diff --git a/Dockerfile-base b/Dockerfile-base
index 2f6b60e..211ac09 100644
--- a/Dockerfile-base
+++ b/Dockerfile-base
@@ -24,7 +24,9 @@ RUN wget https://github.com/torognes/vsearch/archive/v2.4.3.tar.gz && \
     make install && \
     cd ..
 
-RUN git clone git://github.com/nextgenusfs/amptk.git && \
+RUN wget https://github.com/nextgenusfs/amptk/archive/0.10.2.tar.gz && \
+    tar xzf 0.10.2.tar.gz && \
+    mv amptk-0.10.2 amptk && \
     cd amptk && \
     make && \
     cd ..
diff --git a/amptk.py b/amptk.py
index 502fcc4..060dcd9 100755
--- a/amptk.py
+++ b/amptk.py
@@ -59,7 +59,7 @@ def download(url, name):
         sys.stdout.write(status)
     f.close()
 
-version = '0.10.1'
+version = '0.10.2'
 
 default_help = """
 Usage:       amptk <command> <arguments>
@@ -762,6 +762,7 @@ def download(url, name):
              -m, --mapping_file  QIIME-like mapping file
              -t, --taxonomy      Taxonomy calculated elsewhere. 2 Column file.
              --method            Taxonomy method. Default: hybrid [utax, sintax, usearch, hybrid, rdp, blast]
+             --add2db            Add FASTA files to DB on the fly.
              --fasta_db          Alternative database of fasta sequenes to use for global alignment.
              --utax_db           UTAX formatted database. Default: ITS2.udb [See configured DB's below]
              --utax_cutoff       UTAX confidence value threshold. Default: 0.8 [0 to 0.9]
diff --git a/bin/amptk-fastq2sra.py b/bin/amptk-fastq2sra.py
index 8b26663..c9870f6 100755
--- a/bin/amptk-fastq2sra.py
+++ b/bin/amptk-fastq2sra.py
@@ -41,13 +41,6 @@ class col:
 parser.add_argument('-a','--append', help='Append a name to all sample names for a run, i.e. --append run1 would yield Sample_run1')
 args=parser.parse_args()
 
