| Next changeset 1:43e081d32f90 (2015-12-06) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 |
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added:
LICENSE sickle.xml test-data/output.c1.fastq test-data/output.c2.fastq test-data/output.f.fastq test-data/output.r.fastq test-data/output.s.fastq test-data/test.f.fastq test-data/test.fastq test-data/test.r.fastq tool_dependencies.xml |
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| diff -r 000000000000 -r a5f56370e870 LICENSE --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/LICENSE Thu Nov 12 07:05:48 2015 -0500 |
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| @@ -0,0 +1,19 @@ +Permission is hereby granted, free of charge, to any person +obtaining a copy of this software and associated documentation +files (the "Software"), to deal in the Software without +restriction, including without limitation the rights to use, copy, +modify, merge, publish, distribute, sublicense, and/or sell copies +of the Software, and to permit persons to whom the Software is +furnished to do so, subject to the following conditions: + +The above copyright notice and this permission notice shall be +included in all copies or substantial portions of the Software. + +THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, +EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF +MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND +NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS +BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN +ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN +CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE +SOFTWARE. |
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| diff -r 000000000000 -r a5f56370e870 sickle.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/sickle.xml Thu Nov 12 07:05:48 2015 -0500 |
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| b'@@ -0,0 +1,253 @@\n+<tool id="sickle" name="Sickle" version="1.33">\n+ <description>windowed adaptive trimming of FASTQ data</description>\n+ <requirements>\n+ <requirement type="package" version="1.33">sickle</requirement>\n+ </requirements>\n+ <version_command>sickle --version | head -n 1</version_command>\n+ <command>\n+ sickle\n+\n+ #if str($readtype.single_or_paired) == "se":\n+ se -f "${readtype.input_single}" -o "$output_single"\n+\n+ #if $readtype.input_single.ext in ("fastq", "fastqsanger"):\n+ -t sanger\n+ #else if $readtype.input_single.ext == "fastqillumina":\n+ -t illumina\n+ #else if $readtype.input_single.ext == "fastqsolexa":\n+ -t solexa\n+ #end if\n+ #end if\n+\n+ #if str($readtype.single_or_paired) == "pe_combo":\n+ #if $readtype.output_n:\n+ pe -c "${readtype.input_combo}" -M "$output_combo"\n+ #else\n+ pe -c "${readtype.input_combo}" -m "$output_combo" -s "$output_combo_single"\n+ #end if\n+\n+ #if $readtype.input_combo.ext in ("fastq", "fastqsanger"):\n+ -t sanger\n+ #else if $readtype.input_combo.ext == "fastqillumina":\n+ -t illumina\n+ #else if $readtype.input_combo.ext == "fastqsolexa":\n+ -t solexa\n+ #end if\n+ #end if\n+\n+ #if str($readtype.single_or_paired) == "pe_sep":\n+ pe -f "${readtype.input_paired1}" -r "${readtype.input_paired2}" -o "$output_paired1" -p "$output_paired2" -s "$output_paired_single"\n+\n+ #if $readtype.input_paired1.ext in ("fastq", "fastqsanger"):\n+ -t sanger\n+ #else if $readtype.input_paired1.ext == "fastqillumina":\n+ -t illumina\n+ #else if $readtype.input_paired1.ext == "fastqsolexa":\n+ -t solexa\n+ #end if\n+ #end if\n+\n+ #if str($qual_threshold) != "":\n+ -q $qual_threshold\n+ #end if\n+\n+ #if str($length_threshold) != "":\n+ -l $length_threshold\n+ #end if\n+\n+ #if $no_five_prime:\n+ -x\n+ #end if\n+\n+ #if $trunc_n:\n+ -n\n+ #end if\n+ </command>\n+\n+ <inputs>\n+ <conditional name="readtype">\n+ <param name="single_or_paired" type="select" label="Single-end or paired-end reads?" help="Note: Sickle will infer the quality type of the file from its datatype. I.e., if the datatype is fastqsanger, then the quality type is sanger. The default is fastqsanger.">\n+ <option value="se" selected="true">Single-end</option>\n+ <option value="pe_combo">Paired-end (one interleaved input file)</option>\n+ <option value="pe_sep">Paired-end (two separate input files)</option>\n+ </param>\n+\n+ <when value="se">\n+ <param format="fastq" name="input_single" type="data" label="Single-end FASTQ reads" help="(-f)" />\n+ </when>\n+\n+ <when value="pe_combo">\n+ <param format="fastq" name="input_combo" type="data" label="Paired-end interleaved FASTQ reads" help="(-c)" />\n+ <param name="output_n" type="boolean" label="Output only one file with all reads" help="This will output only one file with all the reads, where the reads that did not pass filter will be replaced with a single \'N\', rather than discarded."/>\n+ </when>\n+\n+ <when value="pe_sep">\n+ <param format="fastq" name="input_paired1" type="data" label="Paired-end forward strand FASTQ reads" help="(-f)" />\n+ <param format="fastq" name="input_paired2" type="data" label="Paired-end reverse strand FASTQ reads" help="(-r)" />\n+ </when>\n+ </conditional>\n+\n+ <param name="qual_threshold" value="20" min="0" type="integer" optional="true" label="Quality threshold" help="'..b' of reads. It will also\n+discard reads based upon the length threshold. It takes the quality\n+values and slides a window across them whose length is 0.1 times the\n+length of the read. If this length is less than 1, then the window is\n+set to be equal to the length of the read. Otherwise, the window\n+slides along the quality values until the average quality in the\n+window rises above the threshold, at which point the algorithm\n+determines where within the window the rise occurs and cuts the read\n+and quality there for the 5\'-end cut. Then when the average quality\n+in the window drops below the threshold, the algorithm determines\n+where in the window the drop occurs and cuts both the read and quality\n+strings there for the 3\'-end cut. However, if the length of the\n+remaining sequence is less than the minimum length threshold, then the\n+read is discarded entirely (or replaced with an "N" record). 5\'-end\n+trimming can be disabled. Sickle also has an option to truncate reads\n+with Ns at the first N position.\n+\n+Sickle supports three types of quality values: Illumina, Solexa, and\n+Sanger. Note that the Solexa quality setting is an approximation (the\n+actual conversion is a non-linear transformation). The end\n+approximation is close. Illumina quality refers to qualities encoded\n+with the CASAVA pipeline between versions 1.3 and 1.7. Illumina\n+quality using CASAVA >= 1.8 is Sanger encoded. The quality value will\n+be determined from the datatype of the data, i.e. a fastqsanger datatype\n+is assumed to be Sanger encoded.\n+\n+Note that Sickle will remove the 2nd FASTQ record header (on the "+"\n+line) and replace it with simply a "+". This is the default format for\n+CASAVA >= 1.8.\n+\n+-----\n+\n+**Options**\n+\n+**Single-end**\n+\n+This option takes one single-end input file and outputs one single-end\n+output file of reads that passed the filters.\n+\n+**Paired-End (one interleaved input file)**\n+\n+This option takes as input one interleaved paired-end file. If you then\n+check the "Output only one file with all reads" checkbox, it will output\n+one interleaved file where any read that did not pass filter will be replaced\n+with a FASTQ record where the sequence is a single "N" and the quality is the\n+lowest quality possible for that quality type. This will preserve the paired\n+nature of the data. If you leave the checkbox unchecked, it will output two files,\n+one interleaved file with all the passed pairs and one singletons file where only\n+one of the pair passed filter.