--- a
+++ b/singlecellmultiomics/modularDemultiplexer/demultiplexModules/DamID.py
@@ -0,0 +1,448 @@
+from singlecellmultiomics.modularDemultiplexer.baseDemultiplexMethods import ScatteredUmiBarcodeDemuxMethod, UmiBarcodeDemuxMethod, NonMultiplexable, IlluminaBaseDemultiplexer, phredToFastqHeaderSafeQualities
+from singlecellmultiomics.modularDemultiplexer.demultiplexModules import CELSeq2_c8_u6
+import re
+from singlecellmultiomics.utils import reverse_complement
+
+
+
+
+class DamID2(UmiBarcodeDemuxMethod):
+    def __init__(self, barcodeFileParser, random_primer_read=None,random_primer_length=None, **kwargs):
+        self.barcodeFileAlias = 'DamID2'
+        UmiBarcodeDemuxMethod.__init__(
+            self,
+            umiRead=0,
+            umiStart=0,
+            umiLength=3,
+            barcodeRead=0,
+            barcodeStart=3,
+            barcodeLength=10,
+            random_primer_read=random_primer_read,
+            random_primer_length=random_primer_length,
+            barcodeFileAlias=self.barcodeFileAlias,
+            barcodeFileParser=barcodeFileParser,
+            **kwargs)
+        self.shortName = 'DamID2'
+        self.longName = 'DamID,  CB: 10bp UMI: 3bp'
+        self.autoDetectable = True
+        self.description = '48 barcodes, 3bp umi followed by 10bp barcode, the last two bases of the barcode are CA'
+
+        self.sequenceCapture[0] = slice(
+            self.umiLength + self.barcodeLength - 1,
+            None)  # do map the first base of the barcode
+
+    def demultiplex(self, records, probe=False, **kwargs):
+
+        if probe and records[0].sequence[self.barcodeLength + self.umiLength-2:self.barcodeLength + self.umiLength] != 'CA':
+            raise NonMultiplexable
+
+
+        # add first 2 bases as ligation tag:
+        ligation_start = self.umiLength + self.barcodeLength -2
+        ligation_end = ligation_start + 2
+        ligation_sequence = records[0].sequence[ligation_start:ligation_end]
+        ligation_qualities = records[0].qual[ligation_start:ligation_end]
+
+        taggedRecords = UmiBarcodeDemuxMethod.demultiplex(
+            self, records, probe=probe, **kwargs)
+
+        for rec in taggedRecords:
+            rec.addTagByTag(
+                'lh',
+                ligation_sequence,
+                isPhred=False,
+                make_safe=False)
+            rec.addTagByTag(
+                'lq',
+                ligation_qualities,
+                isPhred=True,
+                make_safe=False)
+            rec.tags['dt'] = 'DamID'
+
+        return taggedRecords
+
+
+class DamID2_NO_OVERHANG(UmiBarcodeDemuxMethod):
+    def __init__(self, barcodeFileParser, random_primer_read=None,random_primer_length=None, **kwargs):
+        self.barcodeFileAlias = 'DamID2_8bp'
+        UmiBarcodeDemuxMethod.__init__(
+            self,
+            umiRead=0,
+            umiStart=0,
+            umiLength=3,
+            barcodeRead=0,
+            barcodeStart=3,
+            barcodeLength=8,
+            random_primer_read=random_primer_read,
+            random_primer_length=random_primer_length,
+            barcodeFileAlias=self.barcodeFileAlias,
+            barcodeFileParser=barcodeFileParser,
+            **kwargs)
+        self.shortName = 'DamID2_8bp_noCA'
+        self.longName = 'DamID,  CB: 8bp UMI: 3bp'
+        self.autoDetectable = True
+        self.description = '48 barcodes, 3bp umi followed by 8bp barcode, no CA overhang in barcodes'
+
+        self.sequenceCapture[0] = slice(
+            self.umiLength + self.barcodeLength - 1,
+            None)  # do map the first base of the barcode
+
+    def demultiplex(self, records, probe=False, **kwargs):
+
+        #if probe and records[0].sequence[self.barcodeLength + self.umiLength-2:self.barcodeLength + self.umiLength] != 'CA':
+        #    raise NonMultiplexable
+
+
+        # add first 2 bases as ligation tag:
+        ligation_start = self.umiLength + self.barcodeLength 
+        ligation_end = ligation_start + 2
+        ligation_sequence = records[0].sequence[ligation_start:ligation_end]
+        ligation_qualities = records[0].qual[ligation_start:ligation_end]
+
+        taggedRecords = UmiBarcodeDemuxMethod.demultiplex(
+            self, records, probe=probe, **kwargs)
+
+        for rec in taggedRecords:
+            rec.addTagByTag(
+                'lh',
+                ligation_sequence,
+                isPhred=False,
+                make_safe=False)
+            rec.addTagByTag(
+                'lq',
+                ligation_qualities,
+                isPhred=True,
