48 lines
1.3 KiB
R
48 lines
1.3 KiB
R
read.gatkreport <- function(filename) {
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con = file(filename, "r", blocking = TRUE);
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lines = readLines(con);
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close(con);
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tableEnv = new.env();
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tableName = NA;
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tableHeader = c();
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tableRows = c();
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for (line in lines) {
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if (length(grep("^#:table[[:space:]]+", line, ignore.case=TRUE)) > 0) {
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headerFields = unlist(strsplit(line, "[[:space:]]+"));
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if (!is.na(tableName)) {
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d = data.frame(tableRows, row.names=NULL, stringsAsFactors=FALSE);
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colnames(d) = tableHeader;
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assign(tableName, d, envir=tableEnv);
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}
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tableName = headerFields[2];
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tableHeader = c();
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tableRows = c();
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} else if (length(grep("^[[:space:]]*$", line)) > 0 | length(grep("^[[:space:]]*#", line)) > 0) {
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# do nothing
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} else if (!is.na(tableName)) {
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row = unlist(strsplit(line, "[[:space:]]+"));
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if (length(tableHeader) == 0) {
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tableHeader = row;
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} else {
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tableRows = rbind(tableRows, row);
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}
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}
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}
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if (!is.na(tableName)) {
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d = data.frame(tableRows, row.names=NULL);
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colnames(d) = tableHeader;
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assign(tableName, d, envir=tableEnv);
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}
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gatkreport = as.list(tableEnv);
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}
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