LongPhase 1.7 Release Notes

[twolinin]

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

Changes

1. Fix the counter issue during the tagging stage and ensure proper closure of the log file. #60
2. Multithread chromosome #59
3. In readCorrection, decide which read to use by passing two snp or more #58
4. Fix pos order #57

• fix the order of SNP, SV, and methylations
• fix the lack of SV and methylations when SNP SV, and modification co-phasing
• fix repeat position of SV and methylation

5. Merging different alignments of a read into a single alignment  #55

• Merging different alignments of a read into a single alignment to enhance phasing integrity.
• Correct the conditions for judging the VCF header.

6. make the baseQuality and edgeWeight modified parameters for users #52

• Add two parameters baseQuality and edgeWeight guide to the --help list. Users can now decide what baseQuality threshold and edgeWeight they want to use.

7. Solve the problem where other variants with the same coordinates are also changed after a variant is phased #49

• The variants used in multiple VCFs will be accessed and stored in their respective chrVariant, even if multiple variants occur at the same coordinate, only one chrVariant from one VCF will be recorded.

8. haplotag supports phased indels and modification VCF. #48

• When utilizing haplotag for read haplotype tagging, it will automatically detect whether the phased SNP file includes phased indels.
• When performing read haplotype tagging with haplotag, it can use the --mod-file option to input the phased modification VCF.
• Correcting the condition in ParsingBam.cpp for determining when a deletion variant that fall within the read's deletion cigar.