diff --git a/requirements.txt b/requirements.txt
index fe38ee6..bc44fad 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -1,4 +1 @@
-autopep8==1.5.7
-pycodestyle==2.8.0
 pysam==0.17.0
-toml==0.10.2
diff --git a/trim.py b/trim.py
deleted file mode 100644
index 14cd24b..0000000
--- a/trim.py
+++ /dev/null
@@ -1,541 +0,0 @@
-import pysam
-import sys
-import time
-import math
-
-# Constants, so we can easily see what type of operation we want
-BAM_CMATCH = 0
-BAM_CINS = 1
-BAM_CDEL = 2
-BAM_CREF_SKIP = 3
-BAM_CSOFT_CLIP = 4
-BAM_CHARD_CLIP = 5
-BAM_CPAD = 6
-BAM_CEQUAL = 7
-BAM_CDIFF = 8
-BAM_CBACK = 9
-
-# Determine which primers overlap with a given start of a read
-
-
-def getOverlappingPrimers(start, primers):
-    overlapping = []
-    for primer in primers:
-        # If the start is between the primer's start and end, it's an overlap
-        # [-----primer[0]-----start-----primer[1]-----] as an example, is an overlap
-        if start >= primer[0] and start <= primer[1]:
-            overlapping.append(primer)
-
-    return overlapping
-
-
-def getPosOnQuery(cigar, pos, seg_start):
-    # Initializations
-    queryPos = 0
-    curPos = seg_start
-
-    # For each operation in our cigar
-    for operation in cigar:
-        # If we consume the reference
-        if consumeReference[operation[0]]:
-            # If our desired position is found somewhere inside the current operation
-            if pos <= curPos + operation[1]:
-                # If we consume the query, we want to advance the position on the query by as much as we need to go
-                if consumeQuery[operation[0]]:
-                    queryPos += (pos - curPos)
-
-                # Return, as our desired position is found in this operation
-                return queryPos
-
-            # Advance past the current operation, as it exists outside of the current operation
-            curPos += operation[1]
-
-        # If we consume the query, we want to advance our query's pointer
-        if consumeQuery[operation[0]]:
-            queryPos += operation[1]
-
-    # We ran out of operations, so it must be here (or outside our query)
-    return queryPos
-
-# Convert a position on the read to a position on the reference
-
-
-def getPosOnReference(cigar, pos, ref_start):
-    curPos = 0
-    referencePos = ref_start
-
-    for operation in cigar:
-        if consumeQuery[operation[0]]:
-            if pos <= curPos + operation[1]:
-                if consumeReference[operation[0]]:
-                    referencePos += (pos - curPos)
-
-                return referencePos
-
-            curPos += operation[1]
-
-        if consumeReference[operation[0]]:
-            referencePos += operation[1]
-
-    return referencePos
-
-
-def cigarToRefLen(cigar):
-    len = 0
-    for operation in cigar:
-        if consumeReference[operation[0]]:
-            len += operation[1]
-
-    return len
-
-
-def cigarToQLen(cigar):
-    len = 0
-    for operation in cigar:
-        if consumeQuery[operation[0]]:
-            len += operation[1]
-
-    return len
-
-
-# Information about cigar operations
-cigarMap = ["M", "I", "D", "N", "S", "H", "P", "=", "X"]
-consumeQuery = [True, True, False, False, True, False, False, True, True]
-consumeReference = [True, False, True, True, False, False, False, True, True]
-
-
-def trim(bam, primer_file, output, min_read_length=30, min_qual_thresh=20, sliding_window=4, include_no_primer=False):
-    ##### Initialize Counters #####
-    removed_reads = 0
-    primer_trimmed_count = 0
-    no_primer_count = 0
-    quality_trimmed_count = 0
-    no_cigar_count = 0
-    unmapped = 0
-
-    ##### Build our primer list #####
-    max_primer_len = 0
-    primers = []
-    for primer in primer_file:
-        data = primer.split()
-        start = int(data[1])
-        # End isn't 0 based in bed
-        end = int(data[2]) - 1
-
-        primers.append((start, end))
-        # Determine the longest primer
-        if end - start + 1 > max_primer_len:
-            max_primer_len = end - start + 1
-
-    starttime = math.floor(time.time())
-    curtime = 0
-    print("Procesesing Reads...")
-
-    processed = 0
-    ##### Iterate Through Reads #####
-    for r in bam:
-        if curtime != math.floor(time.time()):
-            curtime = math.floor(time.time())
-            sys.stdout.write("\r{0} Processed {1} mapped reads, Elapsed Time: {2}:{3}".format(
-                ["|", "/", "-", "\\"][curtime % 4],
-                processed,
-                math.floor((curtime-starttime)/60),
-                (curtime-starttime) % 60)
-            )
-            sys.stdout.flush()
-
-        if r.is_unmapped:
-            unmapped += 1
-            continue
-
-        processed += 1
-
-        # If we have no cigar, we cannot do anything with this read. We will not output it nor do anything with it.
