Remove requirement that zero length reads need color space or flow si… (

#1360)

* Remove requirement that zero length reads need color space or flow signal data.

src/main/java/htsjdk/samtools/SAMRecord.java

@@ -2044,7 +2044,16 @@ public List<SAMValidationError> isValid(final boolean firstOnly) {
             ret.addAll(errors);
             if (firstOnly) return ret;
         }
-        // TODO(mccowan): Is this asking "is this the primary alignment"?
+
+        /*
+        The SAM specification allows both empty bases and qualities.  However, for data generated with color space
+        information (ex. SOLiD sequencing) or flow signal information (ex. Ion Torrent sequencing), we have enforced
+        that certain auxiliary tags are present: CS and CQ for color space data, and FZ for flow signal data.  See section
+        1.6 ("Technology-specific data") in the SAM specification (dated Jan 30 2019).  We have relaxed this constraint
+        to follow the SAM specification and a requested need to represent data in such a spec-compliant way.  For more
+        information, see:
+          1. https://github.com/samtools/htsjdk/issues/1174
+          2. https://github.com/samtools/htsjdk/pull/1360
         if (this.getReadLength() == 0 && !this.isSecondaryAlignment()) {
             final Object fz = getAttribute(SAMTag.FZ.getBinaryTag());
             if (fz == null) {
@@ -2073,6 +2082,8 @@ public List<SAMValidationError> isValid(final boolean firstOnly) {
                 }
             }
         }
+        */
+
         if (this.getReadLength() != getBaseQualities().length &&  !Arrays.equals(getBaseQualities(), NULL_QUALS)) {
             if (ret == null) ret = new ArrayList<>();
             ret.add(new SAMValidationError(SAMValidationError.Type.MISMATCH_READ_LENGTH_AND_QUALS_LENGTH,