/** * Given a read, outputs the base qualities in a string format * * @param read the read * @return a string representation of the base qualities */ public static String convertReadQualToString(GATKSAMRecord read) { return convertReadQualToString(read.getBaseQualities()); }
public void addAlignment(GATKSAMRecord read) { output.println("@" + read.getReadName()); if (read.getReadNegativeStrandFlag()) { output.println(ReadUtils.getBasesReverseComplement(read)); output.println("+"); output.println(ReadUtils.convertReadQualToString(invertQuals(read.getBaseQualities()))); } else { output.println(ReadUtils.convertReadBasesToString(read)); output.println("+"); output.println(ReadUtils.convertReadQualToString(read)); } }