--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/utilities/validateBam.py	Tue May 15 02:39:53 2018 -0400
@@ -0,0 +1,84 @@
+#!/usr/bin/env python
+
+import sys
+import os
+import gzip
+from struct import unpack
+
+BAM_EOF = ['1f', '8b', '08', '04', '00', '00', '00', '00', '00', 'ff', '06', '00', '42', '43', '02', '00', '1b', '00', '03', '00', '00', '00', '00', '00', '00', '00', '00', '00']
+
+def getBytes(fmt,amt):
+	if fmt == '<i' or fmt == '<I':
+		mySize = 4
+	elif fmt == '<c' or fmt == '<b' or fmt == '<B':
+		mySize = 1
+	else:
+		print '\nError, unknown format:',fmt,'\n'
+		exit(1)
+	if amt == 1:
+		fread = f.read(mySize)
+		if not fread:
+			return None
+		return unpack(fmt,fread)[0]
+	else:
+		fread = f.read(mySize*amt)
+		if not fread:
+			return None
+		return unpack(fmt,fread)
+
+# check eof
+IN_BAM = sys.argv[1]
+f = open(IN_BAM,'rb')
+f.seek(os.path.getsize(IN_BAM)-28)
+EOF = [format(ord(n),'02x') for n in f.read()]
+print 'EOF_MARKER:  ', ' '.join(EOF)
+if EOF != BAM_EOF:
+	print '\nWARNING: BAM EOF DOES NOT MATCH EXPECTED STRING.\n'
+f.close()
+
+# check other stuff
+f = gzip.open(IN_BAM,'rb')
+
+print 'MAGIC STRING:', f.read(4)
+l_text = getBytes('<i',1)
+print 'l_text:      ', l_text
+print 'text:      \n', f.read(l_text)
+n_ref = getBytes('<i',1)
+print 'n_ref:       ', n_ref
+
+for i in xrange(n_ref):
+	l_name = getBytes('<i',1)
+	print 'ref'+str(i)+' - l_name:', l_name
+	print 'ref'+str(i)+' - name:  ', f.read(l_name)
+	print 'ref'+str(i)+' - l_ref: ', getBytes('<i',1)
+
+print '\nEXAMINING ALIGNMENT DATA:\n'
+aln_N = 0
+while True:
+	aln_N += 1
+	blockSize = getBytes('<i',1)
+	if blockSize == None:
+		break
+	print '['+str(aln_N)+']:', 'blockSize:', blockSize
+	print '-- refID:', getBytes('<i',1)
+	print '-- pos:  ', getBytes('<i',1)
+	bmqnl = getBytes('<I',1)
+	binv  = (bmqnl>>16)&65535
+	mapq  = (bmqnl>>8)&255
+	lrn   = bmqnl&255
+	print '-- bmqnl:', bmqnl, '(bin='+str(binv)+', mapq='+str(mapq)+', l_readname+1='+str(lrn)+')'
+	flgnc = getBytes('<I',1)
+	flag  = (flgnc>>16)&65535
+	ncig  = flgnc&65535
+	print '-- flgnc:', flgnc, '(flag='+str(flag)+', ncig='+str(ncig)+')'
+	print '-- l_seq:', getBytes('<i',1)
+	print '-- nxtID:', getBytes('<i',1)
+	print '-- nxtPo:', getBytes('<i',1)
+	print '-- tlen: ', getBytes('<i',1)
+	print '-- rname:', str([f.read(lrn)])[1:-1]
+
+	f.read(blockSize-32-lrn)
+	#print [block]
+
+
+f.close()