Update example dataset and a description of README.md/README_JP.md Commit Detail
π Bug Fixes
Update preprocess.genome_fetcher_fetch_seq_coordinates to accurately verify that the entire length of the input sequence is present within the reference sequence. Previously, partial 100% matches were inadvertently accepted; this revision aims to ensure the full alignment of the input sequence with the reference. Commit Detail
Update report.bam_exporter to be case-sensitive and consistent with directory names. This is to avoid errors caused by the difference between report/bam and report/BAM on Ubuntu, which is case-sensitive to directory names. Commit Detail
Thank you @takeiga for reporting the issue #24 !
π§ Maintenance
Change threshold_readnumber at labem_merger.merge_labels from 10 to 5 to capture 1% alleles from 500 total reads. Commit Detail
Update the requirements.txt to install a newer version of the library. Commit Detail
Update report.report_bam and rename to report.bam_exporter: Commit Detail
Use UUID instead of random number for the temporary file name.
Rename realign to recalculate_sam_coodinates_to_reference for the readability of the function name.
Add convert_pos_to_one_indexed to convert the 0-based position to 1-based position and suppress samtools warning.
Warning: [W::sam_parse1] mapped query cannot have zero coordinate; treated as unmapped
Add tests for the write_sam_to_bam function
Move read_sam function from sam_handler to io module. Commit Detail
Rename report.report_mutation, report.report_files to report.mutation_exporter and report.sequence_exporter to be more explicit. Commit Detail
v0.4.3 (2024-03-29)
π Documentation
π Bug Fixes
Update
preprocess.genome_fetcher_fetch_seq_coordinates
to accurately verify that the entire length of the input sequence is present within the reference sequence. Previously, partial 100% matches were inadvertently accepted; this revision aims to ensure the full alignment of the input sequence with the reference. Commit DetailUpdate
report.bam_exporter
to be case-sensitive and consistent with directory names. This is to avoid errors caused by the difference between report/bam and report/BAM on Ubuntu, which is case-sensitive to directory names. Commit Detailπ§ Maintenance
Change
threshold_readnumber
atlabem_merger.merge_labels
from 10 to 5 to capture 1% alleles from 500 total reads. Commit DetailUpdate the
requirements.txt
to install a newer version of the library. Commit DetailUpdate
report.report_bam
and rename toreport.bam_exporter
: Commit Detailrealign
torecalculate_sam_coodinates_to_reference
for the readability of the function name.convert_pos_to_one_indexed
to convert the 0-based position to 1-based position and suppress samtools warning.[W::sam_parse1] mapped query cannot have zero coordinate; treated as unmapped
write_sam_to_bam
functionMove
read_sam
function from sam_handler to io module. Commit DetailRename
report.report_mutation
,report.report_files
toreport.mutation_exporter
andreport.sequence_exporter
to be more explicit. Commit Detail