Update: Concatenation Service (#298)

* Updated attachments concatenation service to work with 'fq' files and updated naming of concatenated paired end files

* Pushing up method name change missed in prev commit

* Updated regex matching for nonzipped_file_extension method, updated tests to check that the concatenated file names match the expected file names

* Added tests for concatenating fq and fq.gz files

* Updated validate_file_extensions method to validate_file_formats which just checks to see if the compression and formats are the same before concatenating, Reverted change which added nonzipped_file_extension to attachment model and added the appropriate extension to the concatenated files. Updated tests

app/services/attachments/concatenation_service.rb

@@ -74,7 +74,7 @@ def validate_params
     def validate_and_concatenate(attachments, is_paired_end)
       return unless attachments.length.positive?
 
-      validate_file_extensions(attachments)
+      validate_file_formats(attachments)
 
       concatenated_attachments = []
 
@@ -117,12 +117,11 @@ def validate_paired_end_files(attachments)
       true
     end
 
-    # Validates if the file extensions all match for the attachments
-    def validate_file_extensions(attachments)
-      expected_extension = attachments.first.metadata['compression'] == 'gzip' ? 'gz' : 'fastq'
+    # Validates if the file formats all match for the attachments
+    def validate_file_formats(attachments)
       attachments.each do |attachment|
-        extension = attachment.file.filename.to_s.split('.')[-1]
-        next unless extension != expected_extension
+        next unless (attachment.metadata['compression'] != attachments.first.metadata['compression']) ||
+                    (attachment.metadata['format'] != attachments.first.metadata['format'])
 
         raise AttachmentConcatenationError,
               I18n.t('services.attachments.concatenation.incorrect_fastq_file_types')
@@ -133,29 +132,49 @@ def validate_file_extensions(attachments)
     # Concatenates the single end reads into a single-end file
     def concatenate_single_end_reads(attachments)
       basename = concatenation_params[:basename]
-      extension = attachments.first.metadata['compression'] == 'gzip' ? '.gz' : ''
+      zipped_extension = attachments.first.metadata['compression'] == 'gzip' ? '.gz' : ''
 
       files = []
-      files << concatenate_attachments(attachments, "#{basename}_1.fastq#{extension}").signed_id
+      files << concatenate_attachments(attachments,
+                                       "#{basename}_1.fastq#{zipped_extension}")
+               .signed_id
 
       Attachments::CreateService.new(current_user, attachable, { files: }).execute
     end
 
     # Concatenates the paired-end reads into a multiple paired-end files
     def concatenate_paired_end_reads(attachments)
-      basename = concatenation_params[:basename]
+      zipped_extension = attachments.first.metadata['compression'] == 'gzip' ? '.gz' : ''
 
-      extension = attachments.first.metadata['compression'] == 'gzip' ? '.gz' : ''
+      fwd_filename, rev_filename = concatenated_paired_end_filenames(
+        attachments.first.metadata['type']
+      )
 
       forward_reads, reverse_reads = attachments_to_paired_end_directional_reads(attachments)
 
       files = []
-      files << concatenate_attachments(forward_reads, "#{basename}_1.fastq#{extension}").signed_id <<
-        concatenate_attachments(reverse_reads, "#{basename}_2.fastq#{extension}").signed_id
+      files <<
+        concatenate_attachments(forward_reads,
+                                "#{fwd_filename}.fastq#{zipped_extension}")
+        .signed_id <<
+        concatenate_attachments(reverse_reads,
+                                "#{rev_filename}.fastq#{zipped_extension}")
+        .signed_id
 
       Attachments::CreateService.new(current_user, attachable, { files: }).execute
     end
 
+    # Gets the filename in the correct format for illumina paired-end and paired-end files
+    def concatenated_paired_end_filenames(attachment_type)
+      basename = concatenation_params[:basename]
+
+      fwd_filename = attachment_type == 'illumina_pe' ? "#{basename}_S1_L001_R1_001" : "#{basename}_1"
+
+      rev_filename = attachment_type == 'illumina_pe' ? "#{basename}_S1_L001_R2_001" : "#{basename}_2"
+
+      [fwd_filename, rev_filename]
+    end
+
     def concatenate_attachments(attachments, filename)
       blobs = retrieve_attachment_blobs(attachments)
       ActiveStorage::Blob.compose(blobs, filename:)

test/fixtures/active_storage/attachments.yml

@@ -73,6 +73,26 @@ attachmentPEREV5_file_test_file_fastq:
   record: attachmentPEREV5 (Attachment)
   blob: attachmentPEREV5_file_test_file_fastq_blob
 