-def FindBarcode(Seq, BarcodeDict):
-    for BarcodeLabel in BarcodeDict.keys():
-        Barcode = BarcodeDict[BarcodeLabel]
-        if Seq.startswith(Barcode):
-            return Barcode, BarcodeLabel
-    return "", ""
-
 log_name = args.out + '.amptk-sra.log'
 if os.path.isfile(log_name):
     os.remove(log_name)
@@ -238,12 +231,12 @@ def FindBarcode(Seq, BarcodeDict):
             #look for forward primer
             if args.require_primer != 'off': #means we only want ones with forward primer and or reverse, but don't remove them             
                 #now search for forward primer
-                foralign = edlib.align(FwdPrimer, seq, mode="HW", k=args.primer_mismatch)
+                foralign = edlib.align(FwdPrimer, seq, mode="HW", k=args.primer_mismatch, additionalEqualities=amptklib.degenNuc)
                 if foralign["editDistance"] < 0:
                     continue
                 if args.require_primer == 'both': 
                     #now search for reverse primer
-                    revalign = edlib.align(ReverseCompRev, seq, mode="HW", task="locations", k=args.primer_mismatch)
+                    revalign = edlib.align(ReverseCompRev, seq, mode="HW", task="locations", k=args.primer_mismatch, additionalEqualities=amptklib.degenNuc)
                     if revalign["editDistance"] < 0:  #reverse primer was not found
                         continue         
             #check size
diff --git a/bin/amptk-process_illumina_folder.py b/bin/amptk-process_illumina_folder.py
index 97e94ed..b940f69 100755
--- a/bin/amptk-process_illumina_folder.py
+++ b/bin/amptk-process_illumina_folder.py
@@ -63,7 +63,7 @@ def processRead(input):
             for title, seq, qual in FastqGeneralIterator(open(input)):
                 Total += 1
                 #first thing is look for forward primer, if found trim it off
-                foralign = edlib.align(FwdPrimer, seq, mode="HW", k=args.primer_mismatch)
+                foralign = edlib.align(FwdPrimer, seq, mode="HW", k=args.primer_mismatch, additionalEqualities=amptklib.degenNuc)
                 #if require primer is on make finding primer in amplicon required if amplicon is larger than read length
                 #if less than read length, can't enforce primer because could have been trimmed via staggered trim in fastq_mergepairs
                 if args.primer == 'on' and len(seq) > ReadLen:
@@ -83,7 +83,7 @@ def processRead(input):
                         Seq = seq
                         Qual = qual
                 #now look for reverse primer
-                revalign = edlib.align(RevPrimer, Seq, mode="HW", task="locations", k=args.primer_mismatch)
+                revalign = edlib.align(RevPrimer, Seq, mode="HW", task="locations", k=args.primer_mismatch, additionalEqualities=amptklib.degenNuc)
                 if revalign["editDistance"] >= 0:
                     RevPrimerFound += 1
                     RevCutPos = revalign["locations"][0][0]
diff --git a/bin/amptk-process_illumina_raw.py b/bin/amptk-process_illumina_raw.py
index 0b32304..f5f4052 100755
--- a/bin/amptk-process_illumina_raw.py
+++ b/bin/amptk-process_illumina_raw.py
@@ -68,7 +68,7 @@ def processRead(input):
                     NoBC += 1
                     continue
                 #first thing is look for forward primer, if found trim it off
-                foralign = edlib.align(FwdPrimer, seq, mode="HW", k=args.primer_mismatch)
+                foralign = edlib.align(FwdPrimer, seq, mode="HW", k=args.primer_mismatch, additionalEqualities=amptklib.degenNuc)
                 #if require primer is on make finding primer in amplicon required if amplicon is larger than read length
                 #if less than read length, can't enforce primer because could have been trimmed via staggered trim in fastq_mergepairs
                 if args.primer == 'on' and len(seq) > ReadLen:
@@ -88,7 +88,7 @@ def processRead(input):
                         Seq = seq
                         Qual = qual
                 #now look for reverse primer
-                revalign = edlib.align(RevPrimer, Seq, mode="HW", task="locations", k=args.primer_mismatch)
+                revalign = edlib.align(RevPrimer, Seq, mode="HW", task="locations", k=args.primer_mismatch, additionalEqualities=amptklib.degenNuc)
                 if revalign["editDistance"] >= 0:
                     RevPrimerFound += 1
                     RevCutPos = revalign["locations"][0][0]
diff --git a/bin/amptk-process_ion.py b/bin/amptk-process_ion.py
index f9c98f3..b84c9e3 100755
--- a/bin/amptk-process_ion.py
+++ b/bin/amptk-process_ion.py
@@ -76,13 +76,13 @@ def processRead(input):
                 Seq = seq[BarcodeLength:]
                 Qual = qual[BarcodeLength:]
                 #now search for forward primer
-                foralign = edlib.align(FwdPrimer, Seq, mode="HW", k=args.primer_mismatch)
+                foralign = edlib.align(FwdPrimer, Seq, mode="HW", k=args.primer_mismatch, additionalEqualities=amptklib.degenNuc)
                 if foralign["editDistance"] < 0:
                     NoPrimer += 1
                     continue
                 ForTrim = foralign["locations"][0][1]+1   
                 #now search for reverse primer
-                revalign = edlib.align(RevPrimer, Seq, mode="HW", task="locations", k=args.primer_mismatch)
+                revalign = edlib.align(RevPrimer, Seq, mode="HW", task="locations", k=args.primer_mismatch, additionalEqualities=amptklib.degenNuc)
                 if revalign["editDistance"] >= 0:  #reverse primer was found
                     RevPrimerFound += 1 
                     #location to trim sequences
@@ -169,7 +169,7 @@ def processRead(input):
 #check if mapping file passed, use this if present, otherwise use command line arguments
 if args.mapping_file:
     if not os.path.isfile(args.mapping_file):
-        amptklib.error("Mapping file is not valid: %s" % args.mapping_file)
+        amptklib.log.error("Mapping file is not valid: %s" % args.mapping_file)
         sys.exit(1)
     mapdata = amptklib.parseMappingFile(args.mapping_file, barcode_file)
     #forward primer in first item in tuple, reverse in second
diff --git a/lib/amptklib.py b/lib/amptklib.py
index bc00094..f86a8ca 100644
--- a/lib/amptklib.py
+++ b/lib/amptklib.py
@@ -10,11 +10,132 @@
 