\n+\n+**Paired-End (two separate input files)**\n+\n+This option takes two separate (forward and reverse) paired-end files as input.\n+The output is three files: Two paired-end files with pairs that passed filter and\n+a singletons file where only one of the pair passed filter.\n+\n+**Quality threshold**\n+\n+Input your desired quality threshold. This threshold is phred-scaled, which is typically\n+values between 0-41 for FASTQ data.\n+\n+**Length threshold**\n+\n+Input your desired length threshold. This is the threshold to determine if a read is kept\n+after all the trimming steps are done.\n+\n+**Disable 5-prime trimming**\n+\n+An option to disable trimming the read on the 5-prime end. This trimming trims the read\n+if the average quality values dip below the quality threshold at the 5-prime end.\n+\n+**Truncate sequences with Ns**\n+\n+This option will trim a read at the first "N" base in the read after doing quality trimming.\n+It is then still subject to the length threshold.\n+\n+-----\n+\n+Copyright: Nikhil Joshi\n+\n+http://bioinformatics.ucdavis.edu\n+\n+http://github.com/najoshi/sickle\n+ </help>\n+ <citations>\n+ <citation type="bibtex">\n+ @unpublished{sickle_link,\n+ author = {Joshi, Nikhil A. and Fass, Joseph N.},\n+ title = {Sickle: A windowed adaptive trimming tool for FASTQ files using quality},\n+ year = 2011,\n+ url = { https://github.com/najoshi/sickle }\n+ }\n+ </citation>\n+ </citations>\n+</tool>\n' |
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| diff -r 000000000000 -r a5f56370e870 test-data/output.c1.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output.c1.fastq Thu Nov 12 07:05:48 2015 -0500 |
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| b'@@ -0,0 +1,9936 @@\n+@2242:2:1101:1532:1981/1\n+TTTTTCCTTCCTTTAAAACCACTTCTTTGATCCAATCCAGAAAGCCTCTCCAATAATTTGATACCACTAAAATGACGGGGAAAGGTCTGATCTTTTTAGTCTGAATAAGCGTAAGCGATTCGAGCAGC\n++\n+P\\ccc^acebegafabfffbcag`gfb`faf]fad^^cedbeff`affhgfdcfe`^aaa\\WHW_be_f_V_dfZ^Z[a`U]aaaT]bb]Z`G]Zb`[b]``]b]]Y_YRTGWGGGHQGQ]OYb_[^a\n+@2242:2:1101:1532:1981/2\n+ATCATCCAGCGGTGAGCATTTTAGGTTCCACACGCATTAAACCCGGTGACGAGGTCTACTCGAAGGCGGAACAAATCTGCAAACTCTTAGC\n++\n+^a_cccaZJQbe[beghihigbJ[bX^^deffffYe\\f_a`dRZU_aa\\bGLT\\T_bZ_bd^`Z^ZX\\ZTTX^[[RYGS]Y]_^R_Y]]bb\n+@2242:2:1101:1908:1977/1\n+GCTGTCGGAAAAGAATTGGAGAAAAGGGATGCTCGCTACCTTGCTTTAAGCTCTCGGATTGCTGCTGAATTTGGGGCACGGAATGTAAAAACCTACTGGTGTGAGAATTTTGAGAAGGTGGTTGGTGGGTGGCCTGTTCCCGTCTGTAG\n++\n+PYS``ca_^ceeeeehaeaXXJbfacZV_cfaebP^cUVcdXbbdeeeebebdeee^[`[ac]]a`baaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa\n+@2242:2:1101:1908:1977/2\n+GGGATGTCGGCTGATACCCCCTCACCC\n++\n+\\a_e\\cacYHOQ_YY`a^Rb___YH^b\n+@2242:2:1101:2236:1971/1\n+GTTTTTGCCGTACCAGTTCCATGCTGGTTGAAGCTGGCTTGACGCTGCCGCAATCGTTAAACGCCATTATCGGCATTATAGATAACAGCGTCATAAAGAAAG\n++\n+PP`accccc_c`ddhXQ`bSdd]ed_d^dcddcdXIYc`QOOXU^_[`cNZ_````^_Z^`YZ^^W\\Y]`GGWZEO]`cc`]G]````]][]^[]````^^`\n+@2242:2:1101:2236:1971/2\n+TATACTTAATACAATGATTGGTATATCGAATACAGCGGCTGCATGATAGCAAGGCCGATAAAGCCGATTAACAAACCGGCAATAATAATGGAAGCCGGTTCAATCA\n++\n+^^Wac`ceeWeegaafffffffhh^ef_egbgefccfa`ced_fhhchS\\\\egf^efUY\\^aVZZX`ac^_]RY^X[__a_aGY]R]]`bGY]R^`_[OTW_bcbb\n+@2242:2:1101:2574:1974/1\n+GGTCGGACGTAGCTGTTACGCACGGCAACCTCGGCCAGACTGCAAAAAACATCAAGGCGCGCCAGGGCGTCGGCAACCGCCAGGACCGG\n++\n+PY\\ac`ccccacdhhhadcbPbcc`[ccccdcccccc_b`bbcccccc_U]`R]``]^NW[^^^^^^^]]]Z]XZ][^^^^]]][^]]^\n+@2242:2:1101:2574:1974/2\n+AAGAACTGGACAACTTGCGGTTGACGGCAAAAAACTCAAAACAGTACCTCGCCAACCTGGAAAAACAGGAGCGAGAGCGTACGGGCATAAAGTCGTTGAAAGTCGGCTATNATCANGCCTTTGGCTACTATATTGAGGNNNNNAATGCNN\n++\n+_a_cccccceeggfd]adafegdgXbcOcegfiiUbfgh[ehficgX_Z_Z`aa`aabccccbZ^aa^`a[aaL[[[[a_^accaV_[b_b_G]_[Xb^b]__]^TT^aGBJQWQBJGJJGYSRGGY^b`c]``bbBBBBBBBBBBBBBB\n+@2242:2:1101:2599:1978/1\n+GTTTCCTATGAGGCGGACAAGGAAAACCCGGGGGCCACCCAGTACCACAAGAACTTCAAGGATTGGCTCACCCGGTTTCAGACCGAGGATCTGGTCGGGTGCTGTGCCCAGACGGACGTCAAAGGCGATCGG\n++\n+P\\ccceegggggihiihiiiiiiiiicfhhiiicccccccacbccccccccccbbcccccccccbccccccaaa_]aaccccbcccccccccccbcccTJO[`b`bb]^```a]accaXXWX]`[WX[]aca\n+@2242:2:1101:2599:1978/2\n+CTCCCATGGAACGAAGACGTCGTCGAAAACCATGTAGGAGTCGCAGCTCCCCGCGTTGAAGCCCTTGGGGAAGCGCTTCCGATCCCGGTAGTTGTGCGCGGTAACCAGCTNTTTCNGCCCGTCCCCATCCCC\n++\n+bbbeeeeegggggiihiiiiiiihiiiiiiiieihhhihdbffhiighggdgeccaccccccccccbcccaca^aaaaccccccac_aX[]`cbb^baaaca_cccc^a_BGQWWBJJW[^TWT[GRX^`^_\n+@2242:2:1101:3233:1997/1\n+TAACCCCTGAGGATGTGGTTACCGGAGGCAGGCATGTAATGGAAGCGGAGATCGAGCTTTCAGAATATATTATGCCAGGCATCGCCGGCCGAGCCCTGAGCGAAGAACATGCAATAGAGACGGCAAAGCTGCTTAACCTTGTTCGTCCC\n++\n+S\\ccccegggggghhfgihiiiiiiiiiiiiifhhihhhfhifiifiihgeece`acccccccccccddeeddbbbbccccccccccccccaccccccccccacca`^bbccbb`bbbbc_[X]a_WXRS]^__`_YY`Y___Y^_^[T\n+@2242:2:1101:3233:1997/2\n+TAAAGGATGGCGACTATGTCCAGAATAGTGAAGCAGGGTATAGACCTCTCTCTGCTTCTTTGTCATGGACAGAAAGGCATCGAGCTCACTCAGCATATACTCTTTCTTCTCGTCCAGAAAGCCATCCACTTGCATGAGGNGGTTCAGACT\n++\n+bbbeeeeegggggiiihiiiiiihiifgghfhfhiiih^cefhiiiiihihhiiiiiiiiihiiiiiigggegeede\\_`bbccccccbc`bccccbbcccccbcccc]`_[a_c^`bRYbGWXbX^bbcbbbGS]b`^BJWGJ[``__]\n+@2242:2:1101:3494:1987/1\n+CTTTCAAGGAAAAATGAAACCCCCGTTCAAGCCCAGGGACCCCAGAAGCGGTTATAGCGAAGCCAACATCATCACCCTCCTGAGACTAGGGGGTTCGCTTGTCTTCTTTATCCTGGCGGTCGTCC\n++\n+PY`cccceccegfaggfhhhdgfaf^cdfcefgbgbeaVeeeafhffhfhhdgdecdY``_]_abc_ccbbc`bY^`^^abY_bbb]_bcccc[X^_aXW[QYY`bcbb`]YbccXW[[ETTTQ^\n+@2242:2:1101:3494:1987/2\n+CCGTTGAATTCGCGAACTTGCCGGCCGGGCTGAAGTTCCAGGTGTAGACCGTCCGGGCCACCCGATAAAAATAGTTCGGGGACATGATAT\n++\n+___`ccccce[eeddf`bddffY_egfgehff_VV^d_\\MM^VZ_ab`_ZRRXW\\_NVT[W[TTTLW[bbc[Y`S]`WTTXTEWYGJ]``\n+@2242:2:1101:3624:1977/1\n+TCGAGGGTTGTCCTGAGGGACGAATTGATGCGTTCTCTCGATCCCAATGTTTCATCAAGGCTCATGTCACCAACCAGATTTCTAAGATTCGTCTGTGCGAGCTTGCTTACGGCTACATAGAAG\n++\n+P\\cc^cc^be_egfgdXdf_edcghhbbXafaegffggag]_\\_cbfbg^gbdbbZ_VHMU]_bb`bbdY]baWWTXXRTZ_R_YYb`]]_baaabb__RX_a[]_b_]]^XRTOXYRa`G]_'..b'TCGGCCTGGGGCTGGGGAGCTTTGGCGTCATGGTAGCC\n++\n+^_^acc^caQ`ccehhidfb[eghhhffdghcggdffdfgN\\`aac_bc_PZ\\WRX`bbb`[TZT^]bY`bbc\n+@2242:2:1101:5665:2357/1\n+GGTCAGCGAGGGCCTGACTCCCGTTCAATGCCGGGGGATCCAAGACTTGATCGAGGAAAAAGACATTCTCCTGAAAATAAAGCTCTTGAAGAAGGAGCTCCAGGAAAGCGAGGTCTAAGGTGAGAAAAACAGCTCTCATCATAATCATAC\n++\n+___ceeeegggggiiiiiihhiieghiihhiiiiiiebccdcccccccccccccccaaccc[accccb`bbbc`bbbccccY_Y_bbbb`bbb]`__a[``bbccab`^_aaXEX__Y`[JSY`bc]bQEWXW]]Y`b]_SS_BBBBBBB\n+@2242:2:1101:5665:2357/2\n+CTTTGTAGAGCTCGTAGGCCAGGTCGATGATAGAGGACTCCGCCTGCTCGGCCAGGCTGTCGTTTCTCCCCTTGACCGAAAGATACTCCTTGTAGGCCTCAATGGCTTCTTCCTCATGGCCCTTCCGCC\n++\n+a__eecdegggcgdddghhhiii`eghffihihiiihiffhhhifhiiihffgihggdgaeedccddbdcab^b_bbcY][acbccc_^`Y`b]_`]b_abbbbbcXPXY`bcRYJSJY[`a[RGXTT^\n+@2242:2:1101:5703:2367/1\n+GGGCATTGCACTCCTCGGGGCAAAGACCGACGGCAAGGCTCTCCTCATAGCTCTCGTGACCAGCGACCTGACAAATCGGTTTCACGCGGGCAATATCG\n++\n+^^_ccceaa[bgefhd]fda`egbhhhc_ce`fhhaZ\\bVZaa_``]Z]_RTZLTR^aYTY`TTWTZZ]R]bYGJSSWTJTO_YRQQEOEOOQ]`b]^\n+@2242:2:1101:5703:2367/2\n+GATACCCGTCAGCTCAACTACCTTAAAGATAGTGACCGACTGTCTCGCCATCTTCAGTTCGTTGATTACACGCGTAATCCTGC\n++\n+_\\^c^cccbcg_JQQ`]aYe]fd]e_d_a[bbPY^^bf_cegWafbaZZZeV\\_ZVMHVVGL^HUZad]_Z\\FRRQ^_RZbY_\n+@2242:2:1101:5687:2369/1\n+GCGCTGCCGGGTTGTTTTCATGGCTTAACGGATAACCTCATTAGCGATATTATAGCCATTCAAGCTGATTTATGCAAATATATATTTTCTTTAATCGGGTTGACAGGCTTTCAA\n++\n+__bec`cceggeeagfddeg`ebdcgffgag`_ef_cae``ff`dfhhha`\\`ZVV^ZVV`bbde`b_bZZZZRZ]R]]]b]]b]_b_`bb_b_]]GTTJQEJY_Y[GJR]_`b\n+@2242:2:1101:5687:2369/2\n+TTGTACAAGCGCACCACCTGAGGCATCATCTTCTTGGTCACCGTGCCTGAGACAATCATCACGTCTGCCTGGCGGGGGCTTGGTCGCATCACTTCCATGCCGAAACGGGAGAAA\n++\n+^ZZ`accaegeecfhhaggdeffbf[acafcgfffhhac_ccaaaffd_fgZ_cdfddghhfddgeeeebabdcc[X_c[^aa]`[aaa_R]S]_`YYY`