add function to read velocyto matrix from STARsolo

chaos.read_solo_meta <-	function(

							id,

							type,

							star_dir = "~/project.isynbio/mengqian/STAR_result",

							filtered = TRUE

){

	if(isTRUE(filtered)){

		filter_str <- "filtered"

	}else{

		filter_str <- "raw"

	}

	solo_dir <- file.path(star_dir,id,"Solo.out/Gene",filter_str)

	if(tolower(type) == "ensg"){

		file.path(solo_dir,"features.tsv.gz") |>

		fread(header = F) %>%

		.$V1

	}else if(tolower(type) == "symbol"){

		file.path(solo_dir,"features.tsv.gz") |>

		fread(header = F) %>%

		.$V2

	}else if(tolower(type) == "barcode"){

		file.path(solo_dir,"barcodes.tsv.gz") |>

		fread(header = F) %>%

		.$V1 %>%

		paste(id,.,sep = ":")

	}

}

chaos.read_solo_velocyto <-	function(

							id,

							star_dir = "~/project.isynbio/mengqian/STAR_result"

){

	mtx_dir <- file.path(star_dir,id,"Solo.out/Velocyto/filtered")

	mtxs <- c("unspliced","spliced","ambiguous")

	parallel::mclapply(

		mtxs,

		\(x){

			paste0(x,".mtx.gz") %>%

			file.path(mtx_dir,.) %>%

			Matrix::readMM() |>

			set_colnames(chaos.read_solo_meta(id,type = "barcode")) |>

			set_rownames(chaos.read_solo_meta(id,type = "symbol"))

		},

		mc.cores = 3

	) |>

	setNames(mtxs)

}

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