 primer_db = {'fITS7': 'GTGARTCATCGAATCTTTG', 'ITS4': 'TCCTCCGCTTATTGATATGC', 'ITS1-F': 'CTTGGTCATTTAGAGGAAGTAA', 'ITS2': 'GCTGCGTTCTTCATCGATGC', 'ITS3': 'GCATCGATGAAGAACGCAGC', 'ITS4-B': 'CAGGAGACTTGTACACGGTCCAG', 'ITS1': 'TCCGTAGGTGAACCTGCGG', 'LR0R': 'ACCCGCTGAACTTAAGC', 'LR2R': 'AAGAACTTTGAAAAGAG', 'JH-LS-369rc': 'CTTCCCTTTCAACAATTTCAC', '16S_V3': 'CCTACGGGNGGCWGCAG', '16S_V4': 'GACTACHVGGGTATCTAATCC', 'ITS3_KYO2': 'GATGAAGAACGYAGYRAA', 'COI-F': 'GGTCAACAAATCATAAAGATATTGG', 'COI-R': 'GGWACTAATCAATTTCCAAATCC', '515FB': 'GTGYCAGCMGCCGCGGTAA', '806RB': 'GGACTACNVGGGTWTCTAAT'}
 
+
+degenNuc = [("R", "A"), ("R", "G"), 
+            ("M", "A"), ("M", "C"),
+            ("W", "A"), ("W", "T"),
+            ("S", "C"), ("S", "G"),
+            ("Y", "C"), ("Y", "T"),
+            ("K", "G"), ("K", "T"),
+            ("V", "A"), ("V", "C"), ("V", "G"),
+            ("H", "A"), ("H", "C"), ("H", "T"),
+            ("D", "A"), ("D", "G"), ("D", "T"),
+            ("B", "C"), ("B", "G"), ("B", "T"),
+            ("N", "G"), ("N", "A"), ("N", "T"), ("N", "C"),
+            ("X", "G"), ("X", "A"), ("X", "T"), ("X", "C")]
+
 class colr:
     GRN = '\033[92m'
     END = '\033[0m'
     WARN = '\033[93m'
     
