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Main fixsnakemake#17

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Congm12 wants to merge 8 commits intomainraphael-group/CalicoST:mainfrom main_fixsnakemakeraphael-group/CalicoST:main_fixsnakemakeCopy head branch name to clipboard

+644-225

Commits

Commits on Dec 2, 2024

• handle the non-gzipped barcodes in preprocessing

  

  Cong Ma

  committed
  af8f384

• update readme

  

  Cong Ma

  committed
  930ca4f

Commits on Dec 8, 2024

• preprocessing step get_snp_matrix.py keep sparse matrix operation to save mem

  

  Cong Ma

  committed
  6ff2d37

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

  committed
  e5cdda0

• add min UMI threshold for constructing haplotype blocks

  

  Cong Ma

  committed
  6d38526

Commits on Dec 12, 2024

• output more intermediate files in parsing inputs

  

  Cong Ma

  committed
  465c351

Commits on Dec 13, 2024

• allow reading other modalities in read_10x_h5

  

  Cong Ma

  committed
  61d6e17

• sub-sample spots and snps

  

  Cong Ma

  committed
  6a4b696