+attachmentPEFWD6_file_test_file_fastq:
+  name: file
+  record: attachmentPEFWD6 (Attachment)
+  blob: attachmentPEFWD6_file_test_file_fastq_blob
+
+attachmentPEREV6_file_test_file_fastq:
+  name: file
+  record: attachmentPEREV6 (Attachment)
+  blob: attachmentPEREV6_file_test_file_fastq_blob
+
+attachmentPEFWD7_file_test_file_fastq:
+  name: file
+  record: attachmentPEFWD7 (Attachment)
+  blob: attachmentPEFWD7_file_test_file_fastq_blob
+
+attachmentPEREV7_file_test_file_fastq:
+  name: file
+  record: attachmentPEREV7 (Attachment)
+  blob: attachmentPEREV7_file_test_file_fastq_blob
+
 attachmentD_file_test_file_fastq:
   name: file
   record: attachmentD (Attachment)
@@ -97,3 +117,13 @@ attachmentH_file_test_file_fastq:
   name: file
   record: attachmentH (Attachment)
   blob: attachmentH_file_test_file_fastq_blob
+
+attachmentI_file_test_file_fastq:
+  name: file
+  record: attachmentI (Attachment)
+  blob: attachmentI_file_test_file_fastq_blob
+
+attachmentJ_file_test_file_fastq:
+  name: file
+  record: attachmentJ (Attachment)
+  blob: attachmentJ_file_test_file_fastq_blob

test/fixtures/active_storage/blobs.yml

@@ -29,6 +29,12 @@ attachmentPEREV4_file_test_file_fastq_blob: <%= ActiveStorage::FixtureSet.blob f
 attachmentPEFWD5_file_test_file_fastq_blob: <%= ActiveStorage::FixtureSet.blob filename: "08-5923-small_S1_L001_R1_001.fastq", service_name: "test" %>
 attachmentPEREV5_file_test_file_fastq_blob: <%= ActiveStorage::FixtureSet.blob filename: "08-5923-small_S1_L001_R2_001.fastq", service_name: "test" %>
 
+attachmentPEFWD6_file_test_file_fastq_blob: <%= ActiveStorage::FixtureSet.blob filename: "test-fq-file_S1_L001_R1_001.fq", service_name: "test" %>
+attachmentPEREV6_file_test_file_fastq_blob: <%= ActiveStorage::FixtureSet.blob filename: "test-fq-file_S1_L001_R2_001.fq", service_name: "test" %>
+
+attachmentPEFWD7_file_test_file_fastq_blob: <%= ActiveStorage::FixtureSet.blob filename: "test-fq-file2_S1_L001_R1_001.fq", service_name: "test" %>
+attachmentPEREV7_file_test_file_fastq_blob: <%= ActiveStorage::FixtureSet.blob filename: "test-fq-file2_S1_L001_R2_001.fq", service_name: "test" %>
+
 attachmentD_file_test_file_fastq_blob: <%= ActiveStorage::FixtureSet.blob filename: "test_file_D.fastq", service_name: "test" %>
 
 attachmentE_gz_file_test_file_fastq_blob: <%= ActiveStorage::FixtureSet.blob filename: "test_file_2.fastq.gz", service_name: "test" %>
@@ -38,3 +44,7 @@ attachmentF_gz_file_test_file_fastq_blob: <%= ActiveStorage::FixtureSet.blob fil
 attachmentG_file_test_file_fastq_blob: <%= ActiveStorage::FixtureSet.blob filename: "test_file_A.fastq", service_name: "test" %>
 
 attachmentH_file_test_file_fastq_blob: <%= ActiveStorage::FixtureSet.blob filename: "test_file_B.fastq", service_name: "test" %>
+
+attachmentI_file_test_file_fastq_blob: <%= ActiveStorage::FixtureSet.blob filename: "test-fq-file_S1_L001_R1_001.fq.gz", service_name: "test" %>
+
+attachmentJ_file_test_file_fastq_blob: <%= ActiveStorage::FixtureSet.blob filename: "test-fq-file2_S1_L001_R1_001.fq.gz", service_name: "test" %>