+#functions for system checks, etc
+def get_version():
+    version = subprocess.Popen(['amptk', 'version'], stdout=subprocess.PIPE).communicate()[0].rstrip()
+    return version
+
+def get_usearch_version(usearch):
+    try:
+        version = subprocess.Popen([usearch, '-version'], stderr=subprocess.PIPE, stdout=subprocess.PIPE).communicate()
+    except OSError:
+        log.error("%s not found in your PATH, exiting." % usearch)
+        sys.exit(1)
+    vers = version[0].replace('usearch v', '')
+    vers2 = vers.split('_')[0]
+    return vers2
+
+def get_vsearch_version():
+    version = subprocess.Popen(['vsearch', '--version'], stderr=subprocess.PIPE, stdout=subprocess.PIPE).communicate()
+    for v in version:
+        if v.startswith('vsearch'):
+            vers = v.replace('vsearch v', '')
+            vers2 = vers.split('_')[0]
+            return vers2
+
+def versiontuple(v):
+    return tuple(map(int, (v.split("."))))
+
+def gvc(input, check):
+    if versiontuple(input) >= versiontuple(check):
+        return True
+    else:
+        return False
+
+def versionDependencyChecks(usearch):
+    #to run amptk need usearch > 9.0.2132 and vsearch > 2.2.0
+    amptk_version = get_version()
+    usearch_version = get_usearch_version(usearch)
+    vsearch_version = get_vsearch_version()
+    usearch_pass = '9.0.2132'
+    vsearch_pass = '2.2.0'
+    if not gvc(usearch_version, usearch_pass):
+        log.error("USEARCH v%s detected, needs to be atleast v%s" % (usearch_version, usearch_pass))
+        sys.exit(1)
+    if not gvc(vsearch_version, vsearch_pass):
+        log.error("VSEARCH v%s detected, needs to be atleast v%s" % (vsearch_version, vsearch_pass))
+        sys.exit(1)
+    log.info("%s, USEARCH v%s, VSEARCH v%s" % (amptk_version, usearch_version, vsearch_version))
+
+def checkRversion():
+    #need to have R version > 3.2
+    cmd = ['Rscript', '--vanilla', os.path.join(parentdir, 'util', 'check_version.R')]
+    proc = subprocess.Popen(cmd, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
+    stdout, stderr = proc.communicate()
+    versions = stdout.replace(' \n', '')
+    Rvers = versions.split(',')[0]
+    dada2 = versions.split(',')[1]
+    return (Rvers, dada2)
+
+def checkfastqsize(input):
+    filesize = os.path.getsize(input)
+    return filesize
+
+def getCPUS():
+    cores = multiprocessing.cpu_count()
+    return cores
+
+def MemoryCheck():
+    import psutil
+    mem = psutil.virtual_memory()
+    RAM = int(mem.total)
+    return round(RAM / 1024000000)
+                   
+def systemOS():
+    if sys.platform == 'darwin':
+        system_os = 'MacOSX '+ platform.mac_ver()[0]
+    elif sys.platform == 'linux':
+        linux_version = platform.linux_distribution()
+        system_os = linux_version[0]+ ' '+linux_version[1]
+    else:
+        system_os = sys.platform
+    return system_os
+
+def SystemInfo():
+    system_os = systemOS()
+    python_vers = str(sys.version_info[0])+'.'+str(sys.version_info[1])+'.'+str(sys.version_info[2])   
+    log.info("OS: %s, %i cores, ~ %i GB RAM. Python: %s" % (system_os, multiprocessing.cpu_count(), MemoryCheck(), python_vers))
+    #print python modules to logfile
+    mod_versions()
+    
+def mod_versions():
+    import pkg_resources
+    modules = ['numpy', 'pandas', 'matplotlib', 'psutil', 'natsort', 'biopython', 'edlib', 'biom-format']
+    results = []
+    for x in modules:
+        try:
+            vers = pkg_resources.get_distribution(x).version
+            hit = "%s v%s" % (x, vers)
+        except pkg_resources.DistributionNotFound:
+            hit = "%s NOT installed!" % x
+        results.append(hit)
+        if x == 'edlib':
+            vers = vers.replace('.post2', '')
+            if not gvc(vers, '1.2.0'):
+                log.error("Edlib v%s detected, at least v1.2.0 required for degenerate nucleotide search, please upgrade.  e.g. pip install -U edlib" % vers)
+                sys.exit(1)
+    log.debug("Python Modules: %s" % ', '.join(results))
+ 
+  
 class gzopen(object):
    """Generic opener that decompresses gzipped files
    if needed. Encapsulates an open file or a GzipFile.
@@ -101,20 +222,6 @@ def Fzip_inplace(input):
     except NameError:
         subprocess.call(cmd)
 
-
-def mod_versions():
-    import pkg_resources
-    modules = ['numpy', 'pandas', 'matplotlib', 'psutil', 'natsort', 'biopython', 'edlib', 'biom-format']
-    results = []
-    for x in modules:
-        try:
-            vers = pkg_resources.get_distribution(x).version
-            hit = "%s v%s" % (x, vers)
-        except pkg_resources.DistributionNotFound:
-            hit = "%s NOT installed!" % x
-        results.append(hit)
-    log.debug("Python Modules: %s" % ', '.join(results))
-
 def fastalen2dict(input):
     Lengths = {}
     with open(input, 'rU') as infile:
@@ -330,8 +437,13 @@ def AlignRevBarcode(Seq, BarcodeDict, mismatch):
     if besthit[2] <= int(mismatch):
         return besthit[0], besthit[1]
     return "", ""
-          
-           
+
+def findFwdPrimer(primer, sequence, mismatch):
+    return edlib.align(primer, sequence, mode="HW", k=mismatch, additionalEqualities=degenNuc)
+
+def findRevPrimer(primer, sequence, mismatch, degen):
+    return edlib.align(primer, sequence, mode="HW", task="locations", k=mismatch, additionalEqualities=degenNuc) 
+      
 def MergeReads(R1, R2, tmpdir, outname, read_length, minlen, usearch, rescue, method, index, mismatch):
     removelist = []
     if mismatch == 0:
@@ -418,30 +530,6 @@ def dictFlip(input):
                 print "duplicate ID found: %s" % i
     return outDict
     