b]MX][^_aacacc\n+@2242:2:1101:5649:2379/1\n+AAGCCTGTGGGAGTGTCATTCCAGTCTCCTGAGCTTGAACTATGCTTCTGAAGAGGTCCGGCAAATGCTCGTCTATTGCCTTTCTCCACCTGTAATCAAGGTAGATCAGGATGGCCGGTGGAAAGGCCGCGGCGATGATTGAGAAGAAGA\n++\n+abbeeeeegggggfghhiiiiiiifhiiihhfhhiihhhiiiihiiiiiiiiiihifghfhiiiggegfgecdccddddcccccccbbbccbcc`cccccc_`bcdc]`bbbb_bcccT_cabb[aa^_aa[aaa]]R]bbGS[bbcBBB\n+@2242:2:1101:5649:2379/2\n+TCCTCACTGGCCCGCTGATGTTGGTGATCATGCTAACGGTAATGGCGATGCTTGGCGGAGGAGACCTTGGATTGCTCAGTCCAGACCTGTTGCTAAACATGCTCACCTACTTGGGCATTCCGTTAGGAGCAATAGTCTTCTTGATCATTC\n++\n+bbbeeeeegggggiiiihhighii^effhihhiiiiiii^egghiiihihfhhhgggccccaaaacccccccbbccccccbcccbcabbbccccY_`bb`bbccbbccbbbb_YQ[b[Y_b`b`aabbbacbbbb]bcc]S]YbRY]Y]Y\n+@2242:2:1101:5633:2394/1\n+TCGGCGTCGGTAGTTTTCGTCCCTGGTTTTGCGATGTCATGGAGCAGCGCCGCCAGCTTTAACAACACCGTTCGCGTGCTGCCGCTGCTGATTTCAGCTTCGAAGTGCTGGATC\n++\n+^__cccP^cebac^[deeU^eedRc_cXZ^a[e`Z_U_``_`Rb]b\\d[a_[Za_Z_T]R]R]``^aa^TJQ[ZXOHOX^RGQXaT]RY`GSGY`YYGSGSO^W^a_Y]___Y_\n+@2242:2:1101:5633:2394/2\n+CGCATCGCCGCCGAACTGGGACTACGCATCGAAGACGATACCGAAG\n++\n+ZZZacc^c``egcfh`R^cebf_ZeGVcZ`fXHT_a_TZZ\\aaab_\n+@2242:2:1101:5545:2405/1\n+CCCGATCAAACAGTCCAGATCACTGAAAATGCAGCCGGAGTAAACCATTCAGCCTTTAAATTTTCAGAAGGTGATAATATAACTCTTCTTGATCTCATAAAAGCGGCATTAATAAGTTCTCATAATAATGCTACTATTGCACTTGCGGAA\n++\n+bbbeeeeeggggghiifghfhihiiiihhbghiihiiiihZeghihiiiiihiiiihhfhhiggdbgfgee_bddcddddddcccbccbcbcb`cbbdcccccc_aac_b_bbdcb_cbbccdccb`bd``bcccbcb__bcccb`_ac]\n+@2242:2:1101:5545:2405/2\n+AAGCCAGCATTTTCAGTATATCCTGTCTTTATCCCTTTTATAAATTCATATTCCAATAGTTTATTGGTATTCTCAAGAGGAATAATTTCATCATCTAATATTATATTATCAGATTTTGTACCGACTATTTCCCTAAAAAGGCTGTTTTCC\n++\n+_bbcceeeeggggihighfiihihhegiiihfffhhiiihiihiiiiiiiiiiihihfhhiiiihhhegiiiiiihifdgghhfhhfggggggeeeeeeebdeecbbdd`ccbcbbc_`cbb__]a]b_`_bbbcX]b]a^`]`[b`X_R\n+@2242:2:1101:5710:2454/1\n+TCCATCCGGTGGCTGAGATGCGCGGATGTTTTGCCAACGTGATGGGGCTGCCCGTGTGTCATCTCGCGCGGGCGTTGCGCGCGTTCAAGTCGCCCGCCGATATTCCTGTCGC\n++\n+abbeeeeeggggghiiiieiiihiiiihdfhichhiificgiihggffeecdcc_aacaccdcbbccacXZ__cOX__ccccaOT[``_]__aacMX[XOOTX_ccbY_`V^\n+@2242:2:1101:5710:2454/2\n+GAATGAGTTCGAGGGTGGGAGTGCTCAAGGGTTTGCTCCTTCAAACGTATGGTAGGCGGGCATCCCGATGCCCACTGCTGGCGCATGGGGATGCGCCCGCTACCGCGACAGAAGCCAAAATATCGGCAAAGACCGGACAGTGGGATCCGA\n++\n+abbeeeedgggggih`fgiehdfghhiihih^fgiiiiihighhiiibggfhhgfffgecZ_bccccccaabbba`bbb]_^_c]a^aac^O[aa__ccaX]acacccac_bRXX[^X`^_bbbV][[Xa``GGET[aX^JSRJQY_XPW\n' |
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| diff -r 000000000000 -r a5f56370e870 test-data/output.c2.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output.c2.fastq Thu Nov 12 07:05:48 2015 -0500 |
| [ |
| b'@@ -0,0 +1,10000 @@\n+@2242:2:1101:1532:1981/1\n+TTTTTCCTTCCTTTAAAACCACTTCTTTGATCCAATCCAGAAAGCCTCTCCAATAATTTGATACCACTAAAATGACGGGGAAAGGTCTGATCTTTTTAGTCTGAATAAGCGTAAGCGATTCGAGCAGC\n++\n+P\\ccc^acebegafabfffbcag`gfb`faf]fad^^cedbeff`affhgfdcfe`^aaa\\WHW_be_f_V_dfZ^Z[a`U]aaaT]bb]Z`G]Zb`[b]``]b]]Y_YRTGWGGGHQGQ]OYb_[^a\n+@2242:2:1101:1532:1981/2\n+ATCATCCAGCGGTGAGCATTTTAGGTTCCACACGCATTAAACCCGGTGACGAGGTCTACTCGAAGGCGGAACAAATCTGCAAACTCTTAGC\n++\n+^a_cccaZJQbe[beghihigbJ[bX^^deffffYe\\f_a`dRZU_aa\\bGLT\\T_bZ_bd^`Z^ZX\\ZTTX^[[RYGS]Y]_^R_Y]]bb\n+@2242:2:1101:1908:1977/1\n+GCTGTCGGAAAAGAATTGGAGAAAAGGGATGCTCGCTACCTTGCTTTAAGCTCTCGGATTGCTGCTGAATTTGGGGCACGGAATGTAAAAACCTACTGGTGTGAGAATTTTGAGAAGGTGGTTGGTGGGTGGCCTGTTCCCGTCTGTAG\n++\n+PYS``ca_^ceeeeehaeaXXJbfacZV_cfaebP^cUVcdXbbdeeeebebdeee^[`[ac]]a`baaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa\n+@2242:2:1101:1908:1977/2\n+GGGATGTCGGCTGATACCCCCTCACCC\n++\n+\\a_e\\cacYHOQ_YY`a^Rb___YH^b\n+@2242:2:1101:2236:1971/1\n+GTTTTTGCCGTACCAGTTCCATGCTGGTTGAAGCTGGCTTGACGCTGCCGCAATCGTTAAACGCCATTATCGGCATTATAGATAACAGCGTCATAAAGAAAG\n++\n+PP`accccc_c`ddhXQ`bSdd]ed_d^dcddcdXIYc`QOOXU^_[`cNZ_````^_Z^`YZ^^W\\Y]`GGWZEO]`cc`]G]````]][]^[]````^^`\n+@2242:2:1101:2236:1971/2\n+TATACTTAATACAATGATTGGTATATCGAATACAGCGGCTGCATGATAGCAAGGCCGATAAAGCCGATTAACAAACCGGCAATAATAATGGAAGCCGGTTCAATCA\n++\n+^^Wac`ceeWeegaafffffffhh^ef_egbgefccfa`ced_fhhchS\\\\egf^efUY\\^aVZZX`ac^_]RY^X[__a_aGY]R]]`bGY]R^`_[OTW_bcbb\n+@2242:2:1101:2574:1974/1\n+GGTCGGACGTAGCTGTTACGCACGGCAACCTCGGCCAGACTGCAAAAAACATCAAGGCGCGCCAGGGCGTCGGCAACCGCCAGGACCGG\n++\n+PY\\ac`ccccacdhhhadcbPbcc`[ccccdcccccc_b`bbcccccc_U]`R]``]^NW[^^^^^^^]]]Z]XZ][^^^^]]][^]]^\n+@2242:2:1101:2574:1974/2\n+AAGAACTGGACAACTTGCGGTTGACGGCAAAAAACTCAAAACAGTACCTCGCCAACCTGGAAAAACAGGAGCGAGAGCGTACGGGCATAAAGTCGTTGAAAGTCGGCTATNATCANGCCTTTGGCTACTATATTGAGGNNNNNAATGCNN\n++\n+_a_cccccceeggfd]adafegdgXbcOcegfiiUbfgh[ehficgX_Z_Z`aa`aabccccbZ^aa^`a[aaL[[[[a_^accaV_[b_b_G]_[Xb^b]__]^TT^aGBJQWQBJGJJGYSRGGY^b`c]``bbBBBBBBBBBBBBBB\n+@2242:2:1101:2599:1978/1\n+GTTTCCTATGAGGCGGACAAGGAAAACCCGGGGGCCACCCAGTACCACAAGAACTTCAAGGATTGGCTCACCCGGTTTCAGACCGAGGATCTGGTCGGGTGCTGTGCCCAGACGGACGTCAAAGGCGATCGG\n++\n+P\\ccceegggggihiihiiiiiiiiicfhhiiicccccccacbccccccccccbbcccccccccbccccccaaa_]aaccccbcccccccccccbcccTJO[`b`bb]^```a]accaXXWX]`[WX[]aca\n+@2242:2:1101:2599:1978/2\n+CTCCCATGGAACGAAGACGTCGTCGAAAACCATGTAGGAGTCGCAGCTCCCCGCGTTGAAGCCCTTGGGGAAGCGCTTCCGATCCCGGTAGTTGTGCGCGGTAACCAGCTNTTTCNGCCCGTCCCCATCCCC\n++\n+bbbeeeeegggggiihiiiiiiihiiiiiiiieihhhihdbffhiighggdgeccaccccccccccbcccaca^aaaaccccccac_aX[]`cbb^baaaca_cccc^a_BGQWWBJJW[^TWT[GRX^`^_\n+@2242:2:1101:3233:1997/1\n+TAACCCCTGAGGATGTGGTTACCGGAGGCAGGCATGTAATGGAAGCGGAGATCGAGCTTTCAGAATATATTATGCCAGGCATCGCCGGCCGAGCCCTGAGCGAAGAACATGCAATAGAGACGGCAAAGCTGCTTAACCTTGTTCGTCCC\n++\n+S\\ccccegggggghhfgihiiiiiiiiiiiiifhhihhhfhifiifiihgeece`acccccccccccddeeddbbbbccccccccccccccaccccccccccacca`^bbccbb`bbbbc_[X]a_WXRS]^__`_YY`Y___Y^_^[T\n+@2242:2:1101:3233:1997/2\n+TAAAGGATGGCGACTATGTCCAGAATAGTGAAGCAGGGTATAGACCTCTCTCTGCTTCTTTGTCATGGACAGAAAGGCATCGAGCTCACTCAGCATATACTCTTTCTTCTCGTCCAGAAAGCCATCCACTTGCATGAGGNGGTTCAGACT\n++\n+bbbeeeeegggggiiihiiiiiihiifgghfhfhiiih^cefhiiiiihihhiiiiiiiiihiiiiiigggegeede\\_`bbccccccbc`bccccbbcccccbcccc]`_[a_c^`bRYbGWXbX^bbcbbbGS]b`^BJWGJ[``__]\n+@2242:2:1101:3494:1987/1\n+CTTTCAAGGAAAAATGAAACCCCCGTTCAAGCCCAGGGACCCCAGAAGCGGTTATAGCGAAGCCAACATCATCACCCTCCTGAGACTAGGGGGTTCGCTTGTCTTCTTTATCCTGGCGGTCGTCC\n++\n+PY`cccceccegfaggfhhhdgfaf^cdfcefgbgbeaVeeeafhffhfhhdgdecdY``_]_abc_ccbbc`bY^`^^abY_bbb]_bcccc[X^_aXW[QYY`bcbb`]YbccXW[[ETTTQ^\n+@2242:2:1101:3494:1987/2\n+CCGTTGAATTCGCGAACTTGCCGGCCGGGCTGAAGTTCCAGGTGTAGACCGTCCGGGCCACCCGATAAAAATAGTTCGGGGACATGATAT\n++\n+___`ccccce[eeddf`bddffY_egfgehff_VV^d_\\MM^VZ_ab`_ZRRXW\\_NVT[W[TTTLW[bbc[Y`S]`WTTXTEWYGJ]``\n+@2242:2:1101:3624:1977/1\n+TCGAGGGTTGTCCTGAGGGACGAATTGATGCGTTCTCTCGATCCCAATGTTTCATCAAGGCTCATGTCACCAACCAGATTTCTAAGATTCGTCTGTGCGAGCTTGCTTACGGCTACATAGAAG\n++\n+P\\cc^cc^be_egfgdXdf_edcghhbbXafaegffggag]_\\_cbfbg^gbdbbZ_VHMU]_bb`bbdY]baWWTXXRTZ_R_YYb`]]_baaabb__RX_a[]_b_]]^XRTOXYRa`G]'..b'TCGGCCTGGGGCTGGGGAGCTTTGGCGTCATGGTAGCC\n++\n+^_^acc^caQ`ccehhidfb[eghhhffdghcggdffdfgN\\`aac_bc_PZ\\WRX`bbb`[TZT^]bY`bbc\n+@2242:2:1101:5665:2357/1\n+GGTCAGCGAGGGCCTGACTCCCGTTCAATGCCGGGGGATCCAAGACTTGATCGAGGAAAAAGACATTCTCCTGAAAATAAAGCTCTTGAAGAAGGAGCTCCAGGAAAGCGAGGTCTAAGGTGAGAAAAACAGCTCTCATCATAATCATAC\n++\n+___ceeeegggggiiiiiihhiieghiihhiiiiiiebccdcccccccccccccccaaccc[accccb`bbbc`bbbccccY_Y_bbbb`bbb]`__a[``bbccab`^_aaXEX__Y`[JSY`bc]bQEWXW]]Y`b]_SS_BBBBBBB\n+@2242:2:1101:5665:2357/2\n+CTTTGTAGAGCTCGTAGGCCAGGTCGATGATAGAGGACTCCGCCTGCTCGGCCAGGCTGTCGTTTCTCCCCTTGACCGAAAGATACTCCTTGTAGGCCTCAATGGCTTCTTCCTCATGGCCCTTCCGCC\n++\n+a__eecdegggcgdddghhhiii`eghffihihiiihiffhhhifhiiihffgihggdgaeedccddbdcab^b_bbcY][acbccc_^`Y`b]_`]b_abbbbbcXPXY`bcRYJSJY[`a[RGXTT^\n+@2242:2:1101:5703:2367/1\n+GGGCATTGCACTCCTCGGGGCAAAGACCGACGGCAAGGCTCTCCTCATAGCTCTCGTGACCAGCGACCTGACAAATCGGTTTCACGCGGGCAATATCG\n++\n+^^_ccceaa[bgefhd]fda`egbhhhc_ce`fhhaZ\\bVZaa_``]Z]_RTZLTR^aYTY`TTWTZZ]R]bYGJSSWTJTO_YRQQEOEOOQ]`b]^\n+@2