test/fixtures/attachments.yml

@@ -9,15 +9,15 @@ attachment2:
   attachable: sample1 (Sample)
 
 attachmentA:
-  metadata: { "compression": "none" }
+  metadata: { "compression": "none", "format": "fastq" }
   attachable: sampleA (Sample)
 
 attachmentB:
-  metadata: { "compression": "none" }
+  metadata: { "compression": "none", "format": "fastq" }
   attachable: sampleA (Sample)
 
 attachmentC:
-  metadata: { "compression": "none" }
+  metadata: { "compression": "none", "format": "fastq" }
   attachable: sampleA (Sample)
 
 attachmentPEFWD1:
@@ -121,21 +121,69 @@ attachmentPEREV5:
   attachable: sampleC (Sample)
 
 attachmentD:
-  metadata: { "compression": "none" }
+  metadata: { "compression": "none", "format": "fastq" }
   attachable: sampleB (Sample)
 
 attachmentE:
-  metadata: { "compression": "gzip" }
+  metadata: { "compression": "gzip", "format": "fastq" }
   attachable: sampleB (Sample)
 
 attachmentF:
-  metadata: { "compression": "gzip" }
+  metadata: { "compression": "gzip", "format": "fastq" }
   attachable: sampleB (Sample)
 
 attachmentG:
-  metadata: { "compression": "none" }
+  metadata: { "compression": "none", "format": "fastq" }
   attachable: sampleC (Sample)
 
 attachmentH:
-  metadata: { "compression": "none" }
+  metadata: { "compression": "none", "format": "fastq" }
+  attachable: sampleC (Sample)
+
+attachmentPEFWD6:
+  metadata:
+    {
+      "type": "illumina_pe",
+      "format": "fastq",
+      "direction": "forward",
+      "compression": "none",
+    }
+  attachable: sampleC (Sample)
+
+attachmentPEREV6:
+  metadata:
+    {
+      "type": "illumina_pe",
+      "format": "fastq",
+      "direction": "reverse",
+      "compression": "none",
+    }
+  attachable: sampleC (Sample)
+
+attachmentPEFWD7:
+  metadata:
+    {
+      "type": "illumina_pe",
+      "format": "fastq",
+      "direction": "forward",
+      "compression": "none",
+    }
+  attachable: sampleC (Sample)
+
+attachmentPEREV7:
+  metadata:
+    {
+      "type": "illumina_pe",
+      "format": "fastq",
+      "direction": "reverse",
+      "compression": "none",
+    }
+  attachable: sampleC (Sample)
+
+attachmentI:
+  metadata: { "compression": "gzip", "format": "fastq" }
+  attachable: sampleC (Sample)
+
+attachmentJ:
+  metadata: { "compression": "gzip", "format": "fastq" }
   attachable: sampleC (Sample)

