Proposed replacement for progress PR

src/main/java/htsjdk/samtools/util/AbstractProgressLogger.java

@@ -18,10 +18,14 @@ abstract public class AbstractProgressLogger implements ProgressLoggerInterface
     private long startTime;
     private final NumberFormat fmt = new DecimalFormat("#,###");
     private final NumberFormat timeFmt = new DecimalFormat("00");
-    private long processed;
-    private long lastStartTime;
-    private String lastChrom;
-    private int lastPos;
+    private long processed = 0;
+    // Set to -1 until the first record is added
+    private long lastStartTime = -1;
+    private String lastChrom = null;
+    private int lastPos = 0;
+    private String lastReadName = null;
+    private long countNonIncreasing = 0;
+    final private long PRINT_READ_NAME_THRESHOLD = 1000;
 
     /**
      * Construct an AbstractProgressLogger.
@@ -60,18 +64,26 @@ private synchronized void record() {
         if (this.lastChrom == null) readInfo = "*/*";
         else readInfo = this.lastChrom + ":" + fmt.format(this.lastPos);
 
+        final String rnInfo;
+
+        if (lastReadName != null && countNonIncreasing > PRINT_READ_NAME_THRESHOLD) {
+            rnInfo = ".  Last read name: " + lastReadName;
+        } else {
+            rnInfo = "";
+        }
+
         final long n = (this.processed % this.n == 0) ? this.n : this.processed % this.n;
 
         log(this.verb, " ", processed, " " + noun + ".  Elapsed time: ", elapsed, "s.  Time for last ", fmt.format(n),
-                ": ", period, "s.  Last read position: ", readInfo);
+                ": ", period, "s.  Last read position: ", readInfo, rnInfo);
     }
 
     /**
      * Logs the last last record if it wasn't previously logged.
      * @return boolean true if logging was triggered, false otherwise
      */
     public synchronized boolean log() {
-        if (this.processed % this.n != 0) {
+        if (processed % this.n != 0) {
             record();
             return true;
         }
@@ -80,14 +92,22 @@ public synchronized boolean log() {
         }
     }
 
-    @Override
-    public synchronized boolean record(final String chrom, final int pos) {
-        this.lastChrom = chrom;
-        this.lastPos = pos;
-        if (this.lastStartTime == -1) {
-            this.lastStartTime = System.currentTimeMillis();
+    protected synchronized boolean record(final String chrom, final int pos, final String rname) {
+        lastChrom = chrom;
+        if (pos >= lastPos) {
+            countNonIncreasing = Math.max(0, countNonIncreasing--);
+        } else {
+            countNonIncreasing++;
+            if (countNonIncreasing == PRINT_READ_NAME_THRESHOLD) {
+                log("Seen many non-increasing record positions. Printing Readnames as well.");
+            }
+        }
+        lastPos = pos;
+        lastReadName = rname;
+        if (lastStartTime == -1) {
+            lastStartTime = System.currentTimeMillis();
         }
-        if (++this.processed % this.n == 0) {
+        if (++processed % n == 0) {
             record();
             return true;
         }
@@ -96,25 +116,31 @@ public synchronized boolean record(final String chrom, final int pos) {
         }
     }
 
+    @Override
+    public synchronized boolean record(final String chrom, final int pos) {
+        return record(chrom, pos, null);
+    }
+
     /**
      * Records that a given record has been processed and triggers logging if necessary.
      * @return boolean true if logging was triggered, false otherwise
      */
     @Override
     public synchronized boolean record(final SAMRecord rec) {
         if (SAMRecord.NO_ALIGNMENT_REFERENCE_NAME.equals(rec.getReferenceName())) {
-            return record(null, 0);
-        }
-        else {
-            return record(rec.getReferenceName(), rec.getAlignmentStart());
+            return record(null, 0, rec.getReadName());
+        } else {
+            return record(rec.getReferenceName(), rec.getAlignmentStart(), rec.getReadName());
         }
     }
 
     /** Records multiple SAMRecords and triggers logging if necessary. */
     @Override
     public boolean record(final SAMRecord... recs) {
         boolean triggered = false;
-        for (final SAMRecord rec : recs) triggered = record(rec) || triggered;
+        for (final SAMRecord rec : recs) {
+            triggered = record(rec) || triggered;
+        }
         return triggered;
     }
 
@@ -132,13 +158,16 @@ public void reset() {
         lastStartTime = -1;
         lastChrom = null;
         lastPos = 0;
+        lastReadName = null;
     }
 
     /** Left pads a string until it is at least the given length. */
     private String pad (String in, final int length) {
-        while (in.length() < length) {
-            in = " " + in;
+        final StringBuilder inBuilder = new StringBuilder(in);
+        while (inBuilder.length() < length) {
+            inBuilder.insert(0, " ");
         }
+        in = inBuilder.toString();
 
         return in;
     }