-def fuzzymatch(seq1, seq2, num_errors):
-    from Bio import pairwise2
-    seq1_a, seq2_a, score, start, end = pairwise2.align.localms(seq1, seq2, 5.0, -4.0, -9.0, -0.5, one_alignment_only=True, gap_char='-')[0]
-    if start < 2: #align needs to start in first 2 bp
-        if end < len(seq1)+2:
-            match_region = seq2_a[start:end]
-            seq_region = seq1_a[start:end]
-            matches = sum((1 if s == match_region[i] else 0) for i, s in enumerate(seq_region))
-            # too many errors -- no trimming
-            if (len(seq1) - matches) <= int(num_errors):
-                return (score, start, end)
-
-def exactmatch(seq1, seq2):
-    from Bio import pairwise2
-    seq1_a, seq2_a, score, start, end = pairwise2.align.localms(seq1, seq2, 5.0, -4.0, -9.0, -0.5, one_alignment_only=True, gap_char='-')[0]
-    match_region = seq2_a[start:end]
-    seq_region = seq1_a[start:end]
-    matches = sum((1 if s == match_region[i] else 0) for i, s in enumerate(seq_region))
-    # too many errors -- no trimming
-    if (len(seq1) - matches) <= 0:
-        return (score, start, end)
-    else:
-        return False
-
 def classifier2dict(input, pcutoff):
     ClassyDict = {}
     with open(input, 'rU') as infile:
@@ -625,62 +713,6 @@ def mapping2dict(input):
                 sys.exit(1)
     return MapDict
 
-def get_version():
-    version = subprocess.Popen(['amptk', 'version'], stdout=subprocess.PIPE).communicate()[0].rstrip()
-    return version
-
-def get_usearch_version(usearch):
-    try:
-        version = subprocess.Popen([usearch, '-version'], stderr=subprocess.PIPE, stdout=subprocess.PIPE).communicate()
-    except OSError:
-        log.error("%s not found in your PATH, exiting." % usearch)
-        sys.exit(1)
-    vers = version[0].replace('usearch v', '')
-    vers2 = vers.split('_')[0]
-    return vers2
-
-def get_vsearch_version():
-    version = subprocess.Popen(['vsearch', '--version'], stderr=subprocess.PIPE, stdout=subprocess.PIPE).communicate()
-    for v in version:
-        if v.startswith('vsearch'):
-            vers = v.replace('vsearch v', '')
-            vers2 = vers.split('_')[0]
-            return vers2
-
-def versiontuple(v):
-    return tuple(map(int, (v.split("."))))
-
-def gvc(input, check):
-    if versiontuple(input) >= versiontuple(check):
-        return True
-    else:
-        return False
-
-def versionDependencyChecks(usearch):
-    #to run amptk need usearch > 9.0.2132 and vsearch > 2.2.0
-    amptk_version = get_version()
-    usearch_version = get_usearch_version(usearch)
-    vsearch_version = get_vsearch_version()
-    usearch_pass = '9.0.2132'
-    vsearch_pass = '2.2.0'
-    if not gvc(usearch_version, usearch_pass):
-        log.error("USEARCH v%s detected, needs to be atleast v%s" % (usearch_version, usearch_pass))
-        sys.exit(1)
-    if not gvc(vsearch_version, vsearch_pass):
-        log.error("VSEARCH v%s detected, needs to be atleast v%s" % (vsearch_version, vsearch_pass))
-        sys.exit(1)
-    log.info("%s, USEARCH v%s, VSEARCH v%s" % (amptk_version, usearch_version, vsearch_version))
-
-def checkRversion():
-    #need to have R version > 3.2
-    cmd = ['Rscript', '--vanilla', os.path.join(parentdir, 'util', 'check_version.R')]
-    proc = subprocess.Popen(cmd, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
-    stdout, stderr = proc.communicate()
-    versions = stdout.replace(' \n', '')
-    Rvers = versions.split(',')[0]
-    dada2 = versions.split(',')[1]
-    return (Rvers, dada2)
-
 def runMultiProgress(function, inputList, cpus):
     #setup pool
     p = multiprocessing.Pool(cpus)
@@ -700,29 +732,6 @@ def runMultiProgress(function, inputList, cpus):
     p.close()
     p.join()
 