test/fixtures/files/test-fq-file2_S1_L001_R1_001.fq

@@ -0,0 +1,18 @@
+@gi|284993440|ref|NC_013768.1|-540/1
+CTGTGGCGGGGACAATTATGATTGGTTTACTTACAGTGTCGCTTTTAATCGGTGTAATTTGGGCGCCGAAAACACGTGGCAGATCACTTGATGATATTACGAAGGAACGTTACGGAAATACAATTGATTAAAGAAAAGGAGCCAGACCAGTGAAACATTATGTTGCAGTAGATATTGGTGCATCAAGTGGTCGATTAATTCTAGGGAAATTGGTGAATGAAAAATTACAATTAGAAGAAATTCACCGTTT
++
+[email protected]>IGHHFFHII=IIBIIFIAHFIIHFFAAC@HDIIIH*IIIHIIHIIHCIHHIHHHHHHHHHEIGIHHIHHHCHHHGHHGFFEFHGHFFE+DGD>AAG6;CG*EEGGGFGFGEGE4ECEGEE1?G?DGGEG*:GEEGDE:?GGEEEEGFGGGDG6GGEGGFEGGC6:GEEHE:HGECDEG?:GEGGDG:GEGE?EEAEEEGC/GAGEEAG
+@gi|284993440|ref|NC_013768.1|-538/1
+CGAAAACACGTGGCAGATCACTTGATGATATTACGAAGGAACGTTACGGAAATACAATTGATTAAAGAAAAGGAGGTAGACCAGTGAAACATTATGTTGCAGTAGATATTGGTGCATCAAGTGGTCGATTAATTCTAGGGAAATTGGTGAATGAAAAATTACAATTAGAAGAAATTCACCGTTTTAAAAATGGTTTTACGTACCGAGATGGACACGAACGCTGGGAAATTGATCAACTAATGCAGGAAAT
++
+??A??BBBDD.DDDDBFGFFFGIIHIIIFEFII0EFIHI0EIH0HHGIFI@HHIHIHFHIHIIEIIGHHIHHIIH+HIIIHIG8HIIG?HEHGIHCIIHHIDBHIHHGHE@FIFFHEEHEH=G;9EC(CGF*GFFGE:DGEE@EGEGGGG@EGGEG8GGCEECCGG6AGE*;FAEDFC?C0CFG0GG;FGEG6E<GC?:0E<?*CECGGE,HHFGHFEG??80AF??GCCGGE*GGE0ECEE/:<GGG?E
+@gi|284993440|ref|NC_013768.1|-536/1
+TATACTCGTTAGCCATTCTAGGCTGATTTGTTGGTCACGAAAAAGGATGTTGATGAGAATGTCCTTTTCGCCTGTTGCTTTTATGGAATGATGGCAGCCGCTGTCTAAAAGTAAAAGTTCTCCTTCATGTAAAGTTTCTTTATTTGCTTCAATGATTTGTTCAGAGCTTCCTGAATACATGTAATTTAGTTCAAGAAATTGATGCGTATGGTATGGGTAGTCGGCAATTCGGTTGTGTTTGCTTATATAA
++
+?<AAABBBBDBD<BDDFEG>FFHII>FIHIGIIFIHEH/HGF,HHHIHIHHDD/II?CIHIACHFI5HG=IHGIIHHIFDHIFHIDGIFCFIEGHHCHHGHHHHCHFGGHHHFHEEHGB?GF.GGF=GGG@DDHGEGCG;GDG=*)EGFEG*GGGEEGBAGEEGDC;GEGG86G?8GEGCGGCFGGGCG?EEEG:GGAFCGED*CE:0G,CHHECHEC,CEEEG:FE(G*AGEEGGGGGGG<EGGGF?:F
+@gi|284993440|ref|NC_013768.1|-534/1
+TAATCCGTCTACTTATCATGCCTTTAATGATCAAACAGCTGAAAAGCCAAAAGGCCATGACAAACTTACAACCGAAAATCAAAGAACTACAAGAAAAATACTCGTCTAAAGATAATGAAACAATACCAAAACTACAACAAGAAACAATGCGTCTATATCAAGAAAATAGCGTAAATCCAATGATGGGTTGTTTACCATTATTAATCCAAATGCCTATTCTACTAGGATTTTACCAAGCGATTAGTAGAAC
++
+??5?ABBBDDD@[email protected]@HFGHFHI?EAFHEIHFIHIGDFBIIII?HHCIIHHIIE/DFEHGI5HHHFHHGIHGHGGD)G8H,FG+GGCGHGCGGGFEHE?EEGGADFED;EG?GG?EEE8EGCCFGGGG?GEFGEGGGG;GC6GGG8AAECFCEGGEEGCGFGACGG?HHCHGEFG6G2A'CGAGEG:/FEG?1GE0GFGEGEEA0CC
+@gi|284993440|ref|NC_013768.1|-532/1
+TTTCTTAGTGGGTGTGTACTTATTTTGGAATTTAGTAGCGGGTGCAATGGGATTCTTTATGCCGTTTGTATATGAAACGGTGGGTGGTCTTTCTAATACACAAGCGAATTTATTGCAAGCTGTATTATGGATACTAACAGCAGCTTCTACATACTTTGGCTTTGCTAAATTTGGTGATCGAGTAAGTCATCGTGGGTTGTTTTTTGTAGGGGCTTTAATGGCAGTTGCTTCTTGGGTTGTACTTACTTTT

