Adding total read count in BAM file to command line output.

src/crop_unmapped.h

@@ -406,6 +406,7 @@ crop_unmapped(double & avgCov,
 
     // Iterate over the input file.
     BamAlignmentRecord record;
+    unsigned totalReads = 0;
     unsigned long alignedBaseCount = 0;
     while (!atEnd(inStream))
     {
@@ -416,6 +417,9 @@ crop_unmapped(double & avgCov,
         if (hasFlagDuplicate(record) or hasFlagSecondary(record) or
                 hasFlagQCNoPass(record) or hasFlagSupplementary(record)) continue;
 
+	// Count 'interesting' reads..
+	totalReads += 1;
+
         if (!hasFlagUnmapped(record))
             alignedBaseCount += length(record.seq);
 
@@ -447,6 +451,10 @@ crop_unmapped(double & avgCov,
     avgCov = (double)alignedBaseCount / (double)genomeLength;
 
     std::ostringstream msg;
+    msg << "BAM file lists alignments for " << totalReads << " reads after duplicate removal and filtering on QC pass flag.";
+    printStatus(msg);
+
+    msg.str("");
     msg << "Map of low quality mates has " << otherReads.size() << " records.";
     printStatus(msg);