-def MemoryCheck():
-    import psutil
-    mem = psutil.virtual_memory()
-    RAM = int(mem.total)
-    return round(RAM / 1024000000)
-                   
-def systemOS():
-    if sys.platform == 'darwin':
-        system_os = 'MacOSX '+ platform.mac_ver()[0]
-    elif sys.platform == 'linux':
-        linux_version = platform.linux_distribution()
-        system_os = linux_version[0]+ ' '+linux_version[1]
-    else:
-        system_os = sys.platform
-    return system_os
-
-def SystemInfo():
-    system_os = systemOS()
-    python_vers = str(sys.version_info[0])+'.'+str(sys.version_info[1])+'.'+str(sys.version_info[2])   
-    log.info("OS: %s, %i cores, ~ %i GB RAM. Python: %s" % (system_os, multiprocessing.cpu_count(), MemoryCheck(), python_vers))
-    #print python modules to logfile
-    mod_versions()    
-
 
 def batch_iterator(iterator, batch_size):
     entry = True #Make sure we loop once
@@ -907,13 +916,6 @@ def guess_csv_dialect(header):
     dialect = csv.Sniffer().sniff(header, delimiters=possible_delims)
     return dialect
 
-def checkfastqsize(input):
-    filesize = os.path.getsize(input)
-    return filesize
-
-def getCPUS():
-    cores = multiprocessing.cpu_count()
-    return cores
     
 def fasta2list(input):
     seqlist = []
@@ -953,10 +955,11 @@ def parseMappingFile(input, output):
                     continue
                 cols = line.split('\t')
                 outfile.write('>%s\n%s\n' % (cols[0], cols[1]))
-                match = exactmatch(cols[1], cols[2])
-                if match:
+                match = edlib.align(cols[1], cols[2], mode="HW", k=0)
+                if match["editDistance"] == 0:
+                    Trim = match["locations"][0][1]+1
                     if fwdprimer == '':
-                        fwdprimer = cols[2][int(match[2]):]
+                        fwdprimer = cols[2][Trim:]
                         revprimer = cols[3]
                 else:
                     print "%s: barcode sequence not in LinkerPrimerSequence" % cols[0]
@@ -974,10 +977,11 @@ def parseMappingFileIllumina(input):
             cols = line.split('\t')
             if not cols[0] in samples:
                 samples.append(cols[0])
-            match = exactmatch(cols[1], cols[2])
-            if match:
+            match = edlib.align(cols[1], cols[2], mode="HW", k=0)
+            if match["editDistance"] == 0:
+                Trim = match["locations"][0][1]+1
                 if fwdprimer == '':
-                    fwdprimer = cols[2][int(match[2]):]
+                    fwdprimer = cols[2][Trim:]
                     revprimer = cols[3]
             else:
                 fwdprimer = cols[2]
diff --git a/util/amptk-get_barcode_counts.py b/util/amptk-get_barcode_counts.py
index 6765e60..5aac5e6 100755
--- a/util/amptk-get_barcode_counts.py
+++ b/util/amptk-get_barcode_counts.py
@@ -76,9 +76,9 @@ def countBarcodes(file):
             