test/fixtures/files/test-fq-file2_S1_L001_R2_001.fq

@@ -0,0 +1,18 @@
+@gi|284993440|ref|NC_013768.1|-540/2
+TCAAAACATAGTCAACGCCCCACGTGTCAATTCCAAGCACACATTCCGAAATCCCCAGTTGCTTTACTTTTTCCAAGCCAATAAAAATTTCCTGCATTAGTTGATCAATTTCCCAGCGTTCGTGTCCATCTCGGTACGAAAAACCATTTTTAAAACGGTGAATTTCTTCTAATTGTAATTTTTCATTCACCAATTTCCCTAGAATTAATCAACCACTTGATGCACCAATATCTACTGCAACATAATGTTT
++
+??A5ABB?D+A-DD@<CFFF.FI>FE/IIFH=IHCHG.II/CIHHBIIHFHHHHH=HHIH5GHI5HHGIFFIHFHFHGEBIIHHFHHCEHHFCFBDCHH+=@HHGG-=*EDHB5GGGEHH2FBDHEF=,B??E.GGFG*FBCEEE82(EGGEE5GEECEEEGGGGEGEEG/G?EAFFDF?CEGGFFA<1(GFGEFE:E:GE?EGG*EEDA(G(GGFE7,G8GE*C?FF*(EE??E?A:*(E/'E*FCG)E
+@gi|284993440|ref|NC_013768.1|-538/2
+ATTTAAAGTTCGTTTTTCGCGATAACTAATTGGATCTGCCAACTTCTCACCGGAAGCCCCTATCAAAACATAGTCAACGCCCCACGTGTCAATTCCAAGCACACTTTCCGAAATCCCCAGTTGCTTTACTTTTTTCAAGCCAATAAAAATTTCCTACATTAGCTGGTCAATTTCCCAGCGTTTGTGTCCATCTCGGTGCGTAAAACCATTTTTAAAACGGTGAAGATCTTCTAATTGTAATTGTTCATTC
++
+???A??<B<D<-BD5-CF>GGFFIHHHHCI>AFI>I9EHDHIDIFEIGI-CHHGHDIDHCAIEFHFFHH-IEIACAFAHECIIHFH+EIHH-HHGDBHIHHH2H#DHFFFHGEHEGEEHB@FDGDG(EFH@EGC*GEG@HCGEEFGBGDA;EFEC#:CEFAE*3G.GEG9E=0*GF*2FCCG(/?A0DFE8(::64?.E<</DA8A6:CHEGHE*0.8EGFGG(**6A6GEC(:G6E*A1(8.G(6(/?E
+@gi|284993440|ref|NC_013768.1|-536/2
+CAAATTTACAGAAGGAGATTGTGAAATGGAAGCGCTTAATAAAAAATTATTTCGCCTAAATTCAAAAAAAAAAATCCAAAAAAGCACTGGCACTTTTGTTCCCGATTTACCCAATGGATCCTTTTTAAAAGAGAACGGCAGCATGGAAATATTAAATGATTATTTCTTCAAAAACAAAGACATTTATATAAGCAAACACAGCCGATTTGCCGACTACCCATACCATACGCATCAATTTCTTGAACTAAAT
++
+??<,??BBBDDDBD-?F+6CG+FHI6FHEHEI9FIHHHGIIFFEIFFAFGFCGHHFHII+G=HHGH--5FI-HAFHGHIHDA+HIH-HHIH<+FHGIHG*;E2HGFHI@FHFGH5EF<H7+FB+HHFGE#GFDGEGC,GEEEG*DGEG*CG0G99GGFEEFC,(?EGEEE(2<G8EGEEGGCGGE/EEF6(CE0CGE?AA#CC:=EH*:?H:EG*?(EGGGG;A*F:G/E6.*E???6CECAG:?*EAEC
+@gi|284993440|ref|NC_013768.1|-534/2
+TGATGTAAACAATCATTGCCAGTGATTTATTTTGCTGTGTTTGCCCCATCATAGAAATTTTTGATGATAAGAATGTTGTAAATGCCGCAACAACCGGTAAGATGTAATATGGATCTGGATTTCCCAGTTGTATCCATAAGAACGAATCTGTTTTGATTTCTGCTGTTCTACTAATCGCTTGGTAAAATCCTAGTATAATAGGCATTTGGATTAATAATGGGAAACAACCCATCATTGGATTTACGCTATT
++
+?????BBBDDDEDEDD6FF@C+IHIFCEHHHEICIHHI/HIHHHHAFHHHHIHHHH@HIHEGICHIHCIIHIGCF-FHH-FFI>BHHEGHIH=IIHHHIHHHG+HH6CHHD+CC?EHHGDFG+GF(EEGE(D,EEGEE3HAD)EE<GD1EFF@FCGGG:E9:G<F?6*F>(GE*C2<AEAG:'6G?#E.6:<?*C(?E**G/(C8CECG/FE@GG=0G(:*:C??(AEECFCEG*G?E:0F.G0(GC/EC
+@gi|284993440|ref|NC_013768.1|-532/2
+CACCTGTACTACCACGAACTAAGAAAAACATCACGCCTTGAACCCCACCACGATATTTTCTTGGGAAAAGTTCTGTGGACCAAAGTGCGTAAAAAGCTTGTGCACCAATACCTGCTGAAATAACCCATAAAGTAACAAATGTCCATAAGCCAACACAAGACATCCCACCTAAAGTGATTACAACCCAAGAAGCAACTGCCATTAACGCACCTACAAAAAACAAACCACGATGACTTACTCGATCACCAAG