242:2:1101:5703:2367/2\n+GATACCCGTCAGCTCAACTACCTTAAAGATAGTGACCGACTGTCTCGCCATCTTCAGTTCGTTGATTACACGCGTAATCCTGC\n++\n+_\\^c^cccbcg_JQQ`]aYe]fd]e_d_a[bbPY^^bf_cegWafbaZZZeV\\_ZVMHVVGL^HUZad]_Z\\FRRQ^_RZbY_\n+@2242:2:1101:5687:2369/1\n+GCGCTGCCGGGTTGTTTTCATGGCTTAACGGATAACCTCATTAGCGATATTATAGCCATTCAAGCTGATTTATGCAAATATATATTTTCTTTAATCGGGTTGACAGGCTTTCAA\n++\n+__bec`cceggeeagfddeg`ebdcgffgag`_ef_cae``ff`dfhhha`\\`ZVV^ZVV`bbde`b_bZZZZRZ]R]]]b]]b]_b_`bb_b_]]GTTJQEJY_Y[GJR]_`b\n+@2242:2:1101:5687:2369/2\n+TTGTACAAGCGCACCACCTGAGGCATCATCTTCTTGGTCACCGTGCCTGAGACAATCATCACGTCTGCCTGGCGGGGGCTTGGTCGCATCACTTCCATGCCGAAACGGGAGAAA\n++\n+^ZZ`accaegeecfhhaggdeffbf[acafcgfffhhac_ccaaaffd_fgZ_cdfddghhfddgeeeebabdcc[X_c[^aa]`[aaa_R]S]_`YYY`b]MX][^_aacacc\n+@2242:2:1101:5649:2379/1\n+AAGCCTGTGGGAGTGTCATTCCAGTCTCCTGAGCTTGAACTATGCTTCTGAAGAGGTCCGGCAAATGCTCGTCTATTGCCTTTCTCCACCTGTAATCAAGGTAGATCAGGATGGCCGGTGGAAAGGCCGCGGCGATGATTGAGAAGAAGA\n++\n+abbeeeeegggggfghhiiiiiiifhiiihhfhhiihhhiiiihiiiiiiiiiihifghfhiiiggegfgecdccddddcccccccbbbccbcc`cccccc_`bcdc]`bbbb_bcccT_cabb[aa^_aa[aaa]]R]bbGS[bbcBBB\n+@2242:2:1101:5649:2379/2\n+TCCTCACTGGCCCGCTGATGTTGGTGATCATGCTAACGGTAATGGCGATGCTTGGCGGAGGAGACCTTGGATTGCTCAGTCCAGACCTGTTGCTAAACATGCTCACCTACTTGGGCATTCCGTTAGGAGCAATAGTCTTCTTGATCATTC\n++\n+bbbeeeeegggggiiiihhighii^effhihhiiiiiii^egghiiihihfhhhgggccccaaaacccccccbbccccccbcccbcabbbccccY_`bb`bbccbbccbbbb_YQ[b[Y_b`b`aabbbacbbbb]bcc]S]YbRY]Y]Y\n+@2242:2:1101:5633:2394/1\n+TCGGCGTCGGTAGTTTTCGTCCCTGGTTTTGCGATGTCATGGAGCAGCGCCGCCAGCTTTAACAACACCGTTCGCGTGCTGCCGCTGCTGATTTCAGCTTCGAAGTGCTGGATC\n++\n+^__cccP^cebac^[deeU^eedRc_cXZ^a[e`Z_U_``_`Rb]b\\d[a_[Za_Z_T]R]R]``^aa^TJQ[ZXOHOX^RGQXaT]RY`GSGY`YYGSGSO^W^a_Y]___Y_\n+@2242:2:1101:5633:2394/2\n+CGCATCGCCGCCGAACTGGGACTACGCATCGAAGACGATACCGAAG\n++\n+ZZZacc^c``egcfh`R^cebf_ZeGVcZ`fXHT_a_TZZ\\aaab_\n+@2242:2:1101:5545:2405/1\n+CCCGATCAAACAGTCCAGATCACTGAAAATGCAGCCGGAGTAAACCATTCAGCCTTTAAATTTTCAGAAGGTGATAATATAACTCTTCTTGATCTCATAAAAGCGGCATTAATAAGTTCTCATAATAATGCTACTATTGCACTTGCGGAA\n++\n+bbbeeeeeggggghiifghfhihiiiihhbghiihiiiihZeghihiiiiihiiiihhfhhiggdbgfgee_bddcddddddcccbccbcbcb`cbbdcccccc_aac_b_bbdcb_cbbccdccb`bd``bcccbcb__bcccb`_ac]\n+@2242:2:1101:5545:2405/2\n+AAGCCAGCATTTTCAGTATATCCTGTCTTTATCCCTTTTATAAATTCATATTCCAATAGTTTATTGGTATTCTCAAGAGGAATAATTTCATCATCTAATATTATATTATCAGATTTTGTACCGACTATTTCCCTAAAAAGGCTGTTTTCC\n++\n+_bbcceeeeggggihighfiihihhegiiihfffhhiiihiihiiiiiiiiiiihihfhhiiiihhhegiiiiiihifdgghhfhhfggggggeeeeeeebdeecbbdd`ccbcbbc_`cbb__]a]b_`_bbbcX]b]a^`]`[b`X_R\n+@2242:2:1101:5710:2454/1\n+TCCATCCGGTGGCTGAGATGCGCGGATGTTTTGCCAACGTGATGGGGCTGCCCGTGTGTCATCTCGCGCGGGCGTTGCGCGCGTTCAAGTCGCCCGCCGATATTCCTGTCGC\n++\n+abbeeeeeggggghiiiieiiihiiiihdfhichhiificgiihggffeecdcc_aacaccdcbbccacXZ__cOX__ccccaOT[``_]__aacMX[XOOTX_ccbY_`V^\n+@2242:2:1101:5710:2454/2\n+GAATGAGTTCGAGGGTGGGAGTGCTCAAGGGTTTGCTCCTTCAAACGTATGGTAGGCGGGCATCCCGATGCCCACTGCTGGCGCATGGGGATGCGCCCGCTACCGCGACAGAAGCCAAAATATCGGCAAAGACCGGACAGTGGGATCCGA\n++\n+abbeeeedgggggih`fgiehdfghhiihih^fgiiiiihighhiiibggfhhgfffgecZ_bccccccaabbba`bbb]_^_c]a^aac^O[aa__ccaX]acacccac_bRXX[^X`^_bbbV][[Xa``GGET[aX^JSRJQY_XPW\n' |
| b |
| diff -r 000000000000 -r a5f56370e870 test-data/output.f.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output.f.fastq Thu Nov 12 07:05:48 2015 -0500 |
| [ |
| b'@@ -0,0 +1,4968 @@\n+@2242:2:1101:1532:1981/1\n+TTTTTCCTTCCTTTAAAACCACTTCTTTGATCCAATCCAGAAAGCCTCTCCAATAATTTGATACCACTAAAATGACGGGGAAAGGTCTGATCTTTTTAGTCTGAATAAGCGTAAGCGATTCGAGCAGC\n++\n+P\\ccc^acebegafabfffbcag`gfb`faf]fad^^cedbeff`affhgfdcfe`^aaa\\WHW_be_f_V_dfZ^Z[a`U]aaaT]bb]Z`G]Zb`[b]``]b]]Y_YRTGWGGGHQGQ]OYb_[^a\n+@2242:2:1101:1908:1977/1\n+GCTGTCGGAAAAGAATTGGAGAAAAGGGATGCTCGCTACCTTGCTTTAAGCTCTCGGATTGCTGCTGAATTTGGGGCACGGAATGTAAAAACCTACTGGTGTGAGAATTTTGAGAAGGTGGTTGGTGGGTGGCCTGTTCCCGTCTGTAG\n++\n+PYS``ca_^ceeeeehaeaXXJbfacZV_cfaebP^cUVcdXbbdeeeebebdeee^[`[ac]]a`baaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa\n+@2242:2:1101:2236:1971/1\n+GTTTTTGCCGTACCAGTTCCATGCTGGTTGAAGCTGGCTTGACGCTGCCGCAATCGTTAAACGCCATTATCGGCATTATAGATAACAGCGTCATAAAGAAAG\n++\n+PP`accccc_c`ddhXQ`bSdd]ed_d^dcddcdXIYc`QOOXU^_[`cNZ_````^_Z^`YZ^^W\\Y]`GGWZEO]`cc`]G]````]][]^[]````^^`\n+@2242:2:1101:2574:1974/1\n+GGTCGGACGTAGCTGTTACGCACGGCAACCTCGGCCAGACTGCAAAAAACATCAAGGCGCGCCAGGGCGTCGGCAACCGCCAGGACCGG\n++\n+PY\\ac`ccccacdhhhadcbPbcc`[ccccdcccccc_b`bbcccccc_U]`R]``]^NW[^^^^^^^]]]Z]XZ][^^^^]]][^]]^\n+@2242:2:1101:2599:1978/1\n+GTTTCCTATGAGGCGGACAAGGAAAACCCGGGGGCCACCCAGTACCACAAGAACTTCAAGGATTGGCTCACCCGGTTTCAGACCGAGGATCTGGTCGGGTGCTGTGCCCAGACGGACGTCAAAGGCGATCGG\n++\n+P\\ccceegggggihiihiiiiiiiiicfhhiiicccccccacbccccccccccbbcccccccccbccccccaaa_]aaccccbcccccccccccbcccTJO[`b`bb]^```a]accaXXWX]`[WX[]aca\n+@2242:2:1101:3233:1997/1\n+TAACCCCTGAGGATGTGGTTACCGGAGGCAGGCATGTAATGGAAGCGGAGATCGAGCTTTCAGAATATATTATGCCAGGCATCGCCGGCCGAGCCCTGAGCGAAGAACATGCAATAGAGACGGCAAAGCTGCTTAACCTTGTTCGTCCC\n++\n+S\\ccccegggggghhfgihiiiiiiiiiiiiifhhihhhfhifiifiihgeece`acccccccccccddeeddbbbbccccccccccccccaccccccccccacca`^bbccbb`bbbbc_[X]a_WXRS]^__`_YY`Y___Y^_^[T\n+@2242:2:1101:3494:1987/1\n+CTTTCAAGGAAAAATGAAACCCCCGTTCAAGCCCAGGGACCCCAGAAGCGGTTATAGCGAAGCCAACATCATCACCCTCCTGAGACTAGGGGGTTCGCTTGTCTTCTTTATCCTGGCGGTCGTCC\n++\n+PY`cccceccegfaggfhhhdgfaf^cdfcefgbgbeaVeeeafhffhfhhdgdecdY``_]_abc_ccbbc`bY^`^^abY_bbb]_bcccc[X^_aXW[QYY`bcbb`]YbccXW[[ETTTQ^\n+@2242:2:1101:3624:1977/1\n+TCGAGGGTTGTCCTGAGGGACGAATTGATGCGTTCTCTCGATCCCAATGTTTCATCAAGGCTCATGTCACCAACCAGATTTCTAAGATTCGTCTGTGCGAGCTTGCTTACGGCTACATAGAAG\n++\n+P\\cc^cc^be_egfgdXdf_edcghhbbXafaegffggag]_\\_cbfbg^gbdbbZ_VHMU]_bb`bbdY]baWWTXXRTZ_R_YYb`]]_baaabb__RX_a[]_b_]]^XRTOXYRa`G]_\n+@2242:2:1101:4155:1969/1\n+GTCTGATTATAGATGCCTACTTCTCAGCCACAAAGATTCGCTGGCTACTGGATAACATCCCGGACGGACAGGAACGCGCCCGGAGGGGCGACCTGCTGTT\n++\n+PPacccdg`e]eeffedhhfdgggg_adgbfh`febegg\\cghhhhhhhhh_fhggghhfhffaadb^aa\\a`a^a^aaa_OXOT[aa]aaaaa^^Y_`b\n+@2242:2:1101:4098:1976/1\n+TATTTCCCTTTTCACTGTTGCTCATTTACCTGACCGGTTGGCGGTTGGGCGGTCGCTTTCTCGGTTGGACCAGCATGCTCCACCTGGCCTCGAATTCTTTAGTCTTGCTCCATACGCGGCGGGCAATGTCGGGAAGTGGATTATTATTT\n++\n+PP`ccccgegfghfgdfhifhiihhiihiihidghhhcefhfehZeaggfgcRZZWT^_b`bacGW__``^W[`^`b]bbb`bca^```baXX[]W`b`bRYY]`SS]_YY_Y_b^a____OXTOGX_YYQTMTT^]b_GSYJSSY_b_\n+@2242:2:1101:4632:1974/1\n+CAGCTCGGAGTCCTCCATGACCAGGTTGCGACGCGCCAGCGGGCGGCCGGACCGGTCCAGAACCAGCAGGCGGAACAGGTTGGCATCCTCTCGGCGCAGCAGGAAGAACTCGCCCC\n++\n+S\\ceeeegggggiiiiiiiiiiiiighhiiiihiiiiigggecccccccccccaaac_ccbbccccccaaccaX[]^^aYbba]`bbbbcY^T^_[TOXTGQ`GW`P^[YY^TX_a\n+@2242:2:1101:4557:1998/1\n+AGATTATAATACCTCGATAAAGTCGTGTCAATATTTTGGGCGAGAGCCTCAGTGTTTGACAAGGGCTCTTTGTTTAAGGTATCCTAAGCTAGCCTAATTAAAAGGAGGTGAAAAGGATATGGCTGAAGAAAAGAAGCCAACCGTGGAGG\n++\n+PYccccegggcgiiiiaffhihhiiihe`ehfafghh`daeg_c`Ybefd]e\\b_dgbZbb`Za^^^`dbdd`b\\Z_]bZ_Z]`b``b`b`]][]_SY`_bcbbacW]QQ]]]`b^abbbb]`b_QSYGR[^b^^BBBBBBBBBBBBBB\n+@2242:2:1101:4928:2000/1\n+CCGTATCGGTTGCAGTTCTGCCAAAGCCCAAAAAAACCGTAATTAAAATTAAGCCCGATGATATAAAAGTAGATTTTTATCGCGCATCAGGTCCGGGAGGACAAAATGTAAACAGGAGGGAAA\n++\n+Pacceeefggggiiihihiiiiiiiiiiidhhiiehfffeghhiiihiiigfgfgeeccccddddddcc_```b_bccccb[acccccbccbbccccT_VQ[[`bab_bcccb]^^aaaa][^\n+@2242:2:1101:5055:1979/1\n+GCACATCGAACATGGCTCAATTGTAACATATATAGAAGCCTGGCTCAACCATTTCGCGCCCAGATAATTTGTCGCTGAAGTAAGAGCGATCATCTCGGCGTGCGCGGGAGGGGCTTT\n++\n+P\\ceeeegggggiiihhiiiiiihhhihiiihihhiifhiiiiihiiifghhhiidffiifdggceeeeeeedc`_cabcbbbcccbcccccccccc^a__TEHTT[EOTa]EOT^`\n+@2242:2:1101:51'..b'GCGGTTGCGCACGCCGGAGGGAGCGAAGGAGGCGGCGCGCGACGAGCTCGGTGTCGTCGACGAGGGCGAGG\n++\n+bbbeeeeegggggfhiiiiihiiiiiiihihhiffccX^_acccccccccacccccccccccccccccaccccc_[_X[aaba[Q^L]_[^_[]a]_cc]aM[_\n+@2242:2:1101:5303:2421/1\n+AATTCCTTGTCCACGAAAGGCAGCAATTGCGCGCCGGGCTCGATGAGCGTCACCTTCACGTCGAGCGCCGAAAAGATGGTGGCGTATTCCACGCCGATGACGCTC\n++\n+bbbeeeeecggegiiiaghheihhiiihdgfihhifhiihge]addddcacacccccbcccccZ]acaacacc_`[_bbY_^aaTO[`bdR]accaTX_bbca[_\n+@2242:2:1101:5304:2442/1\n+CGAGCGTAACTTGCCGGTGTGGATGTTGACTCCGGCGGCCCGCAGGTTTGACGAAGCGGTTGAGATCATGAAAAAGTTCGAGCGGGCCGACTGCCCGATAGTGGTCTCCCGTATGTGGGGTTTTGAGT\n++\n+bbbeeeeegggggiiiidgdgfhiifhfiiiiiihiigeccac_ac[bbabbaacccccOV[]b`_bbbbccccc]Y_bccccccc[aaaaR]^ba_][]_]`aRY]]bbaQT[bcabca]TGW[W^b\n+@2242:2:1101:5332:2460/1\n+TCCACCTTCTGTCCTAATTGTAGGAGTAAATATGGATAATTATACGCTGTTCACACCCGGTCCAGTCGATATCCCCAATGAAATCAATCGGGAAATGAATAAACCTTTAATATATCACCGGGAGAATCGTTTCGCGCAGCTACTTGATGA\n++\n+_bbeeeeeggfggfihfhiigihiiicfffiihfhggfgchfhiiiiigggihhiiegffegd_ddggfeeeedd\\`bbbbcc``bcbcccc__abcbc[Y_]Y``b_]bcdcccddbb^REX_]`]Y[WP[b_]a_EHT`bc`RG]_]_\n+@2242:2:1101:5322:2499/1\n+CGGGCAATTAATCATCGGTTATTTCGATGAATACCCCTCTGGTCAAGTACCGTACCTTGGTGCTCTCATCCCCAGCCCTGTGACGTTCCCCGTTACCTATACCATCTCAGGTCTCGCTGATGATACCTACTACG\n++\n+bbbeeeeeggggghiiiighiiiiiiihiiiiiihiihihhifghfigfghhghiiihhgfgfhiiigfgfgdeeabbbdcccba\\^accbaZ`_cccbbb`bbcb`bY]b_`]`bcaaXb_`Ybbb_GX_bc^\n+@2242:2:1101:5578:2289/1\n+AATTGAGGGCCTTATGGCGGCTGAGACCGGGAACAATGCTGTCGTGCCTGGCGCCATCATCCCTGCGCTCACCCTTGCCATTCC\n++\n+^^^aJ^c]cUc^^d]]dR[__b^Xcb[a^`cFTZ\\RZ^\\`RV^ZKT\\]RZZTX\\\\W[]]TTY\\]YQTZ]LOY[^GX[]`YS]a`\n+@2242:2:1101:5564:2297/1\n+CACGAAGCCGTACAGCGGCTCGCTGAACATCCGCGCCTCGTCAGGCACCGAGCTGTTCGAGTACATCTGCC\n++\n+__beceeeggggghhhhhhhhU^^_cfbcXbbYb__d``NMTUKZZ\\^^YFWNKGKT]WW^RW`b_`Y]_b\n+@2242:2:1101:5670:2333/1\n+CCGTCCGGTCCCAAGGCCGACTACCTGTGGCGGCTCTATGCGCCCGACCGGGCCATGCAAGCCGGCATAGACGACGTGGGAATAGGAGCCCTGTTCGGGCTGACCGACCACAAGTTCG\n++\n+___cacceYceggeegdgfcgfgihfh^afgegh``]bdV^[^^`NZ_aaca[a_bb``b`a_Z_aaT]Yb_OZTLEWWXWXQ]YY_RPGWGWY_]GOTTTXGR]X_]c_^^W[SSS^\n+@2242:2:1101:5665:2357/1\n+GGTCAGCGAGGGCCTGACTCCCGTTCAATGCCGGGGGATCCAAGACTTGATCGAGGAAAAAGACATTCTCCTGAAAATAAAGCTCTTGAAGAAGGAGCTCCAGGAAAGCGAGGTCTAAGGTGAGAAAAACAGCTCTCATCATAATCATAC\n++\n+___ceeeegggggiiiiiihhiieghiihhiiiiiiebccdcccccccccccccccaaccc[accccb`bbbc`bbbccccY_Y_bbbb`bbb]`__a[``bbccab`^_aaXEX__Y`[JSY`bc]bQEWXW]]Y`b]_SS_BBBBBBB\n+@2242:2:1101:5703:2367/1\n+GGGCATTGCACTCCTCGGGGCAAAGACCGACGGCAAGGCTCTCCTCATAGCTCTCGTGACCAGCGACCTGACAAATCGGTTTCACGCGGGCAATATCG\n++\n+^^_ccceaa[bgefhd]fda`egbhhhc_ce`fhhaZ\\bVZaa_``]Z]_RTZLTR^aYTY`TTWTZZ]R]bYGJSSWTJTO_YRQQEOEOOQ]`b]^\n+@2242:2:1101:5687:2369/1\n+GCGCTGCCGGGTTGTTTTCATGGCTTAACGGATAACCTCATTAGCGATATTATAGCCATTCAAGCTGATTTATGCAAATATATATTTTCTTTAATCGGGTTGACAGGCTTTCAA\n++\n+__bec`cceggeeagfddeg`ebdcgffgag`_ef_cae``ff`dfhhha`\\`ZVV^ZVV`bbde`b_bZZZZRZ]R]]]b]]b]_b_`bb_b_]]GTTJQEJY_Y[GJR]_`b\n+@2242:2:1101:5649:2379/1\n+AAGCCTGTGGGAGTGTCATTCCAGTCTCCTGAGCTTGAACTATGCTTCTGAAGAGGTCCGGCAAATGCTCGTCTATTGCCTTTCTCCACCTGTAATCAAGGTAGATCAGGATGGCCGGTGGAAAGGCCGCGGCGATGATTGAGAAGAAGA\n++\n+abbeeeeegggggfghhiiiiiiifhiiihhfhhiihhhiiiihiiiiiiiiiihifghfhiiiggegfgecdccddddcccccccbbbccbcc`cccccc_`bcdc]`bbbb_bcccT_cabb[aa^_aa[aaa]]R]bbGS[bbcBBB\n+@2242:2:1101:5633:2394/1\n+TCGGCGTCGGTAGTTTTCGTCCCTGGTTTTGCGATGTCATGGAGCAGCGCCGCCAGCTTTAACAACACCGTTCGCGTGCTGCCGCTGCTGATTTCAGCTTCGAAGTGCTGGATC\n++\n+^__cccP^cebac^[deeU^eedRc_cXZ^a[e`Z_U_``_`Rb]b\\d[a_[Za_Z_T]R]R]``^aa^TJQ[ZXOHOX^RGQXaT]RY`GSGY`YYGSGSO^W^a_Y]___Y_\n+@2242:2:1101:5545:2405/1\n+CCCGATCAAACAGTCCAGATCACTGAAAATGCAGCCGGAGTAAACCATTCAGCCTTTAAATTTTCAGAAGGTGATAATATAACTCTTCTTGATCTCATAAAAGCGGCATTAATAAGTTCTCATAATAATGCTACTATTGCACTTGCGGAA\n++\n+bbbeeeeeggggghiifghfhihiiiihhbghiihiiiihZeghihiiiiihiiiihhfhhiggdbgfgee_bddcddddddcccbccbcbcb`cbbdcccccc_aac_b_bbdcb_cbbccdccb`bd``bcccbcb__bcccb`_ac]\n+@2242:2:1101:5710:2454/1\n+TCCATCCGGTGGCTGAGATGCGCGGATGTTTTGCCAACGTGATGGGGCTGCCCGTGTGTCATCTCGCGCGGGCGTTGCGCGCGTTCAAGTCGCCCGCCGATATTCCTGTCGC\n++\n+abbeeeeeggggghiiiieiiihiiiihdfhichhiificgiihggffeecdcc_aacaccdcbbccacXZ__cOX__ccccaOT[``_]__aacMX[XOOTX_ccbY_`V^\n' |
| b |
| diff -r 000000000000 -r a5f56370e870 test-data/output.r.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output.r.fastq Thu Nov 12 07:05:48 2015 -0500 |
| [ |
| b'@@ -0,0 +1,4968 @@\n+@2242:2:1101:1532:1981/2\n+ATCATCCAGCGGTGAGCATTTTAGGTTCCACACGCATTAAACCCGGTGACGAGGTCTACTCGAAGGCGGAACAAATCTGCAAACTCTTAGC\n++\n+^a_cccaZJQbe[beghihigbJ[bX^^deffffYe\\f_a`dRZU_aa\\bGLT\\T_bZ_bd^`Z^ZX\\ZTTX^[[RYGS]Y]_^R_Y]]bb\n+@2242:2:1101:1908:1977/2\n+GGGATGTCGGCTGATACCCCCTCACCC\n++\n+\\a_e\\cacYHOQ_YY`a^Rb___YH^b\n+@2242:2:1101:2236:1971/2\n+TATACTTAATACAATGATTGGTATATCGAATACAGCGGCTGCATGATAGCAAGGCCGATAAAGCCGATTAACAAACCGGCAATAATAATGGAAGCCGGTTCAATCA\n++\n+^^Wac`ceeWeegaafffffffhh^ef_egbgefccfa`ced_fhhchS\\\\egf^efUY\\^aVZZX`ac^_]RY^X[__a_aGY]R]]`bGY]R^`_[OTW_bcbb\n+@2242:2:1101:2574:1974/2\n+AAGAACTGGACAACTTGCGGTTGACGGCAAAAAACTCAAAACAGTACCTCGCCAACCTGGAAAAACAGGAGCGAGAGCGTACGGGCATAAAGTCGTTGAAAGTCGGCTATNATCANGCCTTTGGCTACTATATTGAGGNNNNNAATGCNN\n++\n+_a_cccccceeggfd]adafegdgXbcOcegfiiUbfgh[ehficgX_Z_Z`aa`aabccccbZ^aa^`a[aaL[[[[a_^accaV_[b_b_G]_[Xb^b]__]^TT^aGBJQWQBJGJJGYSRGGY^b`c]``bbBBBBBBBBBBBBBB\n+@2242:2:1101:2599:1978/2\n+CTCCCATGGAACGAAGACGTCGTCGAAAACCATGTAGGAGTCGCAGCTCCCCGCGTTGAAGCCCTTGGGGAAGCGCTTCCGATCCCGGTAGTTGTGCGCGGTAACCAGCTNTTTCNGCCCGTCCCCATCCCC\n++\n+bbbeeeeegggggiihiiiiiiihiiiiiiiieihhhihdbffhiighggdgeccaccccccccccbcccaca^aaaaccccccac_aX[]`cbb^baaaca_cccc^a_BGQWWBJJW[^TWT[GRX^`^_\n+@2242:2:1101:3233:1997/2\n+TAAAGGATGGCGACTATGTCCAGAATAGTGAAGCAGGGTATAGACCTCTCTCTGCTTCTTTGTCATGGACAGAAAGGCATCGAGCTCACTCAGCATATACTCTTTCTTCTCGTCCAGAAAGCCATCCACTTGCATGAGGNGGTTCAGACT\n++\n+bbbeeeeegggggiiihiiiiiihiifgghfhfhiiih^cefhiiiiihihhiiiiiiiiihiiiiiigggegeede\\_`bbccccccbc`bccccbbcccccbcccc]`_[a_c^`bRYbGWXbX^bbcbbbGS]b`^BJWGJ[``__]\n+@2242:2:1101:3494:1987/2\n+CCGTTGAATTCGCGAACTTGCCGGCCGGGCTGAAGTTCCAGGTGTAGACCGTCCGGGCCACCCGATAAAAATAGTTCGGGGACATGATAT\n++\n+___`ccccce[eeddf`bddffY_egfgehff_VV^d_\\MM^VZ_ab`_ZRRXW\\_NVT[W[TTTLW[bbc[Y`S]`WTTXTEWYGJ]``\n+@2242:2:1101:3624:1977/2\n+CTACGCTAATTGTTGAAAAAATTAAAGGAGGTCAATGAAAATGGATATAGGAACGATAATTATCATAGTGATTCTGGCAATTGTGGTACTAGTTACTCTTAAAAAGTCGGNAACCNTTATCCGCCAGGCCGAGAAGGGNNNNNTGGAGNN\n++\n+___cecececgggiidgfdh]_ffeeffhfdbeegadgfbfffgbghhhh_fhiiihfhhhhiggcge`dd__ceeedcdcbdcccZT``cc__bc_bbbccb_]abb[]BJJJWBJQWO[`V^aa]^acVOXX_bBBBBBBBBBBBBBB\n+@2242:2:1101:4155:1969/2\n+GGTAAGATTCCATATCAGCCAGCTGTCCACTGTTCCGAACAGCAGGTCGCCCCTCCGGGC\n++\n+a_YaccZcgacggde]aeXecY[gcggfdg`eggI^^OWbeghdfaOX^UZ_e^_`Z`da\n+@2242:2:1101:4098:1976/2\n+ATTGGTCTGCCGGACAAGCAATTCCTGGCGAACTTTCAACGCTGCTTGAAGCGCATTCAAGGAGTCTGTCCAAATAATTGGATTCAGCAAAATGAAAATTGTAAAGAATCNTGCCNCAAATCTGGCTGTTTGTCC\n++\n+___cacececgggdgadgffhfgfbghiihgchicgbaeghhiiihfhddgec^`a`dddcc`abbccccccbccbcddcb_b`_`bcbX^bccbbbcc`bbbbccb`b]BJW^_BJWGWWbbcb`^^GY_bcbb\n+@2242:2:1101:4632:1974/2\n+CCCGCCGGGGCCCTGCAGCACCAGCTCACCCTGGAGCCGGCCAGCCTGCCCCCCCTGGCCGAAGCCCCCGCCGCCACCCCCTCGCTGGGCAGGCTGGTTCC\n++\n+bbbeeeeegggggiiihiiiiiiiiiihiiihhhghfhhfeecccccccc^acccc_accaZacaccccccca]a[[acccT[X]WT[^[GX_XW[]^bY_\n+@2242:2:1101:4557:1998/2\n+TTGAATACCATGAGTACTCGCGGACCCTTCTCGCTTCCCTTATCTAGCATATCGTGAAATTCATGGATAGTAGTGATTTTGTCACCAGCTTTGATGGGTTTATAGTATTCCCAGTCCCC\n++\n+bbbeeeeeggggghhiihiiehhhidgghdghhihihihhifhhhfffhhhihgggfdcedeccbc`d_TZaZab``cbc]`]ZY`bcabbbSS_Y``R[a`b`RSSYbGYYR]`YS_a\n+@2242:2:1101:4928:2000/2\n+TACGGTTAATAATTCGACAAATTCTTCTCTAAAGCCTCAATCATAGAACCTAAATTTCCATTCATAATGCTCTCTAAGTTTTTCCAGGATTTTTTAATCCGATGGTCGGTAATTCTATCTTGGGGAAAATTATAAGTCCNAATTTTTTCT\n++\n+bbbeeeeegggggiiiiiiiiiiiiiiiiiiifiiiiiiiiihiiiiiiihhiiiiihihiihhhiiihihiiiiiigfggggeeedd`ddcddcccbbccccca`bccaccccddccbbcbb`aW[^^]``c__b_cGBJGWW^bbabb\n+@2242:2:1101:5055:1979/2\n+CTTTGCCTTCGGGACTTCCTCGGCCAACAAAAAA\n++\n+bbbeeeeegggggiiiiedY`H[HHPPHHO^eZc\n+@2242:2:1101:5102:1984/2\n+CGGCCAGCCTTCACCTCTTGTTGCTCAACCCGCAGATCCGACTGGCCAGCGCGCCCTCCACATCTGCGGGTGTCTCGCTCGCCCCGAAGGCGCGGTCGTGCAGGCATCTAAGCC\n++\n+b_beeecegggggihfiiiiiiiihg`