-        if r.cigartuples == None:
-            no_cigar_count += 1
-            continue
-
-        # Info for stats
-        primer_trimmed = False
-        quality_trimmed = False
-
-        ##### Primer Trim #####
-        overlapping_start = getOverlappingPrimers(r.reference_start, primers)
-        overlapping_end = getOverlappingPrimers(r.reference_end - 1, primers)
-
-        isize_flag = abs(r.template_length) - \
-            max_primer_len > abs(cigarToQLen(r.cigartuples))
-
-        ref_start_offset = 0
-
-        if not (r.is_paired and isize_flag and r.is_reverse) and len(overlapping_start) > 0:
-            primer_trimmed = True
-            # Determine greatest overlap
-            overlap_end = 0
-            for primer in overlapping_start:
-                if primer[1] > overlap_end:
-                    overlap_end = primer[1]
-            max_delete_start = getPosOnQuery(
-                r.cigartuples, overlap_end + 1, r.reference_start)
-            max_delete_start = max(max_delete_start, 0)
-
-            # Initializations
-            newcigar = []
-            ref_add = 0
-            delLen = max_delete_start
-            pos_start = False
-            start_pos = 0
-
-            # For each operation in our Cigar
-            for operation in r.cigartuples:
-                # If we have nothing left to delete, just append everything
-                if (delLen == 0 and pos_start):
-                    newcigar.append(operation)
-                    continue
-
-                # For convenience, this is the data about our current cigar operation
-                cig = operation[0]
-                n = operation[1]
-
-                # If we have nothing left to delete and are consuming both, we want to just append everything
-                if (delLen == 0 and consumeQuery[cig] and consumeReference[cig]):
-                    pos_start = True
-                    # Remember we need to include this one!
-                    newcigar.append(operation)
-                    continue
-
-                # How much our current trim affects our read's start position
-                ref_add = 0
-
-                # If our operation consumes the query
-                if consumeQuery[cig]:
-                    # How much do we have to delete?
-                    if delLen >= n:
-                        # Our entire operation needs to be deleted
-                        newcigar.append((BAM_CSOFT_CLIP, n))
-                    elif delLen < n and delLen > 0:
-                        # We need to delete some of our segment, but we will still have more later
-                        newcigar.append((BAM_CSOFT_CLIP, delLen))
-                    elif delLen == 0:
-                        # Since we consume the query, we just need to keep clipping
-                        newcigar.append((BAM_CSOFT_CLIP, n))
-                        continue
-
-                    # Update based on how much we just deleted
-                    ref_add = min(delLen, n)
-                    temp = n
-                    n = max(n - delLen, 0)
-                    delLen = max(delLen - temp, 0)
-
-                    # If there is still more left to do, append it
-                    if n > 0:
-                        newcigar.append((cig, n))
-
-                    # If we are done and just consumed, we want to just start appending everything.
-                    if delLen == 0 and consumeQuery[newcigar[-1][0]] and consumeReference[newcigar[-1][0]]:
-                        pos_start = True
-
-                # If our trim consumed the reference, we need to move our read's start position forwards
-                if consumeReference[cig]:
-                    start_pos += ref_add
-
-            # Update our cigar string, since that's what will be written
-            cigarstr = ""
-            propercigar = []
-            for i in range(0, len(newcigar)):
-                if i < len(newcigar)-1 and newcigar[i][0] == newcigar[i+1][0]:
-                    newcigar[i+1] = (newcigar[i+1][0],
-                                     newcigar[i][1] + newcigar[i+1][1])
-                    continue
-
-                cigarstr = cigarstr + \
-                    str(newcigar[i][1]) + cigarMap[newcigar[i][0]]
-                propercigar.append(newcigar[i])
-
-            r.cigarstring = cigarstr
-            r.cigartuples = propercigar
-
-            # Move our position on the reference forward, if needed
-            r.reference_start += start_pos
-            ref_start_offset += start_pos
-
-        if not (r.is_paired and isize_flag and not r.is_reverse) and len(overlapping_end) > 0:
-            primer_trimmed = True
-            # Determine greatest overlap
-            overlap_start = float("inf")
-            for primer in overlapping_end:
-                if primer[0] < overlap_start:
-                    overlap_start = primer[0]
-            max_delete_end = cigarToQLen(
-                r.cigartuples) - getPosOnQuery(r.cigartuples, overlap_start, r.reference_start)
-
-            # Initializations
-            newcigar = []
-            ref_add = 0
-            delLen = max_delete_end
-            pos_start = False
-
-            # For each operation in our Cigar
-            for operation in reversed(r.cigartuples):
-                # If we have nothing left to delete, just append everything
-                if (delLen == 0 and pos_start):
-                    newcigar.append(operation)
-                    continue
-
-                # For convenience, this is the data about our current cigar operation
-                cig = operation[0]
-                n = operation[1]
-
-                # If we have nothing left to delete and are consuming both, we want to just append everything
-                if (delLen == 0 and consumeQuery[cig] and consumeReference[cig]):
-                    pos_start = True
-                    # Remember we need to include this one!