 
     #now let's count the barcodes found and count the number of times they are found.
-    barcode_counts = "%20s:  %s" % ('Sample', 'Count')
+    barcode_counts = "%10s:  %s" % ('Sample', 'Count')
     for k,v in natsorted(BarcodeCount.items(), key=lambda (k,v): v, reverse=True):
-        barcode_counts += "\n%20s:  %s" % (k, str(BarcodeCount[k]))
+        barcode_counts += "\n%10s:  %s" % (k, str(BarcodeCount[k]))
     print("Found %i barcoded samples\n%s" % (len(BarcodeCount), barcode_counts))
 
 def getSeqLength(file):
diff --git a/util/amptk-keep_samples.py b/util/amptk-keep_samples.py
index 4c49b7a..ea97386 100755
--- a/util/amptk-keep_samples.py
+++ b/util/amptk-keep_samples.py
@@ -1,6 +1,6 @@
 #!/usr/bin/env python
 
-import sys, argparse, os, inspect, itertools
+import sys, argparse, os, inspect, itertools, multiprocessing
 from Bio.SeqIO.QualityIO import FastqGeneralIterator
 currentdir = os.path.dirname(os.path.abspath(inspect.getfile(inspect.currentframe())))
 parentdir = os.path.dirname(currentdir)
@@ -50,10 +50,17 @@ def filter_sample(file, output):
                 if args.format == 'fasta':
                     out.write(">%s\n%s\n" % (title, seq))
 
+#check if input compressed, incompress if it is
+if args.input.endswith('.gz'):
+    SeqIn = args.input.replace('.gz', '')
+    amptklib.Funzip(args.input, SeqIn, multiprocessing.cpu_count())
+else:
+    SeqIn = args.input
+
 keepers = []
 if args.threshold:
     print("Keeping samples with more than %i reads" % args.threshold)
-    BC_counts = countBarcodes(args.input)
+    BC_counts = countBarcodes(SeqIn)
     for k,v in BC_counts.items():
         if int(v) >= args.threshold:
             if not k in keepers:
@@ -78,9 +85,19 @@ def filter_sample(file, output):
 #now run filtering 
 keep_count = 0
 total_count = 0
-filter_sample(args.input, args.out)
+
+#rename to base
+if args.out.endswith('.gz'):
+    outfile = args.out.replace('.gz', '')
+else:
+    outfile = args.out
+#run filtering
+filter_sample(SeqIn, outfile)
+#compress and clean
 if args.out.endswith('.gz'): #compress in place
-    amptklib.Fzip_inplace(args.out)
+    amptklib.Fzip_inplace(outfile)
+if args.input.endswith('.gz'):
+    amptklib.removefile(SeqIn)
       
 print("Kept %i reads out of %i total reads" % (keep_count, total_count))
 
diff --git a/util/amptk-remove_samples.py b/util/amptk-remove_samples.py
index 6e5fa1b..69e465b 100755
--- a/util/amptk-remove_samples.py
+++ b/util/amptk-remove_samples.py
@@ -1,6 +1,6 @@
 #!/usr/bin/env python
 
-import sys, argparse, os, inspect, itertools
+import sys, argparse, os, inspect, itertools, multiprocessing
 from Bio.SeqIO.QualityIO import FastqGeneralIterator
 currentdir = os.path.dirname(os.path.abspath(inspect.getfile(inspect.currentframe())))
 parentdir = os.path.dirname(currentdir)
@@ -40,7 +40,7 @@ def countBarcodes(file):
 def filter_sample(file, output):
     global keep_count, total_count
     with open(output, 'w') as out:
-        for title, seq, qual in FastqGeneralIterator(amptklib.gzopen(file)):
+        for title, seq, qual in FastqGeneralIterator(open(file)):
             total_count += 1
             sample = title.split('=',1)[1].split(';')[0]
             if not sample in keep_list:
@@ -50,10 +50,17 @@ def filter_sample(file, output):
                 elif args.format == 'fasta':
                     out.write(">%s\n%s\n" % (title, seq))
 
