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
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?
--- /dev/null
+@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*
--- /dev/null
+@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((''-'
--- /dev/null
+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((''-'
+---
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