v1.7.3

Summary

1. Fix the issue where the phase command calls fai_load() each time it fetches a reference sequence, changing it to call only once.
2. It will no longer fetch reference sequences without SNP cover.

see detail changes

v1.7.2

Summary

Haplotag will add the @PG tag to the header and add option --cram to output CRAM format.
Currently, phase combines different alignments of the same read into a single alignment.

see detail changes

v1.7.1

Summary

If the INFO field of an SV variant does not contain RNAMES, phasing will not be performed for this variant.
Haplotag now includes documentation on tagging specific regions.

see detail changes

v1.7

Summary

Merge different alignments of a read to improve phasing integrity and adjust parameter weights to enhance phasing accuracy. Allow the use of phased modification VCF to increase the proportion of tagged reads. Address some known issues.

phase (-t 24)	v1.6 SW	v1.6 #Block	v1.6 Block N50	v1.7 SW	v1.7 #Block	v1.7 Block N50
HG002 ONT R10.4.1 10x	1,137	7,212	774,928	1,117	7,100	807,877
HG002 ONT R10.4.1 20x	1,225	4,257	1,560,226	1,218	4,132	1,654,808
HG002 ONT R10.4.1 30x	1,194	3,499	1,903,900	1,180	3,372	2,042,500
HG002 ONT R10.4.1 40x	1,211	3,045	2,177,620	1,200	2,915	2,332,195
HG002 ONT R10.4.1 50x	1,216	2,797	2,470,461	1,213	2,679	2,606,645
HG002 ONT R10.4.1 60x	1,197	2,627	2,587,166	1,195	2,513	2,830,210

SW: Switch Error

see detail changes

v1.6

Summary

1. Implement chromosome-level parallelization for the modcall and phase commands. The overall execution time is reduced 71% ~ 88%.
2. Replace malloc with jemalloc.
3. Remove and simplify unused parameters to improve memory usage.
4. Adjust the weighting of low-quality variants in phasing.
5. The VCF generated by modcall can be directly imported into IGV. Additionally, modcall can output all detected coordinates by using the --all parameter.

see detail changes

phase (-t 24)	v1.5.2 (Time)	v1.5.2 (Memory)	v1.6 (Time)	v1.6 (Memory)
HG002 ONT R10.4.1 10x	153s	7.7G	39s	15.1G
HG002 ONT R10.4.1 20x	444s	8.2G	53s	15.6G
HG002 ONT R10.4.1 30x	355s	8.5G	68s	24.4G
HG002 ONT R10.4.1 40x	908s	8.8G	217s	26.6G
HG002 ONT R10.4.1 50x	1043s	9.2G	262s	22.2G
HG002 ONT R10.4.1 60x	640s	9.5G	113s	33.4G

modcall (-t 24)	v1.5.2 (Time)	v1.5.2 (Memory)	v1.6 (Time)	v1.6 (Memory)
HG002 ONT R10.4.1 10x	322s	11.0G	93s	22.2G
HG002 ONT R10.4.1 20x	635s	14.6G	199s	31.6G
HG002 ONT R10.4.1 30x	746s	18.2G	125s	48.1G
HG002 ONT R10.4.1 40x	1308s	21.5G	292s	55.8G
HG002 ONT R10.4.1 50x	1570s	25.0G	317s	68.8G
HG002 ONT R10.4.1 60x	1454s	28.4G	248s	84.0G

*If the device is running low on memory, you can control memory usage by reducing the number of threads (-t).

v1.5.2

This version improves phasing accuracy by refining the graph boundary range and reduces memory usage by 20% to 40% through the elimination of redundant code.

v1.5.1

Release note of v1.5.1
There are two major update in this release.

1. Multi-bam input is now supported. The user can specify multiple BAM files by

longphase phase \
-s SNP.vcf \
-b alignment1.bam \
-b alignment2.bam \
-r reference.fasta \
-t 8 \
-o phased_prefix \
--ont # or --pb for PacBio Hifi

2. A beta version of SNP and modification co-phasing is now released. Feedback are very welcome. The user can detect allele-specific modifications (5mC only at this moment) by a new command modcall, assuming the MM/ML tags are carried to aligned BAM.

longphase modcall \
-b alignment.bam \
-r reference.fasta \
-t 8 \
-o modcall

The SNP and modification co-phasing can then be invoked by providing the modcall-generated VCF. Co-phasing SNPs and modifications can further improve the phasing contiguity.

longphase phase \
-s SNP.vcf \
--mod-file modcall.vcf \
-b alignment.bam \
-r reference.fasta \
-t 8 \
-o phased_prefix \
--ont # or --pb for PacBio Hifi

v1.5

This release includes two main features.

1. Longphase now officially support phasing Nanopore R10.4 with some fine-tuning. This version also works for previous R9.4 data.
2. Co-phasing of SNPs and small indels can now be enabled by '--indels'. See Readme.
3. Resolve issues #8, #26, #27.

v1.4

Major change

This version improves phasing accuracy including switch error and hamming distance. The underlying graph improves phasing integrity by multiple edges instead of second-stage block phasing. Haplotag reads are used in the implementation to improve phasing accuracy.

The phasing accuracy is improved under ONT R9.4.1 with different sequencing depths.

v1.3

Major change

This version mainly improved the phasing accuracy, especially at low-coverage depth (10-20x). The underlying graph model now creates and considers multiple edges from local/flanking SNPs during phasing (see below), which increases the phasing accuracy and robustness at regions of dense ONT errors.

As such the running time increases ~20% on average (2.5-8 minutes for 10-60x with 8 Cores on SSD). The block N50 becomes larger at 10-30x and slightly smaller at 50-60x when compared with previous version. The phasing accuracy (SW: switch error rate) improved at all coverage.

Minor change

1. The haplolag now writes the Phred-scaled phasing quality of each read in the tagged BAM (e.g., PQ:i:40), which was discussed at #19.

2. The program will prompt the user if missing the reference genome. #18