+#check if input compressed, incompress if it is
+if args.input.endswith('.gz'):
+    SeqIn = args.input.replace('.gz', '')
+    amptklib.Funzip(args.input, SeqIn, multiprocessing.cpu_count())
+else:
+    SeqIn = args.input
+
 remove = []
 if args.threshold:
     print("Removing samples with less than %i reads" % args.threshold)
-    BC_counts = countBarcodes(args.input)
+    BC_counts = countBarcodes(SeqIn)
     for k,v in BC_counts.items():
         if int(v) <= args.threshold:
             if not k in remove:
@@ -76,10 +83,21 @@ def filter_sample(file, output):
 #now run filtering 
 keep_count = 0
 total_count = 0
-filter_sample(args.input, args.out)
+
+#rename to base
+if args.out.endswith('.gz'):
+    outfile = args.out.replace('.gz', '')
+else:
+    outfile = args.out
+#run filtering
+filter_sample(SeqIn, outfile)
+#compress and clean
 if args.out.endswith('.gz'): #compress in place
-    amptklib.Fzip_inplace(args.out)
-      
+    amptklib.Fzip_inplace(outfile)
+if args.input.endswith('.gz'):
+    amptklib.removefile(SeqIn)
+
+   
 print("Removed %i samples" % count)
 print("Kept %i reads out of %i total reads" % (keep_count, total_count))
 
diff --git a/util/amptk-split_samples_fastq.py b/util/amptk-split_samples_fastq.py
index 2a2bbbe..f7d483c 100755
--- a/util/amptk-split_samples_fastq.py
+++ b/util/amptk-split_samples_fastq.py
@@ -9,6 +9,7 @@
 import lib.revcomp_lib as revcomp_lib
 import lib.amptklib as amptklib
 from Bio.SeqIO.QualityIO import FastqGeneralIterator
+import edlib
 
 class MyFormatter(argparse.ArgumentDefaultsHelpFormatter):
     def __init__(self,prog):
diff --git a/util/amptk-strip_primer.py b/util/amptk-strip_primer.py
index 3a0c83c..903102f 100755
--- a/util/amptk-strip_primer.py
+++ b/util/amptk-strip_primer.py
@@ -36,13 +36,13 @@ def primerStrip(file):
     with open(goodseq, 'w') as good:
         with open(badseq, 'w') as bad:
             for title, seq, qual in FastqGeneralIterator(open(file)):
-                foralign = edlib.align(args.fwd_primer, seq, mode="HW", k=args.primer_mismatch)
+                foralign = edlib.align(args.fwd_primer, seq, mode="HW", k=args.primer_mismatch, additionalEqualities=amptklib.degenNuc)
                 if foralign["editDistance"] >= 0:
                     ForCutPos = foralign["locations"][0][1]+1
                     Seq = seq[ForCutPos:]
                     Qual = qual[ForCutPos:]
                     #align reverse
-                    revalign = edlib.align(RevPrimer, Seq, mode="HW", task="locations", k=args.primer_mismatch)
+                    revalign = edlib.align(RevPrimer, Seq, mode="HW", task="locations", k=args.primer_mismatch, additionalEqualities=amptklib.degenNuc)
                     if revalign["editDistance"] >= 0:
                         RevCutPos = revalign["locations"][0][0]
                         Seq = Seq[:RevCutPos]
@@ -58,13 +58,13 @@ def revprimerStrip(file):
     with open(goodseq, 'w') as good:
         with open(badseq, 'w') as bad:
             for title, seq, qual in FastqGeneralIterator(open(file)):
-                foralign = edlib.align(args.rev_primer, seq, mode="HW", k=args.primer_mismatch)
+                foralign = edlib.align(args.rev_primer, seq, mode="HW", k=args.primer_mismatch, additionalEqualities=amptklib.degenNuc)
                 if foralign["editDistance"] >= 0:
                     ForCutPos = foralign["locations"][0][1]+1
                     Seq = seq[ForCutPos:]
                     Qual = qual[ForCutPos:]
                     #align reverse
-                    revalign = edlib.align(RevForPrimer, Seq, mode="HW", task="locations", k=args.primer_mismatch)
+                    revalign = edlib.align(RevForPrimer, Seq, mode="HW", task="locations", k=args.primer_mismatch, additionalEqualities=amptklib.degenNuc)
                     if revalign["editDistance"] >= 0:
                         RevCutPos = revalign["locations"][0][0]
                         Seq = Seq[:RevCutPos]