Exemple #1
0
 /**
  * Retrieve the original base qualities of the given read, if present, as stored in the OQ
  * attribute.
  *
  * @param read read to check
  * @return original base qualities as stored in the OQ attribute, or null if the OQ attribute is
  *     not present
  */
 public static byte[] getOriginalBaseQualities(final GATKRead read) {
   if (!read.hasAttribute(ORIGINAL_BASE_QUALITIES_TAG)) {
     return null;
   }
   final String oqString = read.getAttributeAsString(ORIGINAL_BASE_QUALITIES_TAG);
   return oqString.length() > 0 ? SAMUtils.fastqToPhred(oqString) : null;
 }
Exemple #2
0
 /**
  * @return whether or not this read has base insertion or deletion qualities (one of the two is
  *     sufficient to return true)
  */
 public static boolean hasBaseIndelQualities(final GATKRead read) {
   return read.hasAttribute(BQSR_BASE_INSERTION_QUALITIES)
       || read.hasAttribute(BQSR_BASE_DELETION_QUALITIES);
 }