-                    newcigar.append(operation)
-                    continue
-
-                # If our operation consumes the query
-                if consumeQuery[cig]:
-                    # How much do we have to delete?
-                    if delLen >= n:
-                        # Our entire operation needs to be deleted
-                        newcigar.append((BAM_CSOFT_CLIP, n))
-                    elif delLen < n and delLen > 0:
-                        # We need to delete some of our segment, but we will still have more later
-                        newcigar.append((BAM_CSOFT_CLIP, delLen))
-                    elif delLen == 0:
-                        # Since we consume the query, we just need to keep clipping
-                        newcigar.append((BAM_CSOFT_CLIP, n))
-                        continue
-
-                    # Update based on how much we just deleted
-                    temp = n
-                    n = max(n - delLen, 0)
-                    delLen = max(delLen - temp, 0)
-
-                    # If there is still more left to do, append it
-                    if n > 0:
-                        newcigar.append((cig, n))
-
-                    # If we are done and just consumed, we want to just start appending everything.
-                    if delLen == 0 and consumeQuery[newcigar[-1][0]] and consumeReference[newcigar[-1][0]]:
-                        pos_start = True
-
-            # Update our cigar string, since that's what will be written
-            cigarstr = ""
-            propercigar = []
-            for i in reversed(range(0, len(newcigar))):
-                if i > 0 and newcigar[i][0] == newcigar[i-1][0]:
-                    newcigar[i-1] = (newcigar[i-1][0],
-                                     newcigar[i][1] + newcigar[i-1][1])
-                    continue
-
-                cigarstr = cigarstr + \
-                    str(newcigar[i][1]) + cigarMap[newcigar[i][0]]
-                propercigar.append(newcigar[i])
-
-            r.cigarstring = cigarstr
-            r.cigartuples = propercigar
-
-        ##### Quality Trim #####
-        if r.is_reverse:
-            # Initializations
-            sum = 0
-            qual = r.query_alignment_qualities
-            window = sliding_window if sliding_window <= len(
-                qual) else len(qual)
-            truestart = 0
-            trueend = len(qual)
-
-            # Build up our buffer
-            i = trueend
-            for offset in range(1, window):
-                sum += qual[i - offset]
-
-            # Loop through the read, determine when we need to trim
-            while i > truestart:
-                if truestart + window > i:
-                    # We are nearing the end, so we need to shrink our window
-                    window -= 1
-                else:
-                    # Still have more to go, so add in our new value
-                    sum += qual[i - window]
-
-                # Check our current quality score
-                if sum / window < min_qual_thresh:
-                    break
-
-                # Remove the no longer needed quality score, and advance i
-                sum -= qual[i - 1]
-                i -= 1
-
-            # Initialization for trimming
-            newcigar = []
-            del_len = i
-            start_pos = getPosOnReference(
-                r.cigartuples, del_len + r.qstart, r.reference_start)
-
-            # Do we need to trim?
-            if start_pos > r.reference_start:
-                quality_trimmed = True
-                # Iterate over cigar
-                for operation in r.cigartuples:
-                    # Nothing left to trim, just append everything
-                    if (del_len == 0):
-                        newcigar.append(operation)
-                        continue
-
-                    cig = operation[0]
-                    n = operation[1]
-
-                    # These are just clips, so it's not part of our quality trim determination
-                    if cig == BAM_CSOFT_CLIP or cig == BAM_CHARD_CLIP:
-                        newcigar.append(operation)
-                        continue
-
-                    # We consume the query, so we may need to trim
-                    if consumeQuery[cig]:
-                        # How much do we need to delete?
