Move all files to lib directory

Koeng101 · Dec 12, 2023 · 8bdbb6d · 8bdbb6d
1 parent 59bae8a
commit 8bdbb6d
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Showing 155 changed files with 75 additions and 74 deletions.
diff --git a/.golangci.yml b/.golangci.yml
@@ -2,6 +2,7 @@ run:
   timeout: 1m
   skip-dirs:
     - data
+    - api/gen
 linters:
   enable:
     - bodyclose
@@ -26,4 +27,4 @@ linters-settings:
     # https://staticcheck.io/docs/options#checks
     checks:
       - "all"
-      - "-ST1005" # Disable "Incorrectly formatted error string" errors. TODO: Enable this and fix the errors.
+      - "-ST1005" # Disable "Incorrectly formatted error string" errors. TODO: Enable this and fix the errors.
diff --git a/align/align.go → lib/align/align.go b/align/align.go → lib/align/align.go
@@ -66,7 +66,7 @@ Tim
 package align
 
 import (
-	"github.com/koeng101/dnadesign/align/matrix"
+	"github.com/koeng101/dnadesign/lib/align/matrix"
 )
 
 // Scoring is a struct that holds the scoring matrix for match, mismatch, and gap penalties.

diff --git a/align/align_test.go → lib/align/align_test.go b/align/align_test.go → lib/align/align_test.go
@@ -3,9 +3,9 @@ package align_test
 import (
 	"testing"
 
-	"github.com/koeng101/dnadesign/align"
-	"github.com/koeng101/dnadesign/align/matrix"
-	"github.com/koeng101/dnadesign/alphabet"
+	"github.com/koeng101/dnadesign/lib/align"
+	"github.com/koeng101/dnadesign/lib/align/matrix"
+	"github.com/koeng101/dnadesign/lib/alphabet"
 )
 
 func TestNeedlemanWunsch(t *testing.T) {

diff --git a/align/example_test.go → lib/align/example_test.go b/align/example_test.go → lib/align/example_test.go
@@ -4,9 +4,9 @@ package align_test
 import (
 	"fmt"
 
-	"github.com/koeng101/dnadesign/align"
-	"github.com/koeng101/dnadesign/align/matrix"
-	"github.com/koeng101/dnadesign/alphabet"
+	"github.com/koeng101/dnadesign/lib/align"
+	"github.com/koeng101/dnadesign/lib/align/matrix"
+	"github.com/koeng101/dnadesign/lib/alphabet"
 )
 
 func ExampleNeedlemanWunsch() {

diff --git a/align/matrix/matrices.go → lib/align/matrix/matrices.go b/align/matrix/matrices.go → lib/align/matrix/matrices.go
diff --git a/align/matrix/matrix.go → lib/align/matrix/matrix.go b/align/matrix/matrix.go → lib/align/matrix/matrix.go
@@ -6,7 +6,7 @@ package matrix
 import (
 	"fmt"
 
-	"github.com/koeng101/dnadesign/alphabet"
+	"github.com/koeng101/dnadesign/lib/alphabet"
 )
 
 // SubstitutionMatrix is a struct that holds a substitution matrix and the two alphabets that the matrix is defined over.

diff --git a/align/matrix/matrix_test.go → lib/align/matrix/matrix_test.go b/align/matrix/matrix_test.go → lib/align/matrix/matrix_test.go
@@ -3,8 +3,8 @@ package matrix_test
 import (
 	"testing"
 
-	"github.com/koeng101/dnadesign/align/matrix"
-	"github.com/koeng101/dnadesign/alphabet"
+	"github.com/koeng101/dnadesign/lib/align/matrix"
+	"github.com/koeng101/dnadesign/lib/alphabet"
 	"github.com/stretchr/testify/assert"
 )
 

diff --git a/alphabet/alphabet.go → lib/alphabet/alphabet.go b/alphabet/alphabet.go → lib/alphabet/alphabet.go
diff --git a/alphabet/alphabet_test.go → lib/alphabet/alphabet_test.go b/alphabet/alphabet_test.go → lib/alphabet/alphabet_test.go
@@ -4,7 +4,7 @@ import (
 	"reflect"
 	"testing"
 
-	"github.com/koeng101/dnadesign/alphabet"
+	"github.com/koeng101/dnadesign/lib/alphabet"
 )
 
 func TestAlphabet(t *testing.T) {

diff --git a/bio/bio.go → lib/bio/bio.go b/bio/bio.go → lib/bio/bio.go
@@ -16,11 +16,11 @@ import (
 	"io"
 	"math"
 
-	"github.com/koeng101/dnadesign/bio/fasta"
-	"github.com/koeng101/dnadesign/bio/fastq"
-	"github.com/koeng101/dnadesign/bio/genbank"
-	"github.com/koeng101/dnadesign/bio/pileup"
-	"github.com/koeng101/dnadesign/bio/slow5"
+	"github.com/koeng101/dnadesign/lib/bio/fasta"
+	"github.com/koeng101/dnadesign/lib/bio/fastq"
+	"github.com/koeng101/dnadesign/lib/bio/genbank"
+	"github.com/koeng101/dnadesign/lib/bio/pileup"
+	"github.com/koeng101/dnadesign/lib/bio/slow5"
 	"golang.org/x/sync/errgroup"
 )
 

diff --git a/bio/example_test.go → lib/bio/example_test.go b/bio/example_test.go → lib/bio/example_test.go
@@ -8,8 +8,8 @@ import (
 	"os"
 	"strings"
 
-	"github.com/koeng101/dnadesign/bio"
-	"github.com/koeng101/dnadesign/bio/fasta"
+	"github.com/koeng101/dnadesign/lib/bio"
+	"github.com/koeng101/dnadesign/lib/bio/fasta"
 )
 
 // Example_read shows an example of reading a file from disk.

diff --git a/bio/fasta/data/base.fasta → lib/bio/fasta/data/base.fasta b/bio/fasta/data/base.fasta → lib/bio/fasta/data/base.fasta
diff --git a/bio/fasta/data/base.fasta.gz → lib/bio/fasta/data/base.fasta.gz b/bio/fasta/data/base.fasta.gz → lib/bio/fasta/data/base.fasta.gz
diff --git a/bio/fasta/data/uniprot_1mb_test.fasta.gz → lib/bio/fasta/data/uniprot_1mb_test.fasta.gz b/bio/fasta/data/uniprot_1mb_test.fasta.gz → lib/bio/fasta/data/uniprot_1mb_test.fasta.gz
diff --git a/bio/fasta/example_test.go → lib/bio/fasta/example_test.go b/bio/fasta/example_test.go → lib/bio/fasta/example_test.go
@@ -8,7 +8,7 @@ import (
 	"os"
 	"strings"
 
-	"github.com/koeng101/dnadesign/bio/fasta"
+	"github.com/koeng101/dnadesign/lib/bio/fasta"
 )
 
 // This example shows how to open a file with the fasta parser. The sequences

diff --git a/bio/fasta/fasta.go → lib/bio/fasta/fasta.go b/bio/fasta/fasta.go → lib/bio/fasta/fasta.go
diff --git a/bio/fasta/fasta_test.go → lib/bio/fasta/fasta_test.go b/bio/fasta/fasta_test.go → lib/bio/fasta/fasta_test.go
diff --git a/bio/fastq/data/nanosavseq.fastq → lib/bio/fastq/data/nanosavseq.fastq b/bio/fastq/data/nanosavseq.fastq → lib/bio/fastq/data/nanosavseq.fastq
diff --git a/bio/fastq/data/nanosavseq.fastq.gz → lib/bio/fastq/data/nanosavseq.fastq.gz b/bio/fastq/data/nanosavseq.fastq.gz → lib/bio/fastq/data/nanosavseq.fastq.gz
diff --git a/bio/fastq/data/nanosavseq_emptyseq.fastq → lib/bio/fastq/data/nanosavseq_emptyseq.fastq b/bio/fastq/data/nanosavseq_emptyseq.fastq → lib/bio/fastq/data/nanosavseq_emptyseq.fastq
diff --git a/bio/fastq/data/nanosavseq_noidentifier.fastq → .../fastq/data/nanosavseq_noidentifier.fastq b/bio/fastq/data/nanosavseq_noidentifier.fastq → .../fastq/data/nanosavseq_noidentifier.fastq
diff --git a/bio/fastq/data/nanosavseq_noplus.fastq → lib/bio/fastq/data/nanosavseq_noplus.fastq b/bio/fastq/data/nanosavseq_noplus.fastq → lib/bio/fastq/data/nanosavseq_noplus.fastq
diff --git a/bio/fastq/data/nanosavseq_noquality.fastq → ...bio/fastq/data/nanosavseq_noquality.fastq b/bio/fastq/data/nanosavseq_noquality.fastq → ...bio/fastq/data/nanosavseq_noquality.fastq
diff --git a/bio/fastq/data/nanosavseq_noquality2.fastq → ...io/fastq/data/nanosavseq_noquality2.fastq b/bio/fastq/data/nanosavseq_noquality2.fastq → ...io/fastq/data/nanosavseq_noquality2.fastq
diff --git a/bio/fastq/data/nanosavseq_noseq.fastq → lib/bio/fastq/data/nanosavseq_noseq.fastq b/bio/fastq/data/nanosavseq_noseq.fastq → lib/bio/fastq/data/nanosavseq_noseq.fastq
diff --git a/bio/fastq/data/pOpen_v3.fastq.gz → lib/bio/fastq/data/pOpen_v3.fastq.gz b/bio/fastq/data/pOpen_v3.fastq.gz → lib/bio/fastq/data/pOpen_v3.fastq.gz
diff --git a/bio/fastq/example_test.go → lib/bio/fastq/example_test.go b/bio/fastq/example_test.go → lib/bio/fastq/example_test.go
@@ -5,7 +5,7 @@ import (
 	"fmt"
 	"strings"
 
-	"github.com/koeng101/dnadesign/bio/fastq"
+	"github.com/koeng101/dnadesign/lib/bio/fastq"
 )
 
 //go:embed data/nanosavseq.fastq

diff --git a/bio/fastq/fastq.go → lib/bio/fastq/fastq.go b/bio/fastq/fastq.go → lib/bio/fastq/fastq.go
diff --git a/bio/fastq/fastq_test.go → lib/bio/fastq/fastq_test.go b/bio/fastq/fastq_test.go → lib/bio/fastq/fastq_test.go
diff --git a/bio/genbank/data/NC_001141.2_redux.gb → lib/bio/genbank/data/NC_001141.2_redux.gb b/bio/genbank/data/NC_001141.2_redux.gb → lib/bio/genbank/data/NC_001141.2_redux.gb
diff --git a/bio/genbank/data/benchling.gb → lib/bio/genbank/data/benchling.gb b/bio/genbank/data/benchling.gb → lib/bio/genbank/data/benchling.gb
diff --git a/bio/genbank/data/bsub.gbk → lib/bio/genbank/data/bsub.gbk b/bio/genbank/data/bsub.gbk → lib/bio/genbank/data/bsub.gbk
diff --git a/bio/genbank/data/flatGbk_test.seq → lib/bio/genbank/data/flatGbk_test.seq b/bio/genbank/data/flatGbk_test.seq → lib/bio/genbank/data/flatGbk_test.seq
diff --git a/bio/genbank/data/flatGbk_test.seq.gz → lib/bio/genbank/data/flatGbk_test.seq.gz b/bio/genbank/data/flatGbk_test.seq.gz → lib/bio/genbank/data/flatGbk_test.seq.gz
diff --git a/bio/genbank/data/long_comment.seq → lib/bio/genbank/data/long_comment.seq b/bio/genbank/data/long_comment.seq → lib/bio/genbank/data/long_comment.seq
diff --git a/bio/genbank/data/malformed_read_test.gbk → lib/bio/genbank/data/malformed_read_test.gbk b/bio/genbank/data/malformed_read_test.gbk → lib/bio/genbank/data/malformed_read_test.gbk
diff --git a/bio/genbank/data/multiGbk_test.seq → lib/bio/genbank/data/multiGbk_test.seq b/bio/genbank/data/multiGbk_test.seq → lib/bio/genbank/data/multiGbk_test.seq
diff --git a/bio/genbank/data/phix174.gb → lib/bio/genbank/data/phix174.gb b/bio/genbank/data/phix174.gb → lib/bio/genbank/data/phix174.gb
diff --git a/bio/genbank/data/pichia_chr1_head.gb → lib/bio/genbank/data/pichia_chr1_head.gb b/bio/genbank/data/pichia_chr1_head.gb → lib/bio/genbank/data/pichia_chr1_head.gb
diff --git a/bio/genbank/data/puc19.gbk → lib/bio/genbank/data/puc19.gbk b/bio/genbank/data/puc19.gbk → lib/bio/genbank/data/puc19.gbk
diff --git a/bio/genbank/data/puc19_303_regression.gbk → ...bio/genbank/data/puc19_303_regression.gbk b/bio/genbank/data/puc19_303_regression.gbk → ...bio/genbank/data/puc19_303_regression.gbk
diff --git a/bio/genbank/data/puc19_consrtm.gbk → lib/bio/genbank/data/puc19_consrtm.gbk b/bio/genbank/data/puc19_consrtm.gbk → lib/bio/genbank/data/puc19_consrtm.gbk
diff --git a/bio/genbank/data/puc19_snapgene.gb → lib/bio/genbank/data/puc19_snapgene.gb b/bio/genbank/data/puc19_snapgene.gb → lib/bio/genbank/data/puc19_snapgene.gb
diff --git a/bio/genbank/data/sample.gbk → lib/bio/genbank/data/sample.gbk b/bio/genbank/data/sample.gbk → lib/bio/genbank/data/sample.gbk
diff --git a/bio/genbank/data/t4_intron.gb → lib/bio/genbank/data/t4_intron.gb b/bio/genbank/data/t4_intron.gb → lib/bio/genbank/data/t4_intron.gb
diff --git a/bio/genbank/genbank.go → lib/bio/genbank/genbank.go b/bio/genbank/genbank.go → lib/bio/genbank/genbank.go
@@ -20,7 +20,7 @@ import (
 	"strconv"
 	"strings"
 
-	"github.com/koeng101/dnadesign/transform"
+	"github.com/koeng101/dnadesign/lib/transform"
 	"github.com/lunny/log"
 	"github.com/mitchellh/go-wordwrap"
 )

diff --git a/bio/genbank/genbank_test.go → lib/bio/genbank/genbank_test.go b/bio/genbank/genbank_test.go → lib/bio/genbank/genbank_test.go
@@ -14,7 +14,7 @@ import (
 
 	"github.com/google/go-cmp/cmp"
 	"github.com/google/go-cmp/cmp/cmpopts"
-	"github.com/koeng101/dnadesign/transform"
+	"github.com/koeng101/dnadesign/lib/transform"
 	"github.com/stretchr/testify/assert"
 )
 

diff --git a/bio/genbank/multimap.go → lib/bio/genbank/multimap.go b/bio/genbank/multimap.go → lib/bio/genbank/multimap.go
diff --git a/bio/gff/example_test.go → lib/bio/gff/example_test.go b/bio/gff/example_test.go → lib/bio/gff/example_test.go
@@ -7,8 +7,8 @@ import (
 	"path/filepath"
 	"testing"
 
-	"github.com/koeng101/dnadesign/bio/gff"
-	"github.com/koeng101/dnadesign/transform"
+	"github.com/koeng101/dnadesign/lib/bio/gff"
+	"github.com/koeng101/dnadesign/lib/transform"
 )
 
 // This example shows how to open a gff file and search for a gene given its

diff --git a/bio/gff/gff.go → lib/bio/gff/gff.go b/bio/gff/gff.go → lib/bio/gff/gff.go
@@ -22,7 +22,7 @@ import (
 
 	"lukechampine.com/blake3"
 
-	"github.com/koeng101/dnadesign/transform"
+	"github.com/koeng101/dnadesign/lib/transform"
 )
 
 var (

diff --git a/bio/gff/gff_test.go → lib/bio/gff/gff_test.go b/bio/gff/gff_test.go → lib/bio/gff/gff_test.go
diff --git a/bio/pileup/data/test.pileup → lib/bio/pileup/data/test.pileup b/bio/pileup/data/test.pileup → lib/bio/pileup/data/test.pileup
diff --git a/...pileup/data/test_not_enough_fields.pileup → ...pileup/data/test_not_enough_fields.pileup b/...pileup/data/test_not_enough_fields.pileup → ...pileup/data/test_not_enough_fields.pileup
diff --git a/bio/pileup/data/test_position_non_int.pileup → .../pileup/data/test_position_non_int.pileup b/bio/pileup/data/test_position_non_int.pileup → .../pileup/data/test_position_non_int.pileup
diff --git a/bio/pileup/data/test_read_off.pileup → lib/bio/pileup/data/test_read_off.pileup b/bio/pileup/data/test_read_off.pileup → lib/bio/pileup/data/test_read_off.pileup
diff --git a/...pileup/data/test_readcount_non_int.pileup → ...pileup/data/test_readcount_non_int.pileup b/...pileup/data/test_readcount_non_int.pileup → ...pileup/data/test_readcount_non_int.pileup
diff --git a/bio/pileup/data/test_unknown_rune.pileup → lib/bio/pileup/data/test_unknown_rune.pileup b/bio/pileup/data/test_unknown_rune.pileup → lib/bio/pileup/data/test_unknown_rune.pileup
diff --git a/bio/pileup/pileup.go → lib/bio/pileup/pileup.go b/bio/pileup/pileup.go → lib/bio/pileup/pileup.go
diff --git a/bio/pileup/pileup_test.go → lib/bio/pileup/pileup_test.go b/bio/pileup/pileup_test.go → lib/bio/pileup/pileup_test.go
diff --git a/bio/rebase/data/rebase_test.txt → lib/bio/rebase/data/rebase_test.txt b/bio/rebase/data/rebase_test.txt → lib/bio/rebase/data/rebase_test.txt
diff --git a/bio/rebase/example_test.go → lib/bio/rebase/example_test.go b/bio/rebase/example_test.go → lib/bio/rebase/example_test.go
@@ -3,7 +3,7 @@ package rebase_test
 import (
 	"fmt"
 
-	"github.com/koeng101/dnadesign/bio/rebase"
+	"github.com/koeng101/dnadesign/lib/bio/rebase"
 )
 
 // This example reads rebase into an enzymeMap and returns the AarI recognition

diff --git a/bio/rebase/rebase.go → lib/bio/rebase/rebase.go b/bio/rebase/rebase.go → lib/bio/rebase/rebase.go
diff --git a/bio/rebase/rebase_test.go → lib/bio/rebase/rebase_test.go b/bio/rebase/rebase_test.go → lib/bio/rebase/rebase_test.go
diff --git a/bio/slow5/data/example.slow5 → lib/bio/slow5/data/example.slow5 b/bio/slow5/data/example.slow5 → lib/bio/slow5/data/example.slow5
diff --git a/...data/header_tests/test_header_empty.slow5 → ...data/header_tests/test_header_empty.slow5 b/...data/header_tests/test_header_empty.slow5 → ...data/header_tests/test_header_empty.slow5
diff --git a/...s/test_header_not_enough_attributes.slow5 → ...s/test_header_not_enough_attributes.slow5 b/...s/test_header_not_enough_attributes.slow5 → ...s/test_header_not_enough_attributes.slow5
diff --git a/...tests/test_header_numReadGroups_bad.slow5 → ...tests/test_header_numReadGroups_bad.slow5 b/...tests/test_header_numReadGroups_bad.slow5 → ...tests/test_header_numReadGroups_bad.slow5
diff --git a/...ader_tests/test_header_without_tabs.slow5 → ...ader_tests/test_header_without_tabs.slow5 b/...ader_tests/test_header_without_tabs.slow5 → ...ader_tests/test_header_without_tabs.slow5
diff --git a/bio/slow5/data/read_tests/continue.slow5 → lib/bio/slow5/data/read_tests/continue.slow5 b/bio/slow5/data/read_tests/continue.slow5 → lib/bio/slow5/data/read_tests/continue.slow5
diff --git a/bio/slow5/data/read_tests/digitisation.slow5 → .../slow5/data/read_tests/digitisation.slow5 b/bio/slow5/data/read_tests/digitisation.slow5 → .../slow5/data/read_tests/digitisation.slow5
diff --git a/bio/slow5/data/read_tests/endReason.slow5 → ...bio/slow5/data/read_tests/endReason.slow5 b/bio/slow5/data/read_tests/endReason.slow5 → ...bio/slow5/data/read_tests/endReason.slow5
diff --git a/bio/slow5/data/read_tests/end_reason.slow5 → ...io/slow5/data/read_tests/end_reason.slow5 b/bio/slow5/data/read_tests/end_reason.slow5 → ...io/slow5/data/read_tests/end_reason.slow5
diff --git a/.../data/read_tests/end_reason_unknown.slow5 → .../data/read_tests/end_reason_unknown.slow5 b/.../data/read_tests/end_reason_unknown.slow5 → .../data/read_tests/end_reason_unknown.slow5
diff --git a/...low5/data/read_tests/len_raw_signal.slow5 → ...low5/data/read_tests/len_raw_signal.slow5 b/...low5/data/read_tests/len_raw_signal.slow5 → ...low5/data/read_tests/len_raw_signal.slow5
diff --git a/...slow5/data/read_tests/median_before.slow5 → ...slow5/data/read_tests/median_before.slow5 b/...slow5/data/read_tests/median_before.slow5 → ...slow5/data/read_tests/median_before.slow5
diff --git a/bio/slow5/data/read_tests/offset.slow5 → lib/bio/slow5/data/read_tests/offset.slow5 b/bio/slow5/data/read_tests/offset.slow5 → lib/bio/slow5/data/read_tests/offset.slow5
diff --git a/bio/slow5/data/read_tests/range.slow5 → lib/bio/slow5/data/read_tests/range.slow5 b/bio/slow5/data/read_tests/range.slow5 → lib/bio/slow5/data/read_tests/range.slow5
diff --git a/bio/slow5/data/read_tests/raw_signal.slow5 → ...io/slow5/data/read_tests/raw_signal.slow5 b/bio/slow5/data/read_tests/raw_signal.slow5 → ...io/slow5/data/read_tests/raw_signal.slow5
diff --git a/bio/slow5/data/read_tests/read_group.slow5 → ...io/slow5/data/read_tests/read_group.slow5 b/bio/slow5/data/read_tests/read_group.slow5 → ...io/slow5/data/read_tests/read_group.slow5
diff --git a/bio/slow5/data/read_tests/read_number.slow5 → ...o/slow5/data/read_tests/read_number.slow5 b/bio/slow5/data/read_tests/read_number.slow5 → ...o/slow5/data/read_tests/read_number.slow5
diff --git a/...slow5/data/read_tests/sampling_rate.slow5 → ...slow5/data/read_tests/sampling_rate.slow5 b/...slow5/data/read_tests/sampling_rate.slow5 → ...slow5/data/read_tests/sampling_rate.slow5
diff --git a/bio/slow5/data/read_tests/start_mux.slow5 → ...bio/slow5/data/read_tests/start_mux.slow5 b/bio/slow5/data/read_tests/start_mux.slow5 → ...bio/slow5/data/read_tests/start_mux.slow5
diff --git a/bio/slow5/data/read_tests/start_time.slow5 → ...io/slow5/data/read_tests/start_time.slow5 b/bio/slow5/data/read_tests/start_time.slow5 → ...io/slow5/data/read_tests/start_time.slow5
diff --git a/bio/slow5/data/read_tests/unknown.slow5 → lib/bio/slow5/data/read_tests/unknown.slow5 b/bio/slow5/data/read_tests/unknown.slow5 → lib/bio/slow5/data/read_tests/unknown.slow5
diff --git a/bio/slow5/data/test_example.slow5 → lib/bio/slow5/data/test_example.slow5 b/bio/slow5/data/test_example.slow5 → lib/bio/slow5/data/test_example.slow5
diff --git a/bio/slow5/example_test.go → lib/bio/slow5/example_test.go b/bio/slow5/example_test.go → lib/bio/slow5/example_test.go
@@ -4,7 +4,7 @@ import (
 	"fmt"
 	"os"
 
-	"github.com/koeng101/dnadesign/bio/slow5"
+	"github.com/koeng101/dnadesign/lib/bio/slow5"
 )
 
 func ExampleNewParser() {

diff --git a/bio/slow5/slow5.go → lib/bio/slow5/slow5.go b/bio/slow5/slow5.go → lib/bio/slow5/slow5.go
@@ -328,7 +328,7 @@ func (parser *Parser) Next() (*Read, error) {
 			// For whatever reason, this is a string.
 			newRead.ChannelNumber = values[valueIndex]
 		default:
-			return nil, fmt.Errorf("Unknown field to parser '%s' found on line %d. Please report to github.com/koeng101/dnadesign", fieldValue, parser.line)
+			return nil, fmt.Errorf("Unknown field to parser '%s' found on line %d. Please report to github.com/koeng101/dnadesign/lib", fieldValue, parser.line)
 		}
 	}
 	return &newRead, nil

diff --git a/bio/slow5/slow5_test.go → lib/bio/slow5/slow5_test.go b/bio/slow5/slow5_test.go → lib/bio/slow5/slow5_test.go
diff --git a/bio/uniprot/data/check_uniprot → lib/bio/uniprot/data/check_uniprot b/bio/uniprot/data/check_uniprot → lib/bio/uniprot/data/check_uniprot
diff --git a/bio/uniprot/data/test → lib/bio/uniprot/data/test b/bio/uniprot/data/test → lib/bio/uniprot/data/test
diff --git a/bio/uniprot/data/uniprot.xsd → lib/bio/uniprot/data/uniprot.xsd b/bio/uniprot/data/uniprot.xsd → lib/bio/uniprot/data/uniprot.xsd
diff --git a/bio/uniprot/data/uniprot_sprot_mini.xml.gz → ...io/uniprot/data/uniprot_sprot_mini.xml.gz b/bio/uniprot/data/uniprot_sprot_mini.xml.gz → ...io/uniprot/data/uniprot_sprot_mini.xml.gz
diff --git a/bio/uniprot/data/xml_go_generator → lib/bio/uniprot/data/xml_go_generator b/bio/uniprot/data/xml_go_generator → lib/bio/uniprot/data/xml_go_generator
diff --git a/bio/uniprot/example_test.go → lib/bio/uniprot/example_test.go b/bio/uniprot/example_test.go → lib/bio/uniprot/example_test.go
@@ -3,7 +3,7 @@ package uniprot_test
 import (
 	"fmt"
 
-	"github.com/koeng101/dnadesign/bio/uniprot"
+	"github.com/koeng101/dnadesign/lib/bio/uniprot"
 )
 
 // This example shows how to open a uniprot data dump file and read the results

diff --git a/bio/uniprot/uniprot.go → lib/bio/uniprot/uniprot.go b/bio/uniprot/uniprot.go → lib/bio/uniprot/uniprot.go
diff --git a/bio/uniprot/uniprot_test.go → lib/bio/uniprot/uniprot_test.go b/bio/uniprot/uniprot_test.go → lib/bio/uniprot/uniprot_test.go
diff --git a/bio/uniprot/xml.go → lib/bio/uniprot/xml.go b/bio/uniprot/xml.go → lib/bio/uniprot/xml.go
diff --git a/bio/uniprot/xml_test.go → lib/bio/uniprot/xml_test.go b/bio/uniprot/xml_test.go → lib/bio/uniprot/xml_test.go
diff --git a/checks/checks.go → lib/checks/checks.go b/checks/checks.go → lib/checks/checks.go
@@ -6,7 +6,7 @@ package checks
 import (
 	"strings"
 
-	"github.com/koeng101/dnadesign/transform"
+	"github.com/koeng101/dnadesign/lib/transform"
 )
 
 // IsPalindromic accepts a sequence of even length and returns if it is

diff --git a/checks/checks_test.go → lib/checks/checks_test.go b/checks/checks_test.go → lib/checks/checks_test.go
@@ -3,7 +3,7 @@ package checks_test
 import (
 	"testing"
 
-	"github.com/koeng101/dnadesign/checks"
+	"github.com/koeng101/dnadesign/lib/checks"
 )
 
 // This also needs an example test.

diff --git a/clone/clone.go → lib/clone/clone.go b/clone/clone.go → lib/clone/clone.go
@@ -52,9 +52,9 @@ import (
 	"sort"
 	"strings"
 
-	"github.com/koeng101/dnadesign/checks"
-	"github.com/koeng101/dnadesign/seqhash"
-	"github.com/koeng101/dnadesign/transform"
+	"github.com/koeng101/dnadesign/lib/checks"
+	"github.com/koeng101/dnadesign/lib/seqhash"
+	"github.com/koeng101/dnadesign/lib/transform"
 )
 
 // Part is a simple struct that can carry a circular or linear DNA sequence.

diff --git a/clone/clone_test.go → lib/clone/clone_test.go b/clone/clone_test.go → lib/clone/clone_test.go
diff --git a/clone/example_test.go → lib/clone/example_test.go b/clone/example_test.go → lib/clone/example_test.go
@@ -4,8 +4,8 @@ import (
 	"fmt"
 	"log"
 
-	"github.com/koeng101/dnadesign/clone"
-	"github.com/koeng101/dnadesign/seqhash"
+	"github.com/koeng101/dnadesign/lib/clone"
+	"github.com/koeng101/dnadesign/lib/seqhash"
 )
 
 func ExampleGoldenGate() {

diff --git a/data/alteredPichiaTable.json → lib/data/alteredPichiaTable.json b/data/alteredPichiaTable.json → lib/data/alteredPichiaTable.json
diff --git a/data/bsub_codon_test.json → lib/data/bsub_codon_test.json b/data/bsub_codon_test.json → lib/data/bsub_codon_test.json
diff --git a/data/cat.json → lib/data/cat.json b/data/cat.json → lib/data/cat.json
diff --git a/data/ecoli-mg1655-short.gff → lib/data/ecoli-mg1655-short.gff b/data/ecoli-mg1655-short.gff → lib/data/ecoli-mg1655-short.gff
diff --git a/data/ecoli-mg1655.gff → lib/data/ecoli-mg1655.gff b/data/ecoli-mg1655.gff → lib/data/ecoli-mg1655.gff
diff --git a/data/freqB.json → lib/data/freqB.json b/data/freqB.json → lib/data/freqB.json
diff --git a/data/incompletePichiaTable.json → lib/data/incompletePichiaTable.json b/data/incompletePichiaTable.json → lib/data/incompletePichiaTable.json
diff --git a/data/parseLocationRegressionTest.json → lib/data/parseLocationRegressionTest.json b/data/parseLocationRegressionTest.json → lib/data/parseLocationRegressionTest.json
diff --git a/data/phix174.gb → lib/data/phix174.gb b/data/phix174.gb → lib/data/phix174.gb
diff --git a/data/pichiaTable.json → lib/data/pichiaTable.json b/data/pichiaTable.json → lib/data/pichiaTable.json
diff --git a/data/sample.json → lib/data/sample.json b/data/sample.json → lib/data/sample.json
diff --git a/doc.go → lib/doc.go b/doc.go → lib/doc.go
@@ -2,6 +2,6 @@
 Package DnaDesign is a Go package for engineering organisms.
 
 Browse our subpackages to find the functionality and documentation you need:
-https://pkg.go.dev/github.com/koeng101/dnadesign#section-directories
+https://pkg.go.dev/github.com/koeng101/dnadesign/lib#section-directories
 */
 package dnadesign
diff --git a/fold/dna.go → lib/fold/dna.go b/fold/dna.go → lib/fold/dna.go
@@ -1,6 +1,6 @@
 package fold
 
-import "github.com/koeng101/dnadesign/transform"
+import "github.com/koeng101/dnadesign/lib/transform"
 
 var dnaComplement = transform.ComplementBase
 

diff --git a/fold/example_test.go → lib/fold/example_test.go b/fold/example_test.go → lib/fold/example_test.go
@@ -3,7 +3,7 @@ package fold_test
 import (
 	"fmt"
 
-	"github.com/koeng101/dnadesign/fold"
+	"github.com/koeng101/dnadesign/lib/fold"
 )
 
 func ExampleZuker() {

diff --git a/fold/fold.go → lib/fold/fold.go b/fold/fold.go → lib/fold/fold.go
@@ -33,7 +33,7 @@ import (
 	"math"
 	"strings"
 
-	"github.com/koeng101/dnadesign/transform"
+	"github.com/koeng101/dnadesign/lib/transform"
 )
 
 // Zuker folds the DNA sequence and return the lowest free energy score.

diff --git a/fold/fold_test.go → lib/fold/fold_test.go b/fold/fold_test.go → lib/fold/fold_test.go
diff --git a/fold/rna.go → lib/fold/rna.go b/fold/rna.go → lib/fold/rna.go
@@ -1,6 +1,6 @@
 package fold
 
-import "github.com/koeng101/dnadesign/transform"
+import "github.com/koeng101/dnadesign/lib/transform"
 
 var rnaComplement = transform.ComplementBaseRNA
 

diff --git a/fold/seqfold.go → lib/fold/seqfold.go b/fold/seqfold.go → lib/fold/seqfold.go
@@ -5,7 +5,7 @@ import (
 	"math"
 	"strings"
 
-	"github.com/koeng101/dnadesign/checks"
+	"github.com/koeng101/dnadesign/lib/checks"
 )
 
 const (

diff --git a/fold/utils.go → lib/fold/utils.go b/fold/utils.go → lib/fold/utils.go
diff --git a/mash/example_test.go → lib/mash/example_test.go b/mash/example_test.go → lib/mash/example_test.go
@@ -3,7 +3,7 @@ package mash_test
 import (
 	"fmt"
 
-	"github.com/koeng101/dnadesign/mash"
+	"github.com/koeng101/dnadesign/lib/mash"
 )
 
 func ExampleMash() {

diff --git a/mash/mash.go → lib/mash/mash.go b/mash/mash.go → lib/mash/mash.go
diff --git a/mash/mash_test.go → lib/mash/mash_test.go b/mash/mash_test.go → lib/mash/mash_test.go
@@ -3,7 +3,7 @@ package mash_test
 import (
 	"testing"
 
