1.1.0

🔥 Breaking

• Remove to_pdf because the dependencies of weasyprint are complex, and installation fails on macOS (osx-arm64).
  • We would like to leave the saving of HTML to PDF to the browser's functionality.

1.0.4

New features

• None

Maintenance

• fix typo
• add test cases described in README

1.0.3

New feature

• None

Maintenance

• Fixed a bug in the RD calculation
  • For instance, in the case of ["=C-g", "=C"], the correct approach is to separate the REF's CG and C to calculate RD (initially RD=1, next RD=1). However, since it was counting all the Cs (RD=2), it has been modified to calculate them separately.

import cstag

cs_tags = [
    '=A*cg=GTAC',
    '=AC-g=TAC',
    '=ACGT+ggAC',
    ]
chroms = ["chr1", "chr1", "chr1"]
positions = [10, 10, 10]

x = cstag.to_vcf(cs_tags, chroms, positions)
print(x)

#####################
# Before:
#####################
chr1	11	.	CG	C	.	.	DP=4;RD=3;AD=1;VAF=0.25
chr1	11	.	C	G	.	.	DP=4;RD=3;AD=1;VAF=0.25
chr1	13	.	T	TGG	.	.	DP=3;RD=2;AD=1;VAF=0.333

#####################
# After:
#####################
chr1	11	.	CG	C	.	.	DP=2;RD=1;AD=1;VAF=0.5
chr1	11	.	C	G	.	.	DP=3;RD=2;AD=1;VAF=0.333
chr1	13	.	T	TGG	.	.	DP=3;RD=2;AD=1;VAF=0.333

1.0.2

Maintenance

• Fixed a calculation error in RD in to_vcf.call_reference_depth

  • Previously, only the Cs tags that matched the reference were considered, resulting in a match (adding 1 to RD) for sequences like deletions (e.g., =T, -c, -c).
  • Changed the policy to add 1 to RD if the sequence corresponding to v.ref exists in the CS tags.

• Due to the change in cstag.consensus.normalize_read_lengths in v1.0.1, where insufficient read lengths are now padded with None instead of N, a bug arose in to_vcf.call_reference_depth where it referred to None. This has been fixed.

import cstag

cs_tags = [
    '=A*cg=G+aa=T-ac=G',
    '*cg=G+aa=T-ac=G',
    '=G-t=ACG'
    ]
chroms = ['chr1', 'chr1', 'chr1']
positions = [10, 11, 12]

print(cstag.to_vcf(cs_tags, chroms, positions))
# before
# Traceback (most recent call last):
#   File "<stdin>", line 1, in <module>
#   File "/home/kuno/miniconda3/lib/python3.10/site-packages/cstag/to_vcf.py", line 340, in to_vcf
#     return process_cs_tags(cs_tags, chroms, positions)
#   File "/home/kuno/miniconda3/lib/python3.10/site-packages/cstag/to_vcf.py", line 285, in process_cs_tags
#     reference_depth = call_reference_depth(variant_annotations, cs_tags_list, positions_list)
#   File "/home/kuno/miniconda3/lib/python3.10/site-packages/cstag/to_vcf.py", line 202, in call_reference_depth
#     if cs[i][0] in ACGT:
# TypeError: 'NoneType' object is not subscriptable

# after
##fileformat=VCFv4.2
##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
##INFO=<ID=RD,Number=1,Type=Integer,Description="Depth of Ref allele">
##INFO=<ID=AD,Number=1,Type=Integer,Description="Depth of Alt allele">
##INFO=<ID=VAF,Number=1,Type=Float,Description="Variant allele fractions (AD/DP)">
#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO
chr1    11      .       C       G       .       .       DP=2;RD=0;AD=2;VAF=1.0
chr1    12      .       GT      G       .       .       DP=2;RD=1;AD=1;VAF=0.5
chr1    12      .       G       GAA     .       .       DP=3;RD=1;AD=2;VAF=0.667
chr1    13      .       TAC     T       .       .       DP=2;RD=0;AD=2;VAF=1.0

1.0.1

• Made changes in consensus to not consider N due to insufficient read numbers.

cs_tags = [
    '=A*cg=G+aa=T-ac=G',
    '*cg=G+aa=T-ac=G',
    '=G-t=ACG'
    ]
positions = [10, 11, 12]

cstag.consensus(cs_tags, positions)
# result:   =N*cg=G+aa=T-ac=G
# expected: =A*cg=G+aa=T-ac=G

• Modified consensus to split the deletion tags.
  • Added expand_deletion_tags to split the deletions.

cs_tags = [
    '=A*cg=G+aa=T-ac=G',
    '*cg=G+aa=T-ac=G',
    '=G-t=ACG'
    ]
positions = [10, 11, 12]

cstag.consensus(cs_tags, positions)
# result:   =N*cg=G+aa=T-ac=GN
# expected: =N*cg=G+aa=T-ac=G

• Tried other libraries as installing weasyprint is challenging on mac and windows. However, continued using weasyprint as CSS was not applied.
  • fpdf2
  • borb
  • xhtml2pdf

1.0.0

New Features

• Added to_pdf function
• Added COC (Code of Conduct)
• Added GitHub Issue templates (bug and feature)

Maintenance Updates

• Translated Japanese parts to English
• Updated the Docstring for to_vcf
• Replaced to_vcf's NamedTuple with dataclass
  • Honestly, there wasn't much change
• Enhanced tests for to_vcf

0.6.2

New Features

Core Enhancements

• Enhanced cstag.to_vcf to support multiple cs_tags (list[str]). This update introduces additional headers and content for better data representation:

  ##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
  ##INFO=<ID=RD,Number=1,Type=Integer,Description="Depth of Reference Allele">
  ##INFO=<ID=AD,Number=1,Type=Integer,Description="Depth of Alternate Allele">
  ##INFO=<ID=VAF,Number=A,Type=Float,Description="Variant Allele Frequency (AD/DP)">

• Introduced cstag.to_sequence for reconstructing subsequences.

Supplementary Features

• Added validate_cs_tag for CS tag validation.
• Introduced validate_pos for position validation.
• Implemented normalize_positions within cstag.consensus.
• Added Vcf and VcfInfo classes to to_vcf.

Maintenance Updates

• Revised normalize_read_lengths to eliminate deque output.
• Debugged to_html to properly handle =N.

0.6.1

bug fix: cstag.consensus

• POS does not consider CIGAR's softclips, so removed extract_softclips and calculate_read_starts function

0.6.0

• add cstag.to_vcf function

0.5.1

• add prefix
• convert the argument from uppercase to lowercase and standardize the format (e.g. CSTAG -> cs_tag)
• add utils.validator.py
• add python requirements >= 3.7