-                        if del_len >= n:
-                            # All of the current operation
-                            newcigar.append((BAM_CSOFT_CLIP, n))
-                        elif del_len < n:
-                            # Only part of the current operation
-                            newcigar.append((BAM_CSOFT_CLIP, del_len))
-
-                        # Decrease our delete length by how much we've deleted
-                        temp = n
-                        n = max(n - del_len, 0)
-                        del_len = max(del_len - temp, 0)
-
-                        # If we ran out of things to delete, we need to append the rest of the operation
-                        if n > 0:
-                            newcigar.append((cig, n))
-
-                # Update our cigar string, since that's what will be written
-                cigarstr = ""
-                propercigar = []
-                for i in range(0, len(newcigar)):
-                    if i < len(newcigar)-1 and newcigar[i][0] == newcigar[i+1][0]:
-                        newcigar[i+1] = (newcigar[i+1][0],
-                                         newcigar[i][1] + newcigar[i+1][1])
-                        continue
-
-                    cigarstr = cigarstr + \
-                        str(newcigar[i][1]) + cigarMap[newcigar[i][0]]
-                    propercigar.append(newcigar[i])
-
-                r.cigarstring = cigarstr
-                r.cigartuples = propercigar
-
-                # Move our position on the reference forward, if needed
-                r.reference_start = start_pos
-        else:
-            # Initailizations
-            sum = 0
-            qual = r.query_alignment_qualities
-            window = sliding_window if sliding_window <= len(
-                qual) else len(qual)
-            truestart = 0
-            trueend = len(qual)
-
-            # Build up our buffer
-            i = truestart
-            for offset in range(0, window - 1):
-                sum += qual[i + offset]
-
-            # Loop through the read, determine when we need to trim
-            while i < trueend:
-                if trueend - window < i:
-                    # We are nearing the end, so we need to shrink our window
-                    window -= 1
-                else:
-                    # Still have more to go, so add in our new value
-                    sum += qual[i + window - 1]
-
-                # Check our current quality score
-                if sum / window < min_qual_thresh:
-                    break
-
-                # Remove the no longer needed quality score, and advance i
-                sum -= qual[i]
-                i += 1
-
-            # Initialization for trimming
-            newcigar = []
-            del_len = trueend - i
-            start_pos = getPosOnReference(
-                r.cigartuples, del_len, r.reference_start)
-
-            if (del_len > 0):
-                quality_trimmed = True
-
-            # Iterate over cigar
-            for operation in reversed(r.cigartuples):
-                # Nothing left to trim, just append everything
-                if (del_len == 0):
-                    newcigar.append(operation)
-                    continue
-
-                cig = operation[0]
-                n = operation[1]
-
-                # These are just clips, so it's not part of our quality trim determination
-                if cig == BAM_CSOFT_CLIP or cig == BAM_CHARD_CLIP:
-                    newcigar.append(operation)
-                    continue
-
-                # We consume the query, so we may need to trim
-                if consumeQuery[cig]:
-                    # How much do we need to delete?
-                    if del_len >= n:
-                        # All of the current operation
-                        newcigar.append((BAM_CSOFT_CLIP, n))
-                    elif del_len < n:
-                        # Only part of the current operation
-                        newcigar.append((BAM_CSOFT_CLIP, del_len))
-
-                    # Decrease our delete length by how much we've deleted
-                    temp = n
-                    n = max(n - del_len, 0)
-                    del_len = max(del_len - temp, 0)
-
-                    # If we ran out of things to delete, we need to append the rest of the operation
-                    if n > 0:
-                        newcigar.append((cig, n))
-
-            # Update our cigar string, since that's what will be written
-            cigarstr = ""
-            propercigar = []
-            for i in reversed(range(0, len(newcigar))):
-                if i > 0 and newcigar[i][0] == newcigar[i-1][0]:
-                    newcigar[i-1] = (newcigar[i-1][0],
-                                     newcigar[i][1] + newcigar[i-1][1])
-                    continue
-
-                cigarstr = cigarstr + \
-                    str(newcigar[i][1]) + cigarMap[newcigar[i][0]]
-                propercigar.append(newcigar[i])
-
-            r.cigarstring = cigarstr
-            r.cigartuples = propercigar
-
-            # Move our position on the reference forward, if needed
-            r.reference_start = start_pos
-
-        if (primer_trimmed):
-            primer_trimmed_count += 1
-        else:
-            no_primer_count += 1
-
-        if (quality_trimmed):
-            quality_trimmed_count += 1
-
-        # Only output if we exceed the read length
-        if cigarToRefLen(r.cigartuples) >= min_read_length and (primer_trimmed or include_no_primer):
-            output.write(r)
-        else:
-            removed_reads += 1
-
-    print("\nWrapping up...")
-    # Return our statstics (nothing yet)
-    return {"removed_reads": removed_reads, "primer_trimmed_count": primer_trimmed_count, "no_primer_count": no_primer_count, "quality_trimmed_count": quality_trimmed_count, "no_cigar_count": no_cigar_count}