+                make_safe=False)
+            rec.tags['dt'] = 'DamID'
+        return taggedRecords
+    
+class DamID2_c8_u3_cs2(UmiBarcodeDemuxMethod):
+    def __init__(self, barcodeFileParser, random_primer_read=None, random_primer_length=None, **kwargs):
+        self.barcodeFileAlias = 'DamAndT'
+        UmiBarcodeDemuxMethod.__init__(
+            self,
+            umiRead=0,
+            umiStart=0,
+            umiLength=3,
+            barcodeRead=0,
+            barcodeStart=3,
+            barcodeLength=10,
+            random_primer_read=random_primer_read,
+            random_primer_length=random_primer_length,
+            barcodeFileAlias=self.barcodeFileAlias,
+            barcodeFileParser=barcodeFileParser,
+            **kwargs)
+        self.shortName = 'DamAndT'
+        self.longName = 'DamAndT,  CB: 10bp UMI: 3bp'
+        self.autoDetectable = True
+        self.description = 'DamID2 and CS2 Transcriptome'
+
+        self.sequenceCapture[0] = slice(
+            self.umiLength + self.barcodeLength - 2,
+            None)  # do map the first two bases of the barcode
+        
+        self.transcriptome_demux =  CELSeq2_c8_u6(barcodeFileParser=barcodeFileParser,**kwargs)
+        self.damid_demux =  DamID2(barcodeFileParser=barcodeFileParser,**kwargs)
+
+
+    def demultiplex(self, records, probe=False, **kwargs):
+        # Check if the supplied reads are mate-pair:
+        if len(records) != 2:
+            raise NonMultiplexable('Not mate pair')
+
+
+        # Obtain the DAMID barcode and umi:
+        try:
+            damid_tagged_records = self.damid_demux.demultiplex(records, probe=probe, **kwargs)
+        except NonMultiplexable as e:
+            damid_tagged_records = None
+            
+        
+        # Obtain TX barcode and umi
+        try:
+            tx_tagged_records = self.transcriptome_demux.demultiplex(records, probe=probe, **kwargs)
+            # Prune the poly T off R1 start
+            
+            r1 = tx_tagged_records[0]
+            
+            pos = 0
+            for pos, base in enumerate(r1.sequence):
+                if base!='T':
+                    break
+
+            r1.sequence = r1.sequence[pos:]
+            r1.qualities  = r1.qualities[pos:]
+
+        except NonMultiplexable:
+            tx_tagged_records = None
+
+        # Check which of the demuxers yielded results
+        # damid_tagged_records
+        # damid_taggedRecords[0].tags.update(ud)
+        # damid_taggedRecords[1].tags.update(ud)
+        if tx_tagged_records is not None and damid_tagged_records is not None:
+            # Both types
+            tagged_records = damid_tagged_records
+            for rec in tagged_records:
+                rec.tags['dt'] = 'Ambiguous'
+
+        elif tx_tagged_records is not None:
+            tagged_records = tx_tagged_records
+            for rec in tagged_records:
+                rec.tags['dt'] = 'RNA'
+        elif damid_tagged_records is not None:
+            tagged_records = damid_tagged_records
+            for rec in tagged_records:
+                rec.tags['dt'] = 'DamID'
+        elif tx_tagged_records is None and damid_tagged_records is None:
+
+            raise NonMultiplexable('Not DamID or TX')
+        else:
+            raise ValueError('failure')
+
+        return tagged_records
+
+
+class DamID2_SCA(ScatteredUmiBarcodeDemuxMethod):
+    def __init__(self, 
+                 barcodeFileParser, 
+                random_primer_read=None, 
+                random_primer_length=None, 
+                first_umi_len = 3,
+                first_bc_len = 4,
+                second_umi_len = 3,
+                second_barcode_len = 4,
+                barcode_alias=None, 
+                **kwargs):
+        if barcode_alias is None:
+            self.barcodeFileAlias = 'DamID2_scattered_8bp'
+        else:
+            self.barcodeFileAlias= barcode_alias
+
+        # eg 3-ATTG-3-GAAC[GA]
+        
+        self.total_mi_len = first_umi_len+first_bc_len+second_umi_len+second_barcode_len
+        barcode_slices = (
+            ( slice(first_umi_len,first_umi_len+first_bc_len), 
+                slice(first_umi_len+first_bc_len+second_umi_len,first_umi_len+first_bc_len+second_umi_len+second_barcode_len )),  ()
+        )
+        umi_slices = (
+            (slice(0,first_umi_len), 
+                slice(first_umi_len+first_bc_len,first_umi_len+first_bc_len+second_umi_len)
+                ),
+            ()
+        )
+        capture_slices = (
+            slice(self.total_mi_len,None),
+            slice(None)
