custom format of contacts to speed up the load and parse, do not used in this version.

Enhancement#

  • cphasing-rs, slightly speed up pairs2clm
  • rename, use g1, g2, g3 ... to rename duplicates chromosomes, when --unphased specified.
  • hcr_by_contacts, speed up it

Bug fixes#

  • hypergraph, fixed bug that report error of polars prompt of set "skip_nulls=False"

[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.