fhiiiihhfgfhgiiiiiiiihfhgcbcccccbcY`bbbc__cOXX_b_X^aacccacXO[HO[]a[aT_[XT^`bc[``XGS]YR^\n+@2242:2:1101:5256:1987/2\n+CATTAATATGATCGGCTAAACCAATATAGAACCAACAAGCAACCTACCCCGGTTTGCGGATTGGGGTAAAGACCCGACGACCAAAGATCCGAGAATGACACCCAGGCCAGTTCCTGCCATAAGCTGACCAAAACCACTGNNANCCGTACN\n++\n+bbbeeeeefgggghiiiiiffhfhiihhiiieihdfbgfhiifiiihgfffgZaghggeebccbcc]acbbcccac]_]]aa_[`'..b'ccccc`]bccdcccaccccaabccW]`R[`acc_MEEOX_RJGJ[[`[]MEHOQW^[aa]aBBBBBBBB\n+@2242:2:1101:5327:2381/2\n+ACCCTCGCGGAGGTGTGTCGCACTGCCCCCGAGATCGTCGGGCGCGGCGTGCGGG\n++\n+aabeeeeegggggbefghhhifhhiiiiihhfhgggeeecccacaac_[TTOTYa\n+@2242:2:1101:5303:2421/2\n+GGCGTGAGCGCGGCTTTTACGGACGCGGCTATCGCGTGAAGCAGAACATCTCGGCGGAAGATTTGAACCGCCGCCTCGGCATCACGCTGAACCACGAAGTCGAAATTC\n++\n+__ac^ccccgggehdgegh_efhhgd`gdcddbccaa_W^YY`bbccb`bbbaac[aVV__Y`b``bY[]_]LO[[XLTWTTGS_acc]EY]WW_^]TWW_^W^_[_b\n+@2242:2:1101:5304:2442/2\n+CACTGATAACCGCAATCGCACCATTGCCGAATTGACAGGTAAGCACCCCGGTGTCCTCGGTGTCGTAAGGATAATGTCCGCCGGGGCGCGAAACGGCGGCGGTGGCGGCGTGAACCGTGGCCGGGAAAACCATTAATTCAACTACAGAAT\n++\n+bbbeeeeeggggghhiiihiiiiiiiiiiiiiiiiiiiieggfhhhhhhhgdceeeddcc_accccccccccccccdddccaccccccccccccacacaaccT[aW_]TXEXOWY^TQQTO[aaEHT^GXQQJS]]S]Y_cbBBBBBBBB\n+@2242:2:1101:5332:2460/2\n+GGGTTGTGAAGATTATTACCGGTCGGTTTAGAGTTTTAAGTTTTGCTTCGACCGCATCCGGCGTAACGGTTTTTCCGAATTCAACTTTCACAATATGCGTTTTGATCTTATTCATATCACAAATTTCTGCCCATCGTTCACCGAATTTAC\n++\n+aa_cce_cbeeggiiiihhiihcegh^efgf[caeagdffehhhhiifddfghggeeadcaaacY^aacQWZaccccaccabG]bbbcbbbcb_]bY_acaac[W`YSSGJ]]_`Y]GJY`_[`bb`c_`ba`JGQQ^aBBBBBBBBBBB\n+@2242:2:1101:5322:2499/2\n+TTTTGTTGGTGGGTTGGTTGTTGCAAAGTATACATCGTAGGTGACGGTGTCACCTGCATCTGGGTCTCCTCCAATCCAGCTGAGATCAGTGTTGATTGACACATCCGTTGCACCATCTGGTGGGAGAGGGGCATGCGGTTCATACGGTGG\n++\n+abbeeceeg`eggbeghegiiihhfhiiegihihihhiiii^eghihfffdghggegdggdceebddbbddcb^bcccccbbcccbcccbcb_^bbcbbbbbX`bcaGSW_`bc[Y^bbb]XOEQWOW^aETTX[___OM[bYY_^^BBB\n+@2242:2:1101:5578:2289/2\n+ACACGAGACCCCGCCGCAGATTCTTATCCATGAGGTCGCCGAGGATGATCCCGAGTACCAGGGGAGCCATCGGATATTTC\n++\n+\\WY``WOH[QbZ_H[dOOYYXIOOOIX^adbacR\\HWFae_`[`c_]T_ZTKZFKGGT]`Y[T[a_aWXRRWHW^TSR]_\n+@2242:2:1101:5564:2297/2\n+ATGCAGCTGACGTCCGTCGCCCAGCTCGTACCACGCCCCCGCGAAGGGAAACGCCGGCCGATCGACTTCCCGCAGGCCAAGCACCTCTCCGTAGAAACGCTTCGATCGGGCGATGTCTCTGACGCAGAC\n++\n+___eeeeegfgggiiiegfiiihiiiiigghiiihhiiiiigecacccccccccccaccca_ca_acccccaca_accaaa^^^```_^]TQ[^^b`]VXW^[[acaOX_XMETXW_`bb]Y_X]][_^\n+@2242:2:1101:5670:2333/2\n+CCGAAAGGGTGCGCTCGTCGCCGATGGAGAACTGCTCGGCCTGGGGCTGGGGAGCTTTGGCGTCATGGTAGCC\n++\n+^_^acc^caQ`ccehhidfb[eghhhffdghcggdffdfgN\\`aac_bc_PZ\\WRX`bbb`[TZT^]bY`bbc\n+@2242:2:1101:5665:2357/2\n+CTTTGTAGAGCTCGTAGGCCAGGTCGATGATAGAGGACTCCGCCTGCTCGGCCAGGCTGTCGTTTCTCCCCTTGACCGAAAGATACTCCTTGTAGGCCTCAATGGCTTCTTCCTCATGGCCCTTCCGCC\n++\n+a__eecdegggcgdddghhhiii`eghffihihiiihiffhhhifhiiihffgihggdgaeedccddbdcab^b_bbcY][acbccc_^`Y`b]_`]b_abbbbbcXPXY`bcRYJSJY[`a[RGXTT^\n+@2242:2:1101:5703:2367/2\n+GATACCCGTCAGCTCAACTACCTTAAAGATAGTGACCGACTGTCTCGCCATCTTCAGTTCGTTGATTACACGCGTAATCCTGC\n++\n+_\\^c^cccbcg_JQQ`]aYe]fd]e_d_a[bbPY^^bf_cegWafbaZZZeV\\_ZVMHVVGL^HUZad]_Z\\FRRQ^_RZbY_\n+@2242:2:1101:5687:2369/2\n+TTGTACAAGCGCACCACCTGAGGCATCATCTTCTTGGTCACCGTGCCTGAGACAATCATCACGTCTGCCTGGCGGGGGCTTGGTCGCATCACTTCCATGCCGAAACGGGAGAAA\n++\n+^ZZ`accaegeecfhhaggdeffbf[acafcgfffhhac_ccaaaffd_fgZ_cdfddghhfddgeeeebabdcc[X_c[^aa]`[aaa_R]S]_`YYY`b]MX][^_aacacc\n+@2242:2:1101:5649:2379/2\n+TCCTCACTGGCCCGCTGATGTTGGTGATCATGCTAACGGTAATGGCGATGCTTGGCGGAGGAGACCTTGGATTGCTCAGTCCAGACCTGTTGCTAAACATGCTCACCTACTTGGGCATTCCGTTAGGAGCAATAGTCTTCTTGATCATTC\n++\n+bbbeeeeegggggiiiihhighii^effhihhiiiiiii^egghiiihihfhhhgggccccaaaacccccccbbccccccbcccbcabbbccccY_`bb`bbccbbccbbbb_YQ[b[Y_b`b`aabbbacbbbb]bcc]S]YbRY]Y]Y\n+@2242:2:1101:5633:2394/2\n+CGCATCGCCGCCGAACTGGGACTACGCATCGAAGACGATACCGAAG\n++\n+ZZZacc^c``egcfh`R^cebf_ZeGVcZ`fXHT_a_TZZ\\aaab_\n+@2242:2:1101:5545:2405/2\n+AAGCCAGCATTTTCAGTATATCCTGTCTTTATCCCTTTTATAAATTCATATTCCAATAGTTTATTGGTATTCTCAAGAGGAATAATTTCATCATCTAATATTATATTATCAGATTTTGTACCGACTATTTCCCTAAAAAGGCTGTTTTCC\n++\n+_bbcceeeeggggihighfiihihhegiiihfffhhiiihiihiiiiiiiiiiihihfhhiiiihhhegiiiiiihifdgghhfhhfggggggeeeeeeebdeecbbdd`ccbcbbc_`cbb__]a]b_`_bbbcX]b]a^`]`[b`X_R\n+@2242:2:1101:5710:2454/2\n+GAATGAGTTCGAGGGTGGGAGTGCTCAAGGGTTTGCTCCTTCAAACGTATGGTAGGCGGGCATCCCGATGCCCACTGCTGGCGCATGGGGATGCGCCCGCTACCGCGACAGAAGCCAAAATATCGGCAAAGACCGGACAGTGGGATCCGA\n++\n+abbeeeedgggggih`fgiehdfghhiihih^fgiiiiihighhiiibggfhhgfffgecZ_bccccccaabbba`bbb]_^_c]a^aac^O[aa__ccaX]acacccac_bRXX[^X`^_bbbV][[Xa``GGET[aX^JSRJQY_XPW\n' |
| b |
| diff -r 000000000000 -r a5f56370e870 test-data/output.s.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output.s.fastq Thu Nov 12 07:05:48 2015 -0500 |
| [ |
| @@ -0,0 +1,32 @@ +@2242:2:1101:1410:2072/1 +ATTGAAGACGTTCGCACGGATGCTGTCTCTGCGC ++ +\WYaPJQQ`bJ[Ydd[H[PY^b_cc^IOY^_ccc +@2242:2:1101:3714:2244/1 +TACTGAACGGAATGAGCTTGAAATCCAGATCCTTCAGGTTCATGCCGGGGGACAGTGCCAGAAATGTTCCCGCCGAAGTGGAGGACCGCATCCCGCTGTCTTCCAGGGTGCAGCCGGCCTTTTCT ++ +___ec^aaggegcfeeghfhggfffgghhddggfa[^e^cddgdfhhhafa[[`a]]]Z__`]_`b_ZZR]__aa[_[^]R]aa_aa[aaaLX`_]MT[bRY]b]_b_RQGY_GQHOOXOGY__` +@2242:2:1101:5866:2211/1 +GTCGGGGATCGACGGGTTGCGCAGCGCGGAGCTGACCGACGCGATGGCCCGCTCGGCGTGGGAAGGCGTGCACGTGAGGCTGGGGTGATCACACTTGTGCGCATTCCTCGCAATGACAAGC ++ +b_beeeeegggggihi^eghfffffhhggeba^bbcb___aa_U[aacccWaT[T[_aZacaQ`_aacTXT^b[WWW[a^^acacETQYSYbYSGS]Y]]_]RET]b__[_OTXbSGS_W^ +@2242:2:1101:14860:2072/1 +CGGCTGGCTTCGTGCACATCCTCTCCCGCCGGCCCCAGAGGAGGAGATAGGGTTTCTGCTCCTCCTTCGCGATACGAAGCTCGGCGTTCACGCGCACCGACGCCGCC ++ +[_[cacccggc`^[`bbf]dgc`]eha[ef___efgcd`cg[bgG^Z`bb[ZMTZZ]_]`_b`bb^bYGOTOTX[_aQQX]`T[a_a_G]_^WHHEEOOMT[__a_a +@2242:2:1101:15244:2185/1 +TACGACCAGGGCGATTTCGAAACTATCCCGCTCCGGCACATCACCGCCGC ++ +[^ZZa`YWb^^ccWW^b^dW^^_a_bc_Ra^cccch[_[MV^bc^^__]^ +@2242:2:1101:3440:2300/1 +CGGCTCTCGGATGCGGGCGCCCGCAAGGCCGTCGCCGATCGCTACGGACCGCAGGCC ++ +^^_c`ccceeY[cZ_ffh_U_^_aNTL_UbFFKX\^ZUW_QJQ[_aaW_[a[_aaW^ +@2242:2:1101:4206:2262/1 +CACGCCGCCCGCGAGCTGGCGG ++ +___cccccggggehgdagd\e_ +@2242:2:1101:4109:2339/1 +TTGCTCGGTGAGTTGTTCCTTGTGTTTTTGATAATACTCCTCTGTTTGTTCCTGGGTTGGTACTTGTACTATTTCAGAGATATCGTCGAGCTTGACGGCGATATATT ++ +^[_acccc[b`b[dfdeebeggX^`ab^cUPYY^cefdaee_edacfehheeehXZ\b[`T\dheed_ddb^__aZZ__Z`a_GZ_aYNQZ\`^[`aaaaR[a[`ac |
| b |
| diff -r 000000000000 -r a5f56370e870 test-data/test.f.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test.f.fastq Thu Nov 12 07:05:48 2015 -0500 |
| [ |
| b'@@ -0,0 +1,5000 @@\n+@2242:2:1101:1532:1981/1\n+NTTTTTCCTTCCTTTAAAACCACTTCTTTGATCCAATCCAGAAAGCCTCTCCAATAATTTGATACCACTAAAATGACGGGGAAAGGTCTGATCTTTTTAGTCTGAATAAGCGTAAGCGATTCGAGCAGCTCCACCGTGGTCCCAAATCCA\n++2242:2:1101:1532:1981/1\n+BP\\ccc^acebegafabfffbcag`gfb`faf]fad^^cedbeff`affhgfdcfe`^aaa\\WHW_be_f_V_dfZ^Z[a`U]aaaT]bb]Z`G]Zb`[b]``]b]]Y_YRTGWGGGHQGQ]OYb_[^aBBBBBBBBBBBBBBBBBBBBB\n+@2242:2:1101:1908:1977/1\n+NGCTGTCGGAAAAGAATTGGAGAAAAGGGATGCTCGCTACCTTGCTTTAAGCTCTCGGATTGCTGCTGAATTTGGGGCACGGAATGTAAAAACCTACTGGTGTGAGAATTTTGAGAAGGTGGTTGGTGGGTGGCCTGTTCCCGTCTGTAG\n++2242:2:1101:1908:1977/1\n+BPYS``ca_^ceeeeehaeaXXJbfacZV_cfaebP^cUVcdXbbdeeeebebdeee^[`[ac]]a`baaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa\n+@2242:2:1101:2236:1971/1\n+NGTTTTTGCCGTACCAGTTCCATGCTGGTTGAAGCTGGCTTGACGCTGCCGCAATCGTTAAACGCCATTATCGGCATTATAGATAACAGCGTCATAAAGAAAGCTTTTATAGAAATCAGGCAGGATATCATCAAGAGCAGGGGGCTATGC\n++2242:2:1101:2236:1971/1\n+BPP`accccc_c`ddhXQ`bSdd]ed_d^dcddcdXIYc`QOOXU^_[`cNZ_````^_Z^`YZ^^W\\Y]`GGWZEO]`cc`]G]````]][]^[]````^^`BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@2242:2:1101:2574:1974/1\n+NGGTCGGACGTAGCTGTTACGCACGGCAACCTCGGCCAGACTGCAAAAAACATCAAGGCGCGCCAGGGCGTCGGCAACCGCCAGGACCGGCTCGCTGGCGCCGGCCACCTGACAGCCGAGCACTTTTCACAACTCACCCTCAATACACGC\n++2242:2:1101:2574:1974/1\n+BPY\\ac`ccccacdhhhadcbPbcc`[ccccdcccccc_b`bbcccccc_U]`R]``]^NW[^^^^^^^]]]Z]XZ][^^^^]]][^]]^BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@2242:2:1101:2599:1978/1\n+NGTTTCCTATGAGGCGGACAAGGAAAACCCGGGGGCCACCCAGTACCACAAGAACTTCAAGGATTGGCTCACCCGGTTTCAGACCGAGGATCTGGTCGGGTGCTGTGCCCAGACGGACGTCAAAGGCGATCGGATGAAGCGGCGAAGCGA\n++2242:2:1101:2599:1978/1\n+BP\\ccceegggggihiihiiiiiiiiicfhhiiicccccccacbccccccccccbbcccccccccbccccccaaa_]aaccccbcccccccccccbcccTJO[`b`bb]^```a]accaXXWX]`[WX[]acaBBBBBBBBBBBBBBBBB\n+@2242:2:1101:3233:1997/1\n+NTAACCCCTGAGGATGTGGTTACCGGAGGCAGGCATGTAATGGAAGCGGAGATCGAGCTTTCAGAATATATTATGCCAGGCATCGCCGGCCGAGCCCTGAGCGAAGAACATGCAATAGAGACGGCAAAGCTGCTTAACCTTGTTCGTCCC\n++2242:2:1101:3233:1997/1\n+BS\\ccccegggggghhfgihiiiiiiiiiiiiifhhihhhfhifiifiihgeece`acccccccccccddeeddbbbbccccccccccccccaccccccccccacca`^bbccbb`bbbbc_[X]a_WXRS]^__`_YY`Y___Y^_^[T\n+@2242:2:1101:3494:1987/1\n+NCTTTCAAGGAAAAATGAAACCCCCGTTCAAGCCCAGGGACCCCAGAAGCGGTTATAGCGAAGCCAACATCATCACCCTCCTGAGACTAGGGGGTTCGCTTGTCTTCTTTATCCTGGCGGTCGTCCGGCCAAGCACGGGCATGACACTCA\n++2242:2:1101:3494:1987/1\n+BPY`cccceccegfaggfhhhdgfaf^cdfcefgbgbeaVeeeafhffhfhhdgdecdY``_]_abc_ccbbc`bY^`^^abY_bbb]_bcccc[X^_aXW[QYY`bcbb`]YbccXW[[ETTTQ^BBBBBBBBBBBBBBBBBBBBBBBB\n+@2242:2:1101:3624:1977/1\n+NTCGAGGGTTGTCCTGAGGGACGAATTGATGCGTTCTCTCGATCCCAATGTTTCATCAAGGCTCATGTCACCAACCAGATTTCTAAGATTCGTCTGTGCGAGCTTGCTTACGGCTACATAGAAGTTGGCGACTTTATATCAGACAGCCTT\n++2242:2:1101:3624:1977/1\n+BP\\cc^cc^be_egfgdXdf_edcghhbbXafaegffggag]_\\_cbfbg^gbdbbZ_VHMU]_bb`bbdY]baWWTXXRTZ_R_YYb`]]_baaabb__RX_a[]_b_]]^XRTOXYRa`G]_BBBBBBBBBBBBBBBBBBBBBBBBBB\n+@2242:2:1101:4155:1969/1\n+NGTCTGATTATAGATGCCTACTTCTCAGCCACAAAGATTCGCTGGCTACTGGATAACATCCCGGACGGACAGGAACGCGCCCGGAGGGGCGACCTGCTGTTCGGAACAGTGGACAGCTGGCTGATATGGTATCTTACCAGATCGGGAGAG\n++2242:2:1101:4155:1969/1\n+BPPacccdg`e]eeffedhhfdgggg_adgbfh`febegg\\cghhhhhhhhh_fhggghhfhffaadb^aa\\a`a^a^aaa_OXOT[aa]aaaaa^^Y_`bBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@2242:2:1101:4098:1976/1\n+NTATTTCCCTTTTCACTGTTGCTCATTTACCTGACCGGTTGGCGGTTGGGCGGTCGCTTTCTCGGTTGGACCAGCATGCTCCACCTGGCCTCGAATTCTTTAGTCTTGCTCCATACGCGGCGGGCAATGTCGGGAAGTGGATTATTATTT\n++2242:2:1101:4098:1976/1\n+BPP`ccccgegfghfgdfhifhiihhiihiihidghhhcefhfehZeaggfgcRZZWT^_b`bacGW__``^W[`^`b]bbb`bca^```baXX[]W`b`bRYY]`SS]_YY_Y_b^a____OXTOGX_YYQTMTT^]b_GSYJSSY_b_\n+@2242:2:1101:4632:1974/1\n+NCAGCTCGGAGTCCTCCATGACCAGGTTGCGACGCGCCAGCGGGCGGCCGGACCGGTCCAGAACCAGCAGGCGGAACAGGTTGGCATCCTCTCGGCGCAGCAGGAAGAACTCGCCCCGGGGGTTGACGCCCAGAAGCTCGGAGGAGGGGG\n++2242:2:1101:4632:1974/1\n+BS\\ceeeegggggiiiiiiiiiiiiighhiiiihiiiiigggecccccccccccaaac_ccbbccccccaaccaX[]^^aYbba]`bbbbcY^T^_[TOXTGQ`GW`P^[YY^TX_aBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@2242:2:1101:4557:1998/1\n+NAGATTATAATACCTCGATAAAGTCGTGTCAATATTT'..b'feeeedd\\`bbbbcc``bcbcccc__abcbc[Y_]Y``b_]bcdcccddbb^REX_]`]Y[WP[b_]a_EHT`bc`RG]_]_\n+@2242:2:1101:5322:2499/1\n+CGGGCAATTAATCATCGGTTATTTCGATGAATACCCCTCTGGTCAAGTACCGTACCTTGGTGCTCTCATCCCCAGCCCTGTGACGTTCCCCGTTACCTATACCATCTCAGGTCTCGCTGATGATACCTACTACGTGCTTGCGTTCCTTGA\n++2242:2:1101:5322:2499/1\n+bbbeeeeeggggghiiiighiiiiiiihiiiiiihiihihhifghfigfghhghiiihhgfgfhiiigfgfgdeeabbbdcccba\\^accbaZ`_cccbbb`bbcb`bY]b_`]`bcaaXb_`Ybbb_GX_bc^BBBBBBBBBBBBBBBB\n+@2242:2:1101:5578:2289/1\n+AATTGAGGGCCTTATGGCGGCTGAGACCGGGAACAATGCTGTCGTGCCTGGCGCCATCATCCCTGCGCTCACCCTTGCCATTCCAGGCTCTGCCCCTGCCGCCGGTTTGTTAGCAGCCATGTTCATTCACCGCCTCCGGCCCCGCCCCCC\n++2242:2:1101:5578:2289/1\n+^^^aJ^c]cUc^^d]]dR[__b^Xcb[a^`cFTZ\\RZ^\\`RV^ZKT\\]RZZTX\\\\W[]]TTY\\]YQTZ]LOY[^GX[]`YS]a`BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@2242:2:1101:5564:2297/1\n+CACGAAGCCGTACAGCGGCTCGCTGAACATCCGCGCCTCGTCAGGCACCGAGCTGTTCGAGTACATCTGCCAGCAGGCGAACTACGCGCACGAGCTGATGGGCGGCGGAGCTGAGGCCGTGAGGCCAGCGCCGGGGGCGGGGGCCCGCGG\n++2242:2:1101:5564:2297/1\n+__beceeeggggghhhhhhhhU^^_cfbcXbbYb__d``NMTUKZZ\\^^YFWNKGKT]WW^RW`b_`Y]_bBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@2242:2:1101:5670:2333/1\n+CCGTCCGGTCCCAAGGCCGACTACCTGTGGCGGCTCTATGCGCCCGACCGGGCCATGCAAGCCGGCATAGACGACGTGGGAATAGGAGCCCTGTTCGGGCTGACCGACCACAAGTTCGAGGTCATGGCGGGCCTGGCGCCCGCCCAGTAT\n++2242:2:1101:5670:2333/1\n+___cacceYceggeegdgfcgfgihfh^afgegh``]bdV^[^^`NZ_aaca[a_bb``b`a_Z_aaT]Yb_OZTLEWWXWXQ]YY_RPGWGWY_]GOTTTXGR]X_]c_^^W[SSS^BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@2242:2:1101:5665:2357/1\n+GGTCAGCGAGGGCCTGACTCCCGTTCAATGCCGGGGGATCCAAGACTTGATCGAGGAAAAAGACATTCTCCTGAAAATAAAGCTCTTGAAGAAGGAGCTCCAGGAAAGCGAGGTCTAAGGTGAGAAAAACAGCTCTCATCATAATCATAC\n++2242:2:1101:5665:2357/1\n+___ceeeegggggiiiiiihhiieghiihhiiiiiiebccdcccccccccccccccaaccc[accccb`bbbc`bbbccccY_Y_bbbb`bbb]`__a[``bbccab`^_aaXEX__Y`[JSY`bc]bQEWXW]]Y`b]_SS_BBBBBBB\n+@2242:2:1101:5703:2367/1\n+GGGCATTGCACTCCTCGGGGCAAAGACCGACGGCAAGGCTCTCCTCATAGCTCTCGTGACCAGCGACCTGACAAATCGGTTTCACGCGGGCAATATCGTGAAAAGGGACGCCGAAGGTCTAGGGGGGGCCGGCGGGGGGGAGGCTGTAAC\n++2242:2:1101:5703:2367/1\n+^^_ccceaa[bgefhd]fda`egbhhhc_ce`fhhaZ\\bVZaa_``]Z]_RTZLTR^aYTY`TTWTZZ]R]bYGJSSWTJTO_YRQQEOEOOQ]`b]^BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@2242:2:1101:5687:2369/1\n+GCGCTGCCGGGTTGTTTTCATGGCTTAACGGATAACCTCATTAGCGATATTATAGCCATTCAAGCTGATTTATGCAAATATATATTTTCTTTAATCGGGTTGACAGGCTTTCAATCGAGGGGATAATACAGCCCGGCTACTCTACACCCC\n++2242:2:1101:5687:2369/1\n+__bec`cceggeeagfddeg`ebdcgffgag`_ef_cae``ff`dfhhha`\\`ZVV^ZVV`bbde`b_bZZZZRZ]R]]]b]]b]_b_`bb_b_]]GTTJQEJY_Y[GJR]_`bBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@2242:2:1101:5649:2379/1\n+AAGCCTGTGGGAGTGTCATTCCAGTCTCCTGAGCTTGAACTATGCTTCTGAAGAGGTCCGGCAAATGCTCGTCTATTGCCTTTCTCCACCTGTAATCAAGGTAGATCAGGATGGCCGGTGGAAAGGCCGCGGCGATGATTGAGAAGAAGA\n++2242:2:1101:5649:2379/1\n+abbeeeeegggggfghhiiiiiiifhiiihhfhhiihhhiiiihiiiiiiiiiihifghfhiiiggegfgecdccddddcccccccbbbccbcc`cccccc_`bcdc]`bbbb_bcccT_cabb[aa^_aa[aaa]]R]bbGS[bbcBBB\n+@2242:2:1101:5633:2394/1\n+TCGGCGTCGGTAGTTTTCGTCCCTGGTTTTGCGATGTCATGGAGCAGCGCCGCCAGCTTTAACAACACCGTTCGCGTGCTGCCGCTGCTGATTTCAGCTTCGAAGTGCTGGATCAGTCTTTCCGACCACGGCGCGGCGGGCCGGATATGT\n++2242:2:1101:5633:2394/1\n+^__cccP^cebac^[deeU^eedRc_cXZ^a[e`Z_U_``_`Rb]b\\d[a_[Za_Z_T]R]R]``^aa^TJQ[ZXOHOX^RGQXaT]RY`GSGY`YYGSGSO^W^a_Y]___Y_BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@2242:2:1101:5545:2405/1\n+CCCGATCAAACAGTCCAGATCACTGAAAATGCAGCCGGAGTAAACCATTCAGCCTTTAAATTTTCAGAAGGTGATAATATAACTCTTCTTGATCTCATAAAAGCGGCATTAATAAGTTCTCATAATAATGCTACTATTGCACTTGCGGAA\n++2242:2:1101:5545:2405/1\n+bbbeeeeeggggghiifghfhihiiiihhbghiihiiiihZeghihiiiiihiiiihhfhhiggdbgfgee_bddcddddddcccbccbcbcb`cbbdcccccc_aac_b_bbdcb_cbbccdccb`bd``bcccbcb__bcccb`_ac]\n+@2242:2:1101:5710:2454/1\n+TCCATCCGGTGGCTGAGATGCGCGGATGTTTTGCCAACGTGATGGGGCTGCCCGTGTGTCATCTCGCGCGGGCGTTGCGCGCGTTCAAGTCGCCCGCCGATATTCCTGTCGCGTGCCCAGCACACATCCGATACCACCGTCCCGTCTTTC\n++2242:2:1101:5710:2454/1\n+abbeeeeeggggghiiiieiiihiiiihdfhichhiificgiihggffeecdcc_aacaccdcbbccacXZ__cOX__ccccaOT[``_]__aacMX[XOOTX_ccbY_`V^BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n' |
| b |
| diff -r 000000000000 -r a5f56370e870 test-data/test.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test.fastq Thu Nov 12 07:05:48 2015 -0500 |
| [ |
