#how to read a .sam file into R.
#does this work? Untested.
file <- 'accepted_hits.sam'
colnames <- c(
"v1", "v2", "v3", "v4", "v5", "v6", "v7", "v8", "v9", "v10", "v11", "v12",
"v13", "v14", "v15", "v16", "v17", "v18", "v19", "v20", "v21", "v22", "v23",
"v24"
)
sam <- read.table(
file,
header = FALSE,
sep = "",
quote = "'",
dec = ".",
col.names=colnames,
fill=T
)
drops <- c(
"v11","v12","v13","v14","v15","v16","v17","v18","v19","v20","v21","v22",
"v23","v24"
)
sam_2 <- sam[,!(names(sam) %in% drops)]
colnames(sam_2) <- c(
"read_name", "sum_of_flags", "chr", "start", "mapping_quality", "CIGAR",
"mate_alignment_chr", "mate_alignment_start", "inferred_frag_length",
"sequence"
)
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