-	"github.com/koeng101/dnadesign/mash"
+	"github.com/koeng101/dnadesign/lib/mash"
 )
 
 func TestMash(t *testing.T) {

diff --git a/primers/pcr/example_test.go → lib/primers/pcr/example_test.go b/primers/pcr/example_test.go → lib/primers/pcr/example_test.go
@@ -3,7 +3,7 @@ package pcr_test
 import (
 	"fmt"
 
-	"github.com/koeng101/dnadesign/primers/pcr"
+	"github.com/koeng101/dnadesign/lib/primers/pcr"
 )
 
 // This example shows how to design a sequence.

diff --git a/primers/pcr/pcr.go → lib/primers/pcr/pcr.go b/primers/pcr/pcr.go → lib/primers/pcr/pcr.go
@@ -27,8 +27,8 @@ import (
 	"sort"
 	"strings"
 
-	"github.com/koeng101/dnadesign/primers"
-	"github.com/koeng101/dnadesign/transform"
+	"github.com/koeng101/dnadesign/lib/primers"
+	"github.com/koeng101/dnadesign/lib/transform"
 )
 
 // https://doi.org/10.1089/dna.1994.13.75

diff --git a/primers/pcr/pcr_test.go → lib/primers/pcr/pcr_test.go b/primers/pcr/pcr_test.go → lib/primers/pcr/pcr_test.go
diff --git a/primers/primers.go → lib/primers/primers.go b/primers/primers.go → lib/primers/primers.go
@@ -23,8 +23,8 @@ import (
 	"math"
 	"strings"
 
-	"github.com/koeng101/dnadesign/checks"
-	"github.com/koeng101/dnadesign/transform"
+	"github.com/koeng101/dnadesign/lib/checks"
+	"github.com/koeng101/dnadesign/lib/transform"
 )
 
 // For reference: https://www.sigmaaldrich.com/technical-documents/articles/biology/oligos-melting-temp.html

diff --git a/primers/primers_test.go → lib/primers/primers_test.go b/primers/primers_test.go → lib/primers/primers_test.go
@@ -6,8 +6,8 @@ import (
 	"strings"
 	"testing"
 
-	"github.com/koeng101/dnadesign/primers"
-	"github.com/koeng101/dnadesign/transform"
+	"github.com/koeng101/dnadesign/lib/primers"
+	"github.com/koeng101/dnadesign/lib/transform"
 )
 
 func ExampleMarmurDoty() {

diff --git a/random/random.go → lib/random/random.go b/random/random.go → lib/random/random.go
diff --git a/random/random_test.go → lib/random/random_test.go b/random/random_test.go → lib/random/random_test.go
diff --git a/seqhash/example_test.go → lib/seqhash/example_test.go b/seqhash/example_test.go → lib/seqhash/example_test.go
@@ -4,8 +4,8 @@ import (
 	"fmt"
 	"os"
 
-	"github.com/koeng101/dnadesign/bio"
-	"github.com/koeng101/dnadesign/seqhash"
+	"github.com/koeng101/dnadesign/lib/bio"
+	"github.com/koeng101/dnadesign/lib/seqhash"
 )
 
 // This example shows how to seqhash a sequence.

diff --git a/seqhash/seqhash.go → lib/seqhash/seqhash.go b/seqhash/seqhash.go → lib/seqhash/seqhash.go
@@ -92,7 +92,7 @@ import (
 	"sort"
 	"strings"
 
-	"github.com/koeng101/dnadesign/transform"
+	"github.com/koeng101/dnadesign/lib/transform"
 	"lukechampine.com/blake3"
 )
 

diff --git a/seqhash/seqhash_test.go → lib/seqhash/seqhash_test.go b/seqhash/seqhash_test.go → lib/seqhash/seqhash_test.go
@@ -6,7 +6,7 @@ import (
 	"os"
 	"testing"
 
-	"github.com/koeng101/dnadesign/bio"
+	"github.com/koeng101/dnadesign/lib/bio"
 	"github.com/sergi/go-diff/diffmatchpatch"
 )
 

diff --git a/synthesis/codon/codon.go → lib/synthesis/codon/codon.go b/synthesis/codon/codon.go → lib/synthesis/codon/codon.go
@@ -26,7 +26,7 @@ import (
 	"strings"
 	"time"
 
-	"github.com/koeng101/dnadesign/bio/genbank"
+	"github.com/koeng101/dnadesign/lib/bio/genbank"
 	weightedRand "github.com/mroth/weightedrand"
 )
-Original file line number
+Diff line change
@@ Expand Up / @@ -22,7 +22,7 @@ import ( @@
     	"lukechampine.com/blake3"
-    	"github.com/koeng101/dnadesign/transform"
+    	"github.com/koeng101/dnadesign/lib/transform"
     )
     var (
@@ Expand Down @@