| b'@@ -0,0 +1,10000 @@\n+@2242:2:1101:1532:1981/1\n+NTTTTTCCTTCCTTTAAAACCACTTCTTTGATCCAATCCAGAAAGCCTCTCCAATAATTTGATACCACTAAAATGACGGGGAAAGGTCTGATCTTTTTAGTCTGAATAAGCGTAAGCGATTCGAGCAGCTCCACCGTGGTCCCAAATCCA\n++\n+BP\\ccc^acebegafabfffbcag`gfb`faf]fad^^cedbeff`affhgfdcfe`^aaa\\WHW_be_f_V_dfZ^Z[a`U]aaaT]bb]Z`G]Zb`[b]``]b]]Y_YRTGWGGGHQGQ]OYb_[^aBBBBBBBBBBBBBBBBBBBBB\n+@2242:2:1101:1532:1981/2\n+ATCATCCAGCGGTGAGCATTTTAGGTTCCACACGCATTAAACCCGGTGACGAGGTCTACTCGAAGGCGGAACAAATCTGCAAACTCTTAGCCGAAAATGGCTTTGCCGTCATAACNGGAGGAGGAGCTGGGGCCATCGNNNNNGGTAGAN\n++\n+^a_cccaZJQbe[beghihigbJ[bX^^deffffYe\\f_a`dRZU_aa\\bGLT\\T_bZ_bd^`Z^ZX\\ZTTX^[[RYGS]Y]_^R_Y]]bbBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@2242:2:1101:1908:1977/1\n+NGCTGTCGGAAAAGAATTGGAGAAAAGGGATGCTCGCTACCTTGCTTTAAGCTCTCGGATTGCTGCTGAATTTGGGGCACGGAATGTAAAAACCTACTGGTGTGAGAATTTTGAGAAGGTGGTTGGTGGGTGGCCTGTTCCCGTCTGTAG\n++\n+BPYS``ca_^ceeeeehaeaXXJbfacZV_cfaebP^cUVcdXbbdeeeebebdeee^[`[ac]]a`baaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa\n+@2242:2:1101:1908:1977/2\n+GGGATGTCGGCTGATACCCCCTCACCCTCTCCCTCTCCCTCTCCCACCCAGGGGGACGGGGGTTTTAGACCAAATCCTTACTCCGAGCTTACCTTTTGCCTTTTTTTTTTNTTCANTTTCCAATATATAGTTCGCTTTNNNNNCAGATNN\n++\n+\\a_e\\cacYHOQ_YY`a^Rb___YH^bBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@2242:2:1101:2236:1971/1\n+NGTTTTTGCCGTACCAGTTCCATGCTGGTTGAAGCTGGCTTGACGCTGCCGCAATCGTTAAACGCCATTATCGGCATTATAGATAACAGCGTCATAAAGAAAGCTTTTATAGAAATCAGGCAGGATATCATCAAGAGCAGGGGGCTATGC\n++\n+BPP`accccc_c`ddhXQ`bSdd]ed_d^dcddcdXIYc`QOOXU^_[`cNZ_````^_Z^`YZ^^W\\Y]`GGWZEO]`cc`]G]````]][]^[]````^^`BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@2242:2:1101:2236:1971/2\n+TATACTTAATACAATGATTGGTATATCGAATACAGCGGCTGCATGATAGCAAGGCCGATAAAGCCGATTAACAAACCGGCAATAATAATGGAAGCCGGTTCAATCATACCNAGCANCTNGCGCCATCTTAANTCCAGCNNNNNTTNATNN\n++\n+^^Wac`ceeWeegaafffffffhh^ef_egbgefccfa`ced_fhhchS\\\\egf^efUY\\^aVZZX`ac^_]RY^X[__a_aGY]R]]`bGY]R^`_[OTW_bcbbBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@2242:2:1101:2574:1974/1\n+NGGTCGGACGTAGCTGTTACGCACGGCAACCTCGGCCAGACTGCAAAAAACATCAAGGCGCGCCAGGGCGTCGGCAACCGCCAGGACCGGCTCGCTGGCGCCGGCCACCTGACAGCCGAGCACTTTTCACAACTCACCCTCAATACACGC\n++\n+BPY\\ac`ccccacdhhhadcbPbcc`[ccccdcccccc_b`bbcccccc_U]`R]``]^NW[^^^^^^^]]]Z]XZ][^^^^]]][^]]^BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@2242:2:1101:2574:1974/2\n+AAGAACTGGACAACTTGCGGTTGACGGCAAAAAACTCAAAACAGTACCTCGCCAACCTGGAAAAACAGGAGCGAGAGCGTACGGGCATAAAGTCGTTGAAAGTCGGCTATNATCANGCCTTTGGCTACTATATTGAGGNNNNNAATGCNN\n++\n+_a_cccccceeggfd]adafegdgXbcOcegfiiUbfgh[ehficgX_Z_Z`aa`aabccccbZ^aa^`a[aaL[[[[a_^accaV_[b_b_G]_[Xb^b]__]^TT^aGBJQWQBJGJJGYSRGGY^b`c]``bbBBBBBBBBBBBBBB\n+@2242:2:1101:2599:1978/1\n+NGTTTCCTATGAGGCGGACAAGGAAAACCCGGGGGCCACCCAGTACCACAAGAACTTCAAGGATTGGCTCACCCGGTTTCAGACCGAGGATCTGGTCGGGTGCTGTGCCCAGACGGACGTCAAAGGCGATCGGATGAAGCGGCGAAGCGA\n++\n+BP\\ccceegggggihiihiiiiiiiiicfhhiiicccccccacbccccccccccbbcccccccccbccccccaaa_]aaccccbcccccccccccbcccTJO[`b`bb]^```a]accaXXWX]`[WX[]acaBBBBBBBBBBBBBBBBB\n+@2242:2:1101:2599:1978/2\n+CTCCCATGGAACGAAGACGTCGTCGAAAACCATGTAGGAGTCGCAGCTCCCCGCGTTGAAGCCCTTGGGGAAGCGCTTCCGATCCCGGTAGTTGTGCGCGGTAACCAGCTNTTTCNGCCCGTCCCCATCCCCCGGAATNNNNNAGGCGAN\n++\n+bbbeeeeegggggiihiiiiiiihiiiiiiiieihhhihdbffhiighggdgeccaccccccccccbcccaca^aaaaccccccac_aX[]`cbb^baaaca_cccc^a_BGQWWBJJW[^TWT[GRX^`^_BBBBBBBBBBBBBBBBBB\n+@2242:2:1101:3233:1997/1\n+NTAACCCCTGAGGATGTGGTTACCGGAGGCAGGCATGTAATGGAAGCGGAGATCGAGCTTTCAGAATATATTATGCCAGGCATCGCCGGCCGAGCCCTGAGCGAAGAACATGCAATAGAGACGGCAAAGCTGCTTAACCTTGTTCGTCCC\n++\n+BS\\ccccegggggghhfgihiiiiiiiiiiiiifhhihhhfhifiifiihgeece`acccccccccccddeeddbbbbccccccccccccccaccccccccccacca`^bbccbb`bbbbc_[X]a_WXRS]^__`_YY`Y___Y^_^[T\n+@2242:2:1101:3233:1997/2\n+TAAAGGATGGCGACTATGTCCAGAATAGTGAAGCAGGGTATAGACCTCTCTCTGCTTCTTTGTCATGGACAGAAAGGCATCGAGCTCACTCAGCATATACTCTTTCTTCTCGTCCAGAAAGCCATCCACTTGCATGAGGNGGTTCAGACT\n++\n+bbbeeeeegggggiiihiiiiiihiifgghfhfhiiih^cefhiiiiihihhiiiiiiiiihiiiiiigggegeede\\_`bbccccccbc`bccccbbcccccbcccc]`_[a_c^`bRYbGWXbX^bbcbbbG'..b'BB\n+@2242:2:1101:5703:2367/1\n+GGGCATTGCACTCCTCGGGGCAAAGACCGACGGCAAGGCTCTCCTCATAGCTCTCGTGACCAGCGACCTGACAAATCGGTTTCACGCGGGCAATATCGTGAAAAGGGACGCCGAAGGTCTAGGGGGGGCCGGCGGGGGGGAGGCTGTAAC\n++\n+^^_ccceaa[bgefhd]fda`egbhhhc_ce`fhhaZ\\bVZaa_``]Z]_RTZLTR^aYTY`TTWTZZ]R]bYGJSSWTJTO_YRQQEOEOOQ]`b]^BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@2242:2:1101:5703:2367/2\n+GATACCCGTCAGCTCAACTACCTTAAAGATAGTGACCGACTGTCTCGCCATCTTCAGTTCGTTGATTACACGCGTAATCCTGCCGTAAACCTAGTTCCCCTCGTTGCTGACCATCTTTTCTTCGTCTCGCAATTCAGGGCAAACACACTG\n++\n+_\\^c^cccbcg_JQQ`]aYe]fd]e_d_a[bbPY^^bf_cegWafbaZZZeV\\_ZVMHVVGL^HUZad]_Z\\FRRQ^_RZbY_BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@2242:2:1101:5687:2369/1\n+GCGCTGCCGGGTTGTTTTCATGGCTTAACGGATAACCTCATTAGCGATATTATAGCCATTCAAGCTGATTTATGCAAATATATATTTTCTTTAATCGGGTTGACAGGCTTTCAATCGAGGGGATAATACAGCCCGGCTACTCTACACCCC\n++\n+__bec`cceggeeagfddeg`ebdcgffgag`_ef_cae``ff`dfhhha`\\`ZVV^ZVV`bbde`b_bZZZZRZ]R]]]b]]b]_b_`bb_b_]]GTTJQEJY_Y[GJR]_`bBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@2242:2:1101:5687:2369/2\n+TTGTACAAGCGCACCACCTGAGGCATCATCTTCTTGGTCACCGTGCCTGAGACAATCATCACGTCTGCCTGGCGGGGGCTTGGTCGCATCACTTCCATGCCGAAACGGGAGAAATCGAAACGGCTGGCGCCGCGCGGGATCATCTCCCAG\n++\n+^ZZ`accaegeecfhhaggdeffbf[acafcgfffhhac_ccaaaffd_fgZ_cdfddghhfddgeeeebabdcc[X_c[^aa]`[aaa_R]S]_`YYY`b]MX][^_aacaccBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@2242:2:1101:5649:2379/1\n+AAGCCTGTGGGAGTGTCATTCCAGTCTCCTGAGCTTGAACTATGCTTCTGAAGAGGTCCGGCAAATGCTCGTCTATTGCCTTTCTCCACCTGTAATCAAGGTAGATCAGGATGGCCGGTGGAAAGGCCGCGGCGATGATTGAGAAGAAGA\n++\n+abbeeeeegggggfghhiiiiiiifhiiihhfhhiihhhiiiihiiiiiiiiiihifghfhiiiggegfgecdccddddcccccccbbbccbcc`cccccc_`bcdc]`bbbb_bcccT_cabb[aa^_aa[aaa]]R]bbGS[bbcBBB\n+@2242:2:1101:5649:2379/2\n+TCCTCACTGGCCCGCTGATGTTGGTGATCATGCTAACGGTAATGGCGATGCTTGGCGGAGGAGACCTTGGATTGCTCAGTCCAGACCTGTTGCTAAACATGCTCACCTACTTGGGCATTCCGTTAGGAGCAATAGTCTTCTTGATCATTC\n++\n+bbbeeeeegggggiiiihhighii^effhihhiiiiiii^egghiiihihfhhhgggccccaaaacccccccbbccccccbcccbcabbbccccY_`bb`bbccbbccbbbb_YQ[b[Y_b`b`aabbbacbbbb]bcc]S]YbRY]Y]Y\n+@2242:2:1101:5633:2394/1\n+TCGGCGTCGGTAGTTTTCGTCCCTGGTTTTGCGATGTCATGGAGCAGCGCCGCCAGCTTTAACAACACCGTTCGCGTGCTGCCGCTGCTGATTTCAGCTTCGAAGTGCTGGATCAGTCTTTCCGACCACGGCGCGGCGGGCCGGATATGT\n++\n+^__cccP^cebac^[deeU^eedRc_cXZ^a[e`Z_U_``_`Rb]b\\d[a_[Za_Z_T]R]R]``^aa^TJQ[ZXOHOX^RGQXaT]RY`GSGY`YYGSGSO^W^a_Y]___Y_BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@2242:2:1101:5633:2394/2\n+CGCATCGCCGCCGAACTGGGACTACGCATCGAAGACGATACCGAAGAGCTTATCCGCCGGTACAGCCGGCTGGTAACGACCGTCGCCGGCGAACGGGCAAGGGGAGAGCGGCAGCGGCTGCGCGCCGTCCCCCCCGCCGGCCGCCGCCGC\n++\n+ZZZacc^c``egcfh`R^cebf_ZeGVcZ`fXHT_a_TZZ\\aaab_BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@2242:2:1101:5545:2405/1\n+CCCGATCAAACAGTCCAGATCACTGAAAATGCAGCCGGAGTAAACCATTCAGCCTTTAAATTTTCAGAAGGTGATAATATAACTCTTCTTGATCTCATAAAAGCGGCATTAATAAGTTCTCATAATAATGCTACTATTGCACTTGCGGAA\n++\n+bbbeeeeeggggghiifghfhihiiiihhbghiihiiiihZeghihiiiiihiiiihhfhhiggdbgfgee_bddcddddddcccbccbcbcb`cbbdcccccc_aac_b_bbdcb_cbbccdccb`bd``bcccbcb__bcccb`_ac]\n+@2242:2:1101:5545:2405/2\n+AAGCCAGCATTTTCAGTATATCCTGTCTTTATCCCTTTTATAAATTCATATTCCAATAGTTTATTGGTATTCTCAAGAGGAATAATTTCATCATCTAATATTATATTATCAGATTTTGTACCGACTATTTCCCTAAAAAGGCTGTTTTCC\n++\n+_bbcceeeeggggihighfiihihhegiiihfffhhiiihiihiiiiiiiiiiihihfhhiiiihhhegiiiiiihifdgghhfhhfggggggeeeeeeebdeecbbdd`ccbcbbc_`cbb__]a]b_`_bbbcX]b]a^`]`[b`X_R\n+@2242:2:1101:5710:2454/1\n+TCCATCCGGTGGCTGAGATGCGCGGATGTTTTGCCAACGTGATGGGGCTGCCCGTGTGTCATCTCGCGCGGGCGTTGCGCGCGTTCAAGTCGCCCGCCGATATTCCTGTCGCGTGCCCAGCACACATCCGATACCACCGTCCCGTCTTTC\n++\n+abbeeeeeggggghiiiieiiihiiiihdfhichhiificgiihggffeecdcc_aacaccdcbbccacXZ__cOX__ccccaOT[``_]__aacMX[XOOTX_ccbY_`V^BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@2242:2:1101:5710:2454/2\n+GAATGAGTTCGAGGGTGGGAGTGCTCAAGGGTTTGCTCCTTCAAACGTATGGTAGGCGGGCATCCCGATGCCCACTGCTGGCGCATGGGGATGCGCCCGCTACCGCGACAGAAGCCAAAATATCGGCAAAGACCGGACAGTGGGATCCGA\n++\n+abbeeeedgggggih`fgiehdfghhiihih^fgiiiiihighhiiibggfhhgfffgecZ_bccccccaabbba`bbb]_^_c]a^aac^O[aa__ccaX]acacccac_bRXX[^X`^_bbbV][[Xa``GGET[aX^JSRJQY_XPW\n' |
| b |
| diff -r 000000000000 -r a5f56370e870 test-data/test.r.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test.r.fastq Thu Nov 12 07:05:48 2015 -0500 |
| [ |
| b'@@ -0,0 +1,5000 @@\n+@2242:2:1101:1532:1981/2\n+ATCATCCAGCGGTGAGCATTTTAGGTTCCACACGCATTAAACCCGGTGACGAGGTCTACTCGAAGGCