added pair-end power to read_fastq

git-svn-id: http://biopieces.googlecode.com/svn/trunk@2117 74ccb610-7750-0410-82ae-013aeee3265d

diff --git a/bp_bin/read_fastq b/bp_bin/read_fastq
index 78a3fcceaf689bcf198e2544fb45316e8c92cb4b..0c5b9b2cff975de128aa8306db786d7af5ef1882 100755 (executable)
--- a/bp_bin/read_fastq
+++ b/bp_bin/read_fastq
@@ -31,16 +31,19 @@
 require 'maasha/biopieces'
 require 'maasha/fastq'
 
+MAX_TEST = 1_000
+
 allowed_enc = 'auto,base_33,base_64'
 
 casts = []
 casts << {:long=>'data_in',  :short=>'i', :type=>'files!', :mandatory=>false, :default=>nil,    :allowed=>nil,         :disallowed=>nil}
+casts << {:long=>'data_in2', :short=>'j', :type=>'files!', :mandatory=>false, :default=>nil,    :allowed=>nil,         :disallowed=>nil}
 casts << {:long=>'num',      :short=>'n', :type=>'uint',   :mandatory=>false, :default=>nil,    :allowed=>nil,         :disallowed=>'0'}
 casts << {:long=>'encoding', :short=>'e', :type=>'string', :mandatory=>false, :default=>'auto', :allowed=>allowed_enc, :disallowed=>nil}
 
 options = Biopieces.options_parse(ARGV, casts)
 
-MAX_TEST = 1_000
+encoding = options[:encoding].to_sym
 
 num  = 0
 last = false
@@ -52,11 +55,59 @@ Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output|
     end
   end
 
-  if options[:data_in]
-    options[:data_in].each do |file|
-      encoding = options[:encoding].downcase.to_sym
+  if options[:data_in] and options[:data_in2]
+    raise "data_in files differ" if options[:data_in].size != options[:data_in2].size
+
+    (0 ... options[:data_in].size).each do |i|
+      file1 = options[:data_in][i]
+      file2 = options[:data_in2][i]
+
+      io1 = Fastq.open(file1, 'r')
+      io2 = Fastq.open(file2, 'r')
+
+      while not io1.eof? and not io2.eof?
+        entry1 = io1.get_entry
+        entry2 = io2.get_entry
+
+        if encoding == :auto
+          if entry1.qual_base33? or entry2.qual_base33?
+            encoding = :base_33
+          elsif entry1.qual_base64? or entry2.qual_base64?
+            encoding = :base_64
+          else
+            raise SeqError, "Could not auto-detect quality score encoding"
+          end
+        end
+
+        entry1.qual_convert!(encoding, :base_33)
+        entry2.qual_convert!(encoding, :base_33)
+        entry1.qual_coerce!(:base_33)
+        entry2.qual_coerce!(:base_33)
 
-      Fastq.open(file, mode='r') do |fastq|
+        if num < MAX_TEST
+          raise SeqError, "Quality score outside valid range" unless entry1.qual_valid?(:base_33)
+          raise SeqError, "Quality score outside valid range" unless entry2.qual_valid?(:base_33)
+        end
+
+        output.puts entry1.to_bp
+        output.puts entry2.to_bp
+
+        num += 2
+
+        if options[:num] and num >= options[:num]
+          last = true
+          break
+        end
+      end
+
+      io1.close
+      io2.close
+
+      break if last
+    end
+  elsif options[:data_in]
+    options[:data_in].each do |file|
+      Fastq.open(file, 'r') do |fastq|
         fastq.each do |entry|
           if encoding == :auto
             if entry.qual_base33?

diff --git a/bp_test/in/read_fastq.in.3 b/bp_test/in/read_fastq.in.3
new file mode 100644 (file)
index 0000000..7f8f581
--- /dev/null
+++ b/bp_test/in/read_fastq.in.3
@@ -0,0 +1,20 @@
+@M01168:16:000000000-A1R9L:1:1101:14862:1868 1:N:0:14
+TGGGGAATATTGGACAATGGGGGCAACCCTGATCCAGCAATACCGCGTGTGTGAAGAAGGCCTGAGGGTTGTAAAGCACTTTCAATTGTGAAGAAAAGTTAACGGTTAATAACCGTTAGCCTTGACGTTAACTTTAGAAGAAGCACCGGCTAACTCCGTGCCAGCAGCCGCGGTAATACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGTGCGTAGGCGGTTTATTCAGTCAGATGTGCA
++
+<??????BDDDDDDDDGGGGGGGHHIIIEHIHHFGGHFHHGHFHHDHEHEHHFAFFGFFHFHHFFHHHEFEEHHHHHHHHHHHHFFFHFHHHHHHHHHHHHGBDEGGGGGGGGGGGGGGGGEGEGGGGGCEGGGGECCECEEECGGG<ADGCGGGEGGEGGGGGEGCE8>2>DC<EEEGGC?<DGCCCEC:C?CCEGGGGCC)?EGEE:?C84.'80*:C8?C>??2CE22.48C:?*CC?:C*:?C?C*1
+@M01168:16:000000000-A1R9L:1:1101:13906:2139 1:N:0:14
+TAGGGAATCTTGCACAATGGAGGAAACTCTGATGCAGCGATGCCGCGTGAGTGAAGAAGGCCTTTGGGTTGTAAAGCTCTTTCGTCGGGGAAGAAAATGACTGTACCCGAATAAGAAGGTCCGGCTAACTTCGTGCCAGCAGCCGCGGTAATACGAAGGGACCTAGCGTAGTTCGGAATTACTGGGCTTAAAGAGTTCGTAGGTGGTTAAAAACGTTGGTGGTGAAATCCCAGAGCTTAACGCTGGAACTG
++
+<???9?BBBDBDDBDDFFFFFFHHHIFHFHHIHHFHHHHEDDEGHHHCEHE?EFHFGHFHFHIHIIIHCECEHHHIFHIIIHGHFHHHHHHEEFFFFFEEFFFEFFFEEEEEFFFFFFFCEFBEEDEFFFFFFEFEFFEEFFFFDDDDA?EEEFFEEEDECAEE?:ADAA>AEEFDA?CEEF:?CA8EEEEAEEE:AACEFFECEEEE?:?CA).0:AE88).0::CEEEEEC?A*:AA:*)..?>AEEF:
+@M01168:16:000000000-A1R9L:1:1101:14865:2158 1:N:0:14
+TAGGGAATCTTGCACAATGGAGGAAACTCTGATGCAGCGATGCCGCGTGAGTGAAGAAGGCCTTTGGGTTGTAAAGCTCTTTCGTCGGGGAAGAAAATGACTGTACCCGAATAAGAAGGTCCGGCTAACTTCGTGCCAGCAGCCGCGGTAATACGAAGGGACCTAGCGTAGTTCGGAATTACTGGGCTTAAAGAGTTCGTAGGTGGTTAAAAAAGTTGGTGGTGAAATCCCAGAGCTTAACTCTGGAACTG
++
+?????BBBBBDDBDDBFFFFFFECHFHFHFHGHHFGD?>CFHHHHHH>DEEFFFFDFFHF@FHHHIFHEEHHHIIHHHIHIHHHDEHHHHFEEFFF?FEEEEFEEFFEE:>CEEFEFFFBEEEEEDEFE::AE:?AECEFEF?A>;D88;CEEEEFEA;AECEEECE;0?>0:AADAAECEFFEEECEAACE:CA:*?C8?CE::CE8ACCA:4?:AC:8888):*:?EA*::8**1**11??:E?CA:?1
+@M01168:16:000000000-A1R9L:1:1101:17246:2253 1:N:0:14
+TAGGGAATCTTGCACAATGGGGGAAACCCTGATGCAGCGATGCCGCGTGAGTGAAGAAGGCCCTTGGGTTGTAAAGCTCTTTCGTCGGGGAAGAAAATGACTGTACCCGAATAAGAAGGTCCGGCTAACTTCGTGCCAGCAGCCGCGGTAATACGAAGGGAACTAGCGTAGTTCGGAATTACTGGGCTTAAAGAGTTCGTAGGTGGTTAAAAAAGTTGATGGTGAAATCCCAAGGCTCAACCTTGGAACTG
++
+5<???B-<-?<BBBBBFFF;>CEEECC;EFFH=EGBE=CEFHD@CDCE>+>5C=FBAEADHFEHHHHHHECCG=CD=CCF=DC=DDACEE5:DEEEECBECEC3?3;?B:@CEEECEEC?CC????E?CAAAE?ACEEEEEEEE????A;)::ACAEE?EA*8:CEE')08AECE?EEE?:??::ACE*?*?*:A/:*88A?A?CCAE:?C**4A/:AEC::*/0/?::?**0.)*:8:///::*/:?:?0
+@M01168:16:000000000-A1R9L:1:1101:13072:2276 1:N:0:14
+TGGGGAATTTTGCGCAATGGGCGAAAGCCTGACGCAGCAACGCCGCGGGATCGAAGAAGCTCTGCGGAGTGTAAAGATCTGTCATAAGGGAAGAATAACGAGTATTCTAACAAAATATTCGTCTGACGGTACCTTATAAGAAAGCCACGGCTAACTTCGTGCCAGCAGCCGCGGTAATACGAGGGGGGCAAGCGTTATCCGGAATCATTGGGCGTAAAGGGGTCGTATGAGGACTGATCAGATGGAATTGA
++
+55?????B?BB<-5@BC9CFFB>+C>C>E?@B=>,>5>FE,>77>CE)<<:CD=@DEFHDDBCFFEE8:=@,BD=,3;BEEEE?;BCCECCCE?B;?B3:AA88?:**:CAAA88:::::??8*)AC).8?)*:???:0?CEAAE8**4;8;AA:??:8:??8?EE:AC?;42.)4?*::8).'''..'.8C8A)8AAE:A;?'0:?CAEE?8''4A8?*8'0)''8*0*/:C8:CEC?::*0/*0/*:A*

diff --git a/bp_test/in/read_fastq.in.4 b/bp_test/in/read_fastq.in.4
new file mode 100644 (file)
index 0000000..59c747c
--- /dev/null
+++ b/bp_test/in/read_fastq.in.4
@@ -0,0 +1,20 @@
+@M01168:16:000000000-A1R9L:1:1101:14862:1868 2:N:0:14
+CCTGTTTGCTACCCACGCTTTCGTACCTCAGCGTCAGTATTGGTCCAGAAAGCTGCCTTCGCCATTGATGTTCCTTCTGATATCTACGCATTTCACCGCTACACCAGAAATTCCACTTTCCTCTACCATACTCTAGTTGACCAGTTTCAAATGCAGTTCCCAGGTTAAGCCCGGGGCTTTCACATCTGACTTAATAAACCGCCTACGCACGCTTTACGCCCAGTAATTCCACTTAACGCTTGCACCCTCCG
++
+?????BB<-<BDDDDDFEEFFFHFFHI;F;EGHHDHEF9?ECDC?FFFFFGGFGHIH?GFDEE>EHHFFCGFHHIIIIIHHHHIHDHFHHHHDDGGGHHHHHHHHHFFF@FFD>BFDFBFB?=DDE=DEDEEDBDEBECFEA=CBEAACFCA,,==CE==,,=)*1?A:::?8D8'4;AA::CACEEE?A?AACEEEEC*'48).0)'A;D?A))*108..?*1*1:::**010:1*)5).)**0*.8C))
+@M01168:16:000000000-A1R9L:1:1101:13906:2139 2:N:0:14
+ACTCTTCGCTACCCATGCTTTCGTTCCTCAGCGTCAGTAATGATCCAGAAAGCTGCCTTCGCAATCGGTATTCTTTCTAATATCTACGAATTTCACCTCTACACTAGAAATTCTGCTTTCCTCTATCATACTCTAGCTAAAAAGTTTTGATGGCAGTTCCAGAGTTAAGCTCTGGGATTTCACCACCAACTTTTTTAACCACCTACGAACTCTTTAAGCCCAGTAATTCCGAACTACGCTAGGTCCCTTCG
++
+,5<??BB?DDABDBDDFFFFFFHFHIHFHHIIHEHEHF?E?0CDFGFFHHIHFFFHHHGD@E@EDBFH>5EGHHHIIIGGCGHHHFHIHHAFBCGGGGHHFFFHFFFHFHFF?DDBDFH.?FFFFFBFFFEDEEEFEFF=BDEEEECCEEA=AB=?CEC=AC,<5=BE:CE*?*?E?*?:*:*1:8?A?AEEFEE>E:*1:8AEEE?)?8?:?:CEAEAAE*81?*?CEE:8??**1)5.).8A*:A:?**
+@M01168:16:000000000-A1R9L:1:1101:14865:2158 2:N:0:14
+CCTCTTCGCTACCCATGCTTTCGTTCCTCAGTGTCAGTAATGATCCAGAAAGCTGCCTTCGCAATCGGTATTCTTTCTAATATCTACGAATTTCACCTCTACACTAGAAATTCTGCTTTCCTCTATCATACTCTAGCTAAAAAGTTTTGATGGCAGTTCCAGAGTTAAGCTCTGGGATTTCACCACCAACTTTTTTAACCACCTACGAACTCTTTAAGCCCAGTAATTCCGAACTACGCTAGGTCCCTTCG
++
+??,<??B?BB?BBBBBFF?FFFH;FHFFHBG0C9AFHC?F=?CC?FF=C?EBFGGHDHHHFDDEDD@E>CFHHHIHHH??AEGFHC?FEFFFBCEGHHFHHFGHHHFHHFCD.@DDFHH?FFFF=C?BFFFDFF?BFD=;DDEEDEEEEEE;CCBEEEEB?B??B?C?B;E?EBA:/:AC?A:*?EACAA*?CEC;*/0*:?ACCAA?C?EEEEEE:A:*800:AA:AEE:)04??:A;8A?CA/0*::A8
+@M01168:16:000000000-A1R9L:1:1101:17246:2253 2:N:0:14
+CCTCTTCGCTACCCATGCTTTCGTTCCTCAGTGTCAGTAATGATCCAGAAAGTTGCCTTCGCTTTTGATGTTCTTTCTAATATCTACGAATTTCACCTCTACACTAGAAATTCCACTTTCCTCTATCATACTCTAGCTAAAAAGTTTTGATGGCAGTTCCAAGGTTGAGCCTTGGGATTTCACCATCAACTTTTTTAACCACCTACGAACTCTTTAAGCCCAGTAATTCCGAACTACGCTAGGTCCCTTCG
++
+?????BB??BBDBBBBBFFFFFHFHIIFFBD0A09CGFGG?0CDDGHDGFHHGEFGHHIIHE@CFHH+AEGHFHIIHHCEFHHHGDHHHIIHHIHBGGHHDGFHHHHBBGFFDDFDFHFCFFH?.CCFFHHHHFFFFFFDDBFEDDEEEEFE.4,?BA==A==*5=A,BB,A=CAACEEFEEF*AEEC0*AEEEC;C10**080??)88'ACECAA::::*8?C:?EF::?A)2A:*)'.84AAA0?EEA*
+@M01168:16:000000000-A1R9L:1:1101:13072:2276 2:N:0:14
+CCTGTTTGCTCCCCACGCTTTCGTTCCTCAGCGTCAGTATAGGCCCAGTAAGCTGCCTTCGCCTTTGATGTTCCTCCTGATATCTACGCATTTCACCGCTACACCAGGAATTCCGCTTACCTCTACCTCACTCAAGACTGACAGTATTGAAACCGTTCCCCCGGTTAAGCCGCGGTCTTTTAATTCCAACTGATCAGTCCGCCTACGAACCCTTTACGCCCAATGATTCTAGATAACACTTGCCCCACGCG
++
+,<5<<<>>-5-@@@@@CEEEEEEAACE/A>C-7@7CE999A.9AEEE+C=CFFD@BD@=E+9C5>EACC=A5CA@ED>CEDDEEEDDDDE9DDEEDDDDDCCEDE@D99DDD99;991D*3@9*2*0@;88*0**9@@@@;*87*;@8;(/;69'-///6(8'2-46;6(6'''.('/6((//..6666(66<<;<E<(((-((/(/(/''/6.6666-.-6((6(((6.((((/(((/(/6?<6((''-'

diff --git a/bp_test/out/read_fastq.out.4 b/bp_test/out/read_fastq.out.4
new file mode 100644 (file)
index 0000000..ac2f9a3
--- /dev/null
+++ b/bp_test/out/read_fastq.out.4
@@ -0,0 +1,50 @@
+SEQ_NAME: M01168:16:000000000-A1R9L:1:1101:14862:1868 1:N:0:14
+SEQ: TGGGGAATATTGGACAATGGGGGCAACCCTGATCCAGCAATACCGCGTGTGTGAAGAAGGCCTGAGGGTTGTAAAGCACTTTCAATTGTGAAGAAAAGTTAACGGTTAATAACCGTTAGCCTTGACGTTAACTTTAGAAGAAGCACCGGCTAACTCCGTGCCAGCAGCCGCGGTAATACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGTGCGTAGGCGGTTTATTCAGTCAGATGTGCA
+SEQ_LEN: 251
+SCORES: <??????BDDDDDDDDGGGGGGGHHIIIEHIHHFGGHFHHGHFHHDHEHEHHFAFFGFFHFHHFFHHHEFEEHHHHHHHHHHHHFFFHFHHHHHHHHHHHHGBDEGGGGGGGGGGGGGGGGEGEGGGGGCEGGGGECCECEEECGGG<ADGCGGGEGGEGGGGGEGCE8>2>DC<EEEGGC?<DGCCCEC:C?CCEGGGGCC)?EGEE:?C84.'80*:C8?C>??2CE22.48C:?*CC?:C*:?C?C*1
+---
+SEQ_NAME: M01168:16:000000000-A1R9L:1:1101:14862:1868 2:N:0:14
+SEQ: CCTGTTTGCTACCCACGCTTTCGTACCTCAGCGTCAGTATTGGTCCAGAAAGCTGCCTTCGCCATTGATGTTCCTTCTGATATCTACGCATTTCACCGCTACACCAGAAATTCCACTTTCCTCTACCATACTCTAGTTGACCAGTTTCAAATGCAGTTCCCAGGTTAAGCCCGGGGCTTTCACATCTGACTTAATAAACCGCCTACGCACGCTTTACGCCCAGTAATTCCACTTAACGCTTGCACCCTCCG
+SEQ_LEN: 251
+SCORES: ?????BB<-<BDDDDDFEEFFFHFFHI;F;EGHHDHEF9?ECDC?FFFFFGGFGHIH?GFDEE>EHHFFCGFHHIIIIIHHHHIHDHFHHHHDDGGGHHHHHHHHHFFF@FFD>BFDFBFB?=DDE=DEDEEDBDEBECFEA=CBEAACFCA,,==CE==,,=)*1?A:::?8D8'4;AA::CACEEE?A?AACEEEEC*'48).0)'A;D?A))*108..?*1*1:::**010:1*)5).)**0*.8C))
+---
+SEQ_NAME: M01168:16:000000000-A1R9L:1:1101:13906:2139 1:N:0:14
+SEQ: TAGGGAATCTTGCACAATGGAGGAAACTCTGATGCAGCGATGCCGCGTGAGTGAAGAAGGCCTTTGGGTTGTAAAGCTCTTTCGTCGGGGAAGAAAATGACTGTACCCGAATAAGAAGGTCCGGCTAACTTCGTGCCAGCAGCCGCGGTAATACGAAGGGACCTAGCGTAGTTCGGAATTACTGGGCTTAAAGAGTTCGTAGGTGGTTAAAAACGTTGGTGGTGAAATCCCAGAGCTTAACGCTGGAACTG
+SEQ_LEN: 251
+SCORES: <???9?BBBDBDDBDDFFFFFFHHHIFHFHHIHHFHHHHEDDEGHHHCEHE?EFHFGHFHFHIHIIIHCECEHHHIFHIIIHGHFHHHHHHEEFFFFFEEFFFEFFFEEEEEFFFFFFFCEFBEEDEFFFFFFEFEFFEEFFFFDDDDA?EEEFFEEEDECAEE?:ADAA>AEEFDA?CEEF:?CA8EEEEAEEE:AACEFFECEEEE?:?CA).0:AE88).0::CEEEEEC?A*:AA:*)..?>AEEF:
+---
+SEQ_NAME: M01168:16:000000000-A1R9L:1:1101:13906:2139 2:N:0:14
+SEQ: ACTCTTCGCTACCCATGCTTTCGTTCCTCAGCGTCAGTAATGATCCAGAAAGCTGCCTTCGCAATCGGTATTCTTTCTAATATCTACGAATTTCACCTCTACACTAGAAATTCTGCTTTCCTCTATCATACTCTAGCTAAAAAGTTTTGATGGCAGTTCCAGAGTTAAGCTCTGGGATTTCACCACCAACTTTTTTAACCACCTACGAACTCTTTAAGCCCAGTAATTCCGAACTACGCTAGGTCCCTTCG
+SEQ_LEN: 251
+SCORES: ,5<??BB?DDABDBDDFFFFFFHFHIHFHHIIHEHEHF?E?0CDFGFFHHIHFFFHHHGD@E@EDBFH>5EGHHHIIIGGCGHHHFHIHHAFBCGGGGHHFFFHFFFHFHFF?DDBDFH.?FFFFFBFFFEDEEEFEFF=BDEEEECCEEA=AB=?CEC=AC,<5=BE:CE*?*?E?*?:*:*1:8?A?AEEFEE>E:*1:8AEEE?)?8?:?:CEAEAAE*81?*?CEE:8??**1)5.).8A*:A:?**
+---
+SEQ_NAME: M01168:16:000000000-A1R9L:1:1101:14865:2158 1:N:0:14
+SEQ: TAGGGAATCTTGCACAATGGAGGAAACTCTGATGCAGCGATGCCGCGTGAGTGAAGAAGGCCTTTGGGTTGTAAAGCTCTTTCGTCGGGGAAGAAAATGACTGTACCCGAATAAGAAGGTCCGGCTAACTTCGTGCCAGCAGCCGCGGTAATACGAAGGGACCTAGCGTAGTTCGGAATTACTGGGCTTAAAGAGTTCGTAGGTGGTTAAAAAAGTTGGTGGTGAAATCCCAGAGCTTAACTCTGGAACTG
+SEQ_LEN: 251
+SCORES: ?????BBBBBDDBDDBFFFFFFECHFHFHFHGHHFGD?>CFHHHHHH>DEEFFFFDFFHF@FHHHIFHEEHHHIIHHHIHIHHHDEHHHHFEEFFF?FEEEEFEEFFEE:>CEEFEFFFBEEEEEDEFE::AE:?AECEFEF?A>;D88;CEEEEFEA;AECEEECE;0?>0:AADAAECEFFEEECEAACE:CA:*?C8?CE::CE8ACCA:4?:AC:8888):*:?EA*::8**1**11??:E?CA:?1
+---
+SEQ_NAME: M01168:16:000000000-A1R9L:1:1101:14865:2158 2:N:0:14
+SEQ: CCTCTTCGCTACCCATGCTTTCGTTCCTCAGTGTCAGTAATGATCCAGAAAGCTGCCTTCGCAATCGGTATTCTTTCTAATATCTACGAATTTCACCTCTACACTAGAAATTCTGCTTTCCTCTATCATACTCTAGCTAAAAAGTTTTGATGGCAGTTCCAGAGTTAAGCTCTGGGATTTCACCACCAACTTTTTTAACCACCTACGAACTCTTTAAGCCCAGTAATTCCGAACTACGCTAGGTCCCTTCG
+SEQ_LEN: 251
+SCORES: ??,<??B?BB?BBBBBFF?FFFH;FHFFHBG0C9AFHC?F=?CC?FF=C?EBFGGHDHHHFDDEDD@E>CFHHHIHHH??AEGFHC?FEFFFBCEGHHFHHFGHHHFHHFCD.@DDFHH?FFFF=C?BFFFDFF?BFD=;DDEEDEEEEEE;CCBEEEEB?B??B?C?B;E?EBA:/:AC?A:*?EACAA*?CEC;*/0*:?ACCAA?C?EEEEEE:A:*800:AA:AEE:)04??:A;8A?CA/0*::A8
+---
+SEQ_NAME: M01168:16:000000000-A1R9L:1:1101:17246:2253 1:N:0:14
+SEQ: TAGGGAATCTTGCACAATGGGGGAAACCCTGATGCAGCGATGCCGCGTGAGTGAAGAAGGCCCTTGGGTTGTAAAGCTCTTTCGTCGGGGAAGAAAATGACTGTACCCGAATAAGAAGGTCCGGCTAACTTCGTGCCAGCAGCCGCGGTAATACGAAGGGAACTAGCGTAGTTCGGAATTACTGGGCTTAAAGAGTTCGTAGGTGGTTAAAAAAGTTGATGGTGAAATCCCAAGGCTCAACCTTGGAACTG
+SEQ_LEN: 251
+SCORES: 5<???B-<-?<BBBBBFFF;>CEEECC;EFFH=EGBE=CEFHD@CDCE>+>5C=FBAEADHFEHHHHHHECCG=CD=CCF=DC=DDACEE5:DEEEECBECEC3?3;?B:@CEEECEEC?CC????E?CAAAE?ACEEEEEEEE????A;)::ACAEE?EA*8:CEE')08AECE?EEE?:??::ACE*?*?*:A/:*88A?A?CCAE:?C**4A/:AEC::*/0/?::?**0.)*:8:///::*/:?:?0
+---
