Main fixsnakemake#17

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Congm12 wants to merge 11 commits intomainfrom

main_fixsnakemake

Commits on Dec 2, 2024

handle the non-gzipped barcodes in preprocessing
Cong Ma
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update readme
Cong Ma
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Commits on Dec 8, 2024

preprocessing step get_snp_matrix.py keep sparse matrix operation to save mem
Cong Ma
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Commits on Dec 10, 2024

sparse matrix operations for allele counts and transcript counts, sparse intermediate count matrices for haplotype blocks, pd dataframe operations to vectors
Cong Ma
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add min UMI threshold for constructing haplotype blocks
Cong Ma
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Commits on Dec 12, 2024

output more intermediate files in parsing inputs
Cong Ma
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Commits on Dec 13, 2024

allow reading other modalities in read_10x_h5
Cong Ma
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sub-sample spots and snps
Cong Ma
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Commits on Jan 11, 2025

add a separate wrapper for plot spatial clones that takes figsize and point size as input
Cong Ma
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Commits on Apr 17, 2025