/**
* Composes the main output header.
*
* @param commandLine the tool command line.
* @param groupBy the group-by argument used.
* @param countColumnNames the column names.
* @return never {@code null}.
*/
private static String composeMatrixOutputHeader(
final String commandLine,
final TargetOutInfo targetOutInfo,
final GroupBy groupBy,
final List<String> countColumnNames) {
final String countColumnHeaderString =
String.join(COLUMN_SEPARATOR, countColumnNames).replace("%", "%%");
final String formatString =
String.join(
LINE_SEPARATOR,
"##fileFormat = tsv",
"##commandLine = %s",
"##title = Read counts per target and %s",
String.join(COLUMN_SEPARATOR, targetOutInfo.headerString(), countColumnHeaderString));
return String.format(formatString, commandLine, groupBy.toString());
}
/**
* Composes the row summary output header.
*
* @param commandLine the execution command line.
* @param groupBy the value of the group-by argument used.
* @param columnCount number of count-column involved in the analysis.
* @return never {@code null}.
*/
private static String composeRowOutputHeader(
final String commandLine,
final TargetOutInfo targetOutInfo,
final GroupBy groupBy,
final int columnCount) {
return String.format(
String.join(
LINE_SEPARATOR,
"##fileFormat = tsv",
"##commandLine = %s",
"##title = Summary counts per target",
"##metaData = {",
"## groupBy = %s,",
"## columnCount = %d",
"##}",
String.join(
COLUMN_SEPARATOR,
targetOutInfo.headerString(),
SUM_COLUMN_NAME,
AVG_COL_BP_COLUMN_NAME)),
commandLine,
groupBy,
columnCount);
}