+        )
+
+
+        ScatteredUmiBarcodeDemuxMethod.__init__(
+            self,
+            barcode_slices = barcode_slices, # 2-len Tuple of List of slices where the cell barcode is present in the read (slice(), slice(), ...], [ slice())
+            umi_slices = umi_slices, # 2-len List of slices where the UMI is present in the read [slice(), slice(), ...], [slice()] # 
+            capture_slices = capture_slices, # Slices which indicate what region of read 1 and read2 to store in the final read (required)
+            barcodeFileAlias=self.barcodeFileAlias,
+            barcodeFileParser=barcodeFileParser,
+            **kwargs)
+        self.shortName = 'DamID2_3u4b3u6b'
+        self.longName = 'DamID, 3bp UMI, 4bp CB, 3bp UMI, 6bp CB'
+        self.autoDetectable = True
+        self.description = 'DamID, starting with a 3bp UMI, 4bp CB, 3bp UMI, 6bp CB'
+
+
+    def demultiplex(self, records, probe=False, **kwargs):
+
+        #if probe and records[0].sequence[self.barcodeLength + self.umiLength-2:self.barcodeLength + self.umiLength] != 'CA':
+        #    raise NonMultiplexable
+
+
+        # add first 2 bases as ligation tag:
+        ligation_start = self.total_mi_len
+        ligation_end = self.total_mi_len+2
+        ligation_sequence = records[0].sequence[ligation_start:ligation_end]
+        ligation_qualities = records[0].qual[ligation_start:ligation_end]
+
+        taggedRecords = ScatteredUmiBarcodeDemuxMethod.demultiplex(
+            self, records, probe=probe, **kwargs)
+
+        for rec in taggedRecords:
+            rec.addTagByTag(
+                'lh',
+                ligation_sequence,
+                isPhred=False,
+                make_safe=False)
+            rec.addTagByTag(
+                'lq',
+                ligation_qualities,
+                isPhred=True,
+                make_safe=False)
+
+        return taggedRecords
+    
+
+class DamID2andT_SCA6(DamID2_c8_u3_cs2):
+    def __init__(self, barcodeFileParser, random_primer_read=None, random_primer_length=None, **kwargs):
+        
+        self.transcriptome_demux =  DamID2_SCA(barcodeFileParser=barcodeFileParser,barcode_alias='CS2_scattered_8bp',
+                                                first_umi_len = 3,
+                                                first_bc_len = 4,
+                                                second_umi_len = 3,
+                                                second_barcode_len = 4,
+                                               **kwargs)
+        self.damid_demux =  DamID2_SCA(barcodeFileParser=barcodeFileParser,
+                                       second_barcode_len=6,
+                                       barcode_alias='DamID2_scattered_10bp',
+                                       **kwargs)
+        self.autoDetectable = True
+
+        self.shortName = 'DamID2andT_3u4b3u6b'
+        self.longName = 'DamID and transcriptome, 3bp UMI, 4bp CB, 3bp UMI, 6bp CB'
+        self.autoDetectable = True
+        self.description = 'DamID and transcriptome, starting with a 3bp UMI, 4bp CB, 3bp UMI, 6bp CB'
+        self.indexSummary = self.transcriptome_demux.indexSummary + ', ' + self.damid_demux.indexSummary
+        self.barcodeSummary = self.transcriptome_demux.barcodeSummary + ', ' + self.damid_demux.barcodeSummary
+
+    def demultiplex(self, records, probe=False, **kwargs):
+        # Check if the supplied reads are mate-pair:
+        if len(records) != 2:
+            raise NonMultiplexable('Not mate pair')
+
+
+        # Obtain the DAMID barcode and umi:
+        try:
+            damid_tagged_records = self.damid_demux.demultiplex(records, probe=probe, **kwargs)
+        except NonMultiplexable as e:
+            damid_tagged_records = None
+            
+        
+        # Obtain TX barcode and umi
+        try:
+            tx_tagged_records = self.transcriptome_demux.demultiplex(records, probe=probe, **kwargs)
+            # Prune the poly T off R1 start
+            
+            r1 = tx_tagged_records[0]
+            
+            pos = 0
+            for pos, base in enumerate(r1.sequence):
+                if base!='T':
+                    break
+
+            r1.sequence = r1.sequence[pos:]
+            r1.qualities  = r1.qualities[pos:]
+
+        except NonMultiplexable:
+            tx_tagged_records = None
+
+        # Check which of the demuxers yielded results
+        # damid_tagged_records
+        # damid_taggedRecords[0].tags.update(ud)
+        # damid_taggedRecords[1].tags.update(ud)
+        if tx_tagged_records is not None and damid_tagged_records is not None:
+            # Both types
+            for tx_tagged_record, damid_tagged_record in zip(tx_tagged_records, damid_tagged_records):
+                tx_tagged_record.tags.update(damid_tagged_record.tags)
+            tagged_records = tx_tagged_record
+        elif tx_tagged_records is not None:
+            tagged_records = tx_tagged_records
+            for rec in tagged_records:
+                rec.tags['dt'] = 'RNA'
+        elif damid_tagged_records is not None:
+            tagged_records = damid_tagged_records
+            for rec in tagged_records:
+                rec.tags['dt'] = 'DamID'
+        elif tx_tagged_records is None and damid_tagged_records is None:
+
+            raise NonMultiplexable('Not DamID or TX')
+        else:
+            raise ValueError('failure')
+
+        return tagged_records
+    
+
+class DamID2andT_SCA(DamID2_c8_u3_cs2):
+    def __init__(self, barcodeFileParser, random_primer_read=None, random_primer_length=None, **kwargs):
+        
+        self.transcriptome_demux =  DamID2_SCA(barcodeFileParser=barcodeFileParser,barcode_alias='CS2_scattered_8bp',
+                                                first_umi_len = 3,
+                                                first_bc_len = 4,
+                                                second_umi_len = 3,
+                                                second_barcode_len = 4,
+                                               **kwargs)
+        
+        self.damid_demux =  DamID2_SCA(barcodeFileParser=barcodeFileParser,
+                                       first_umi_len = 3,
+                                                first_bc_len = 4,
+                                                second_umi_len = 3,
+                                                second_barcode_len = 4,
+                                                barcode_alias='DamID2_scattered_8bp',
+                                       **kwargs
+                                       )
+        self.autoDetectable = True
+
+        self.shortName = 'DamID2andT_3u4b3u4b'
+        self.longName = 'DamID and transcriptome, 3bp UMI, 4bp CB, 3bp UMI, 4bp CB'
+        self.autoDetectable = True
+        self.description = 'DamID and transcriptome, starting with a 3bp UMI, 4bp CB, 3bp UMI, 4bp CB'
+        self.indexSummary = self.transcriptome_demux.indexSummary + ', ' + self.damid_demux.indexSummary
+        self.barcodeSummary = self.transcriptome_demux.barcodeSummary + ', ' + self.damid_demux.barcodeSummary
+
+    def demultiplex(self, records, probe=False, **kwargs):
+        # Check if the supplied reads are mate-pair:
+        if len(records) != 2:
+            raise NonMultiplexable('Not mate pair')
+
+
+        # Obtain the DAMID barcode and umi:
+        try:
+            damid_tagged_records = self.damid_demux.demultiplex(records, probe=probe, **kwargs)
+            
+        except NonMultiplexable as e:
+            damid_tagged_records = None
+            
+        
+        # Obtain TX barcode and umi
+        try:
+            tx_tagged_records = self.transcriptome_demux.demultiplex(records, probe=probe, **kwargs)
+            # Prune the poly T off R1 start
+            
+            r1 = tx_tagged_records[0]
+            
+            pos = 0
+            for pos, base in enumerate(r1.sequence):
+                if base!='T':
+                    break
+
+            r1.sequence = r1.sequence[pos:]
+            r1.qualities  = r1.qualities[pos:]
+
+        except NonMultiplexable:
+            tx_tagged_records = None
+
+        # Check which of the demuxers yielded results
+        # damid_tagged_records
+        # damid_taggedRecords[0].tags.update(ud)
+        # damid_taggedRecords[1].tags.update(ud)
+        if tx_tagged_records is not None and damid_tagged_records is not None:
+            # Both types
+            tagged_records = damid_tagged_records
+            for rec in tagged_records:
+                rec.tags['dt'] = 'Ambiguous'
+
+        elif tx_tagged_records is not None:
+            tagged_records = tx_tagged_records
+            for rec in tagged_records:
+                rec.tags['dt'] = 'RNA'
+        elif damid_tagged_records is not None:
+            tagged_records = damid_tagged_records
+            for rec in tagged_records:
+                rec.tags['dt'] = 'DamID'
+        elif tx_tagged_records is None and damid_tagged_records is None:
+
+            raise NonMultiplexable('Not DamID or TX')
+        else:
+            raise ValueError('failure')
+
+        return tagged_records
+