test/fixtures/files/test-fq-file_S1_L001_R1_001.fq

@@ -0,0 +1,18 @@
+@gi|662858600|ref|NC_013766.2|-540/1
+CTGTGGCGGGGACAATTATGATTGGTTTACTTACAGTGTCGCTTTTAATCGGTGTAATTTGGGCGCCGAAAACACGTGGCAGATCACTTGATGATATTACGAAGGAACGTTACGGAAATACAATTGATTAAAGAAAAGGAGCCAGACCAGTGAAACATTATGTTGCAGTAGATATTGGTGCATCAAGTGGTCGATTAATTCTAGGGAAATTGGTGAATGAAAAATTACAATTAGAAGAAATTCACCGTTT
++
+[email protected]>IGHHFFHII=IIBIIFIAHFIIHFFAAC@HDIIIH*IIIHIIHIIHCIHHIHHHHHHHHHEIGIHHIHHHCHHHGHHGFFEFHGHFFE+DGD>AAG6;CG*EEGGGFGFGEGE4ECEGEE1?G?DGGEG*:GEEGDE:?GGEEEEGFGGGDG6GGEGGFEGGC6:GEEHE:HGECDEG?:GEGGDG:GEGE?EEAEEEGC/GAGEEAG
+@gi|662858600|ref|NC_013766.2|-538/1
+CGAAAACACGTGGCAGATCACTTGATGATATTACGAAGGAACGTTACGGAAATACAATTGATTAAAGAAAAGGAGGTAGACCAGTGAAACATTATGTTGCAGTAGATATTGGTGCATCAAGTGGTCGATTAATTCTAGGGAAATTGGTGAATGAAAAATTACAATTAGAAGAAATTCACCGTTTTAAAAATGGTTTTACGTACCGAGATGGACACGAACGCTGGGAAATTGATCAACTAATGCAGGAAAT
++
+??A??BBBDD.DDDDBFGFFFGIIHIIIFEFII0EFIHI0EIH0HHGIFI@HHIHIHFHIHIIEIIGHHIHHIIH+HIIIHIG8HIIG?HEHGIHCIIHHIDBHIHHGHE@FIFFHEEHEH=G;9EC(CGF*GFFGE:DGEE@EGEGGGG@EGGEG8GGCEECCGG6AGE*;FAEDFC?C0CFG0GG;FGEG6E<GC?:0E<?*CECGGE,HHFGHFEG??80AF??GCCGGE*GGE0ECEE/:<GGG?E
+@gi|662858600|ref|NC_013766.2|-536/1
+TATACTCGTTAGCCATTCTAGGCTGATTTGTTGGTCACGAAAAAGGATGTTGATGAGAATGTCCTTTTCGCCTGTTGCTTTTATGGAATGATGGCAGCCGCTGTCTAAAAGTAAAAGTTCTCCTTCATGTAAAGTTTCTTTATTTGCTTCAATGATTTGTTCAGAGCTTCCTGAATACATGTAATTTAGTTCAAGAAATTGATGCGTATGGTATGGGTAGTCGGCAATTCGGTTGTGTTTGCTTATATAA
++
+?<AAABBBBDBD<BDDFEG>FFHII>FIHIGIIFIHEH/HGF,HHHIHIHHDD/II?CIHIACHFI5HG=IHGIIHHIFDHIFHIDGIFCFIEGHHCHHGHHHHCHFGGHHHFHEEHGB?GF.GGF=GGG@DDHGEGCG;GDG=*)EGFEG*GGGEEGBAGEEGDC;GEGG86G?8GEGCGGCFGGGCG?EEEG:GGAFCGED*CE:0G,CHHECHEC,CEEEG:FE(G*AGEEGGGGGGG<EGGGF?:F
+@gi|662858600|ref|NC_013766.2|-534/1
+TAATCCGTCTACTTATCATGCCTTTAATGATCAAACAGCTGAAAAGCCAAAAGGCCATGACAAACTTACAACCGAAAATCAAAGAACTACAAGAAAAATACTCGTCTAAAGATAATGAAACAATACCAAAACTACAACAAGAAACAATGCGTCTATATCAAGAAAATAGCGTAAATCCAATGATGGGTTGTTTACCATTATTAATCCAAATGCCTATTCTACTAGGATTTTACCAAGCGATTAGTAGAAC
++
+??5?ABBBDDD@[email protected]@HFGHFHI?EAFHEIHFIHIGDFBIIII?HHCIIHHIIE/DFEHGI5HHHFHHGIHGHGGD)G8H,FG+GGCGHGCGGGFEHE?EEGGADFED;EG?GG?EEE8EGCCFGGGG?GEFGEGGGG;GC6GGG8AAECFCEGGEEGCGFGACGG?HHCHGEFG6G2A'CGAGEG:/FEG?1GE0GFGEGEEA0CC
+@gi|662858600|ref|NC_013766.2|-532/1
+TTTCTTAGTGGGTGTGTACTTATTTTGGAATTTAGTAGCGGGTGCAATGGGATTCTTTATGCCGTTTGTATATGAAACGGTGGGTGGTCTTTCTAATACACAAGCGAATTTATTGCAAGCTGTATTATGGATACTAACAGCAGCTTCTACATACTTTGGCTTTGCTAAATTTGGTGATCGAGTAAGTCATCGTGGGTTGTTTTTTGTAGGGGCTTTAATGGCAGTTGCTTCTTGGGTTGTACTTACTTTT

test/fixtures/files/test-fq-file_S1_L001_R2_001.fq

@@ -0,0 +1,18 @@
+@gi|662858600|ref|NC_013766.2|-540/2
+TCAAAACATAGTCAACGCCCCACGTGTCAATTCCAAGCACACATTCCGAAATCCCCAGTTGCTTTACTTTTTCCAAGCCAATAAAAATTTCCTGCATTAGTTGATCAATTTCCCAGCGTTCGTGTCCATCTCGGTACGAAAAACCATTTTTAAAACGGTGAATTTCTTCTAATTGTAATTTTTCATTCACCAATTTCCCTAGAATTAATCAACCACTTGATGCACCAATATCTACTGCAACATAATGTTT
++
+??A5ABB?D+A-DD@<CFFF.FI>FE/IIFH=IHCHG.II/CIHHBIIHFHHHHH=HHIH5GHI5HHGIFFIHFHFHGEBIIHHFHHCEHHFCFBDCHH+=@HHGG-=*EDHB5GGGEHH2FBDHEF=,B??E.GGFG*FBCEEE82(EGGEE5GEECEEEGGGGEGEEG/G?EAFFDF?CEGGFFA<1(GFGEFE:E:GE?EGG*EEDA(G(GGFE7,G8GE*C?FF*(EE??E?A:*(E/'E*FCG)E
+@gi|662858600|ref|NC_013766.2|-538/2
+ATTTAAAGTTCGTTTTTCGCGATAACTAATTGGATCTGCCAACTTCTCACCGGAAGCCCCTATCAAAACATAGTCAACGCCCCACGTGTCAATTCCAAGCACACTTTCCGAAATCCCCAGTTGCTTTACTTTTTTCAAGCCAATAAAAATTTCCTACATTAGCTGGTCAATTTCCCAGCGTTTGTGTCCATCTCGGTGCGTAAAACCATTTTTAAAACGGTGAAGATCTTCTAATTGTAATTGTTCATTC
++
+???A??<B<D<-BD5-CF>GGFFIHHHHCI>AFI>I9EHDHIDIFEIGI-CHHGHDIDHCAIEFHFFHH-IEIACAFAHECIIHFH+EIHH-HHGDBHIHHH2H#DHFFFHGEHEGEEHB@FDGDG(EFH@EGC*GEG@HCGEEFGBGDA;EFEC#:CEFAE*3G.GEG9E=0*GF*2FCCG(/?A0DFE8(::64?.E<</DA8A6:CHEGHE*0.8EGFGG(**6A6GEC(:G6E*A1(8.G(6(/?E
+@gi|662858600|ref|NC_013766.2|-536/2
+CAAATTTACAGAAGGAGATTGTGAAATGGAAGCGCTTAATAAAAAATTATTTCGCCTAAATTCAAAAAAAAAAATCCAAAAAAGCACTGGCACTTTTGTTCCCGATTTACCCAATGGATCCTTTTTAAAAGAGAACGGCAGCATGGAAATATTAAATGATTATTTCTTCAAAAACAAAGACATTTATATAAGCAAACACAGCCGATTTGCCGACTACCCATACCATACGCATCAATTTCTTGAACTAAAT
++
+??<,??BBBDDDBD-?F+6CG+FHI6FHEHEI9FIHHHGIIFFEIFFAFGFCGHHFHII+G=HHGH--5FI-HAFHGHIHDA+HIH-HHIH<+FHGIHG*;E2HGFHI@FHFGH5EF<H7+FB+HHFGE#GFDGEGC,GEEEG*DGEG*CG0G99GGFEEFC,(?EGEEE(2<G8EGEEGGCGGE/EEF6(CE0CGE?AA#CC:=EH*:?H:EG*?(EGGGG;A*F:G/E6.*E???6CECAG:?*EAEC
+@gi|662858600|ref|NC_013766.2|-534/2
+TGATGTAAACAATCATTGCCAGTGATTTATTTTGCTGTGTTTGCCCCATCATAGAAATTTTTGATGATAAGAATGTTGTAAATGCCGCAACAACCGGTAAGATGTAATATGGATCTGGATTTCCCAGTTGTATCCATAAGAACGAATCTGTTTTGATTTCTGCTGTTCTACTAATCGCTTGGTAAAATCCTAGTATAATAGGCATTTGGATTAATAATGGGAAACAACCCATCATTGGATTTACGCTATT
++
+?????BBBDDDEDEDD6FF@C+IHIFCEHHHEICIHHI/HIHHHHAFHHHHIHHHH@HIHEGICHIHCIIHIGCF-FHH-FFI>BHHEGHIH=IIHHHIHHHG+HH6CHHD+CC?EHHGDFG+GF(EEGE(D,EEGEE3HAD)EE<GD1EFF@FCGGG:E9:G<F?6*F>(GE*C2<AEAG:'6G?#E.6:<?*C(?E**G/(C8CECG/FE@GG=0G(:*:C??(AEECFCEG*G?E:0F.G0(GC/EC
+@gi|662858600|ref|NC_013766.2|-532/2
+CACCTGTACTACCACGAACTAAGAAAAACATCACGCCTTGAACCCCACCACGATATTTTCTTGGGAAAAGTTCTGTGGACCAAAGTGCGTAAAAAGCTTGTGCACCAATACCTGCTGAAATAACCCATAAAGTAACAAATGTCCATAAGCCAACACAAGACATCCCACCTAAAGTGATTACAACCCAAGAAGCAACTGCCATTAACGCACCTACAAAAAACAAACCACGATGACTTACTCGATCACCAAG