+SEQ_NAME: M01168:16:000000000-A1R9L:1:1101:17246:2253 2:N:0:14
+SEQ: CCTCTTCGCTACCCATGCTTTCGTTCCTCAGTGTCAGTAATGATCCAGAAAGTTGCCTTCGCTTTTGATGTTCTTTCTAATATCTACGAATTTCACCTCTACACTAGAAATTCCACTTTCCTCTATCATACTCTAGCTAAAAAGTTTTGATGGCAGTTCCAAGGTTGAGCCTTGGGATTTCACCATCAACTTTTTTAACCACCTACGAACTCTTTAAGCCCAGTAATTCCGAACTACGCTAGGTCCCTTCG
+SEQ_LEN: 251
+SCORES: ?????BB??BBDBBBBBFFFFFHFHIIFFBD0A09CGFGG?0CDDGHDGFHHGEFGHHIIHE@CFHH+AEGHFHIIHHCEFHHHGDHHHIIHHIHBGGHHDGFHHHHBBGFFDDFDFHFCFFH?.CCFFHHHHFFFFFFDDBFEDDEEEEFE.4,?BA==A==*5=A,BB,A=CAACEEFEEF*AEEC0*AEEEC;C10**080??)88'ACECAA::::*8?C:?EF::?A)2A:*)'.84AAA0?EEA*
+---
+SEQ_NAME: M01168:16:000000000-A1R9L:1:1101:13072:2276 1:N:0:14
+SEQ: TGGGGAATTTTGCGCAATGGGCGAAAGCCTGACGCAGCAACGCCGCGGGATCGAAGAAGCTCTGCGGAGTGTAAAGATCTGTCATAAGGGAAGAATAACGAGTATTCTAACAAAATATTCGTCTGACGGTACCTTATAAGAAAGCCACGGCTAACTTCGTGCCAGCAGCCGCGGTAATACGAGGGGGGCAAGCGTTATCCGGAATCATTGGGCGTAAAGGGGTCGTATGAGGACTGATCAGATGGAATTGA
+SEQ_LEN: 251
+SCORES: 55?????B?BB<-5@BC9CFFB>+C>C>E?@B=>,>5>FE,>77>CE)<<:CD=@DEFHDDBCFFEE8:=@,BD=,3;BEEEE?;BCCECCCE?B;?B3:AA88?:**:CAAA88:::::??8*)AC).8?)*:???:0?CEAAE8**4;8;AA:??:8:??8?EE:AC?;42.)4?*::8).'''..'.8C8A)8AAE:A;?'0:?CAEE?8''4A8?*8'0)''8*0*/:C8:CEC?::*0/*0/*:A*
+---
+SEQ_NAME: M01168:16:000000000-A1R9L:1:1101:13072:2276 2:N:0:14
+SEQ: CCTGTTTGCTCCCCACGCTTTCGTTCCTCAGCGTCAGTATAGGCCCAGTAAGCTGCCTTCGCCTTTGATGTTCCTCCTGATATCTACGCATTTCACCGCTACACCAGGAATTCCGCTTACCTCTACCTCACTCAAGACTGACAGTATTGAAACCGTTCCCCCGGTTAAGCCGCGGTCTTTTAATTCCAACTGATCAGTCCGCCTACGAACCCTTTACGCCCAATGATTCTAGATAACACTTGCCCCACGCG
+SEQ_LEN: 251
+SCORES: ,<5<<<>>-5-@@@@@CEEEEEEAACE/A>C-7@7CE999A.9AEEE+C=CFFD@BD@=E+9C5>EACC=A5CA@ED>CEDDEEEDDDDE9DDEEDDDDDCCEDE@D99DDD99;991D*3@9*2*0@;88*0**9@@@@;*87*;@8;(/;69'-///6(8'2-46;6(6'''.('/6((//..6666(66<<;<E<(((-((/(/(/''/6.6666-.-6((6(((6.((((/(((/(/6?<6((''-'
+---

diff --git a/bp_test/test/test_read_fastq b/bp_test/test/test_read_fastq
index cf7d324101df4cb54f24f46ce2ad240a8ca696a9..05b0325945748d5caf7062a19e50c0d01fd3b201 100755 (executable)
--- a/bp_test/test/test_read_fastq
+++ b/bp_test/test/test_read_fastq
@@ -25,3 +25,7 @@ clean
 run "$bp -i $in.1 -n 1 -O $tmp"
 assert_no_diff $tmp $out.3
 clean
+
+run "$bp -i $in.3 -j $in.4 -O $tmp"
+assert_no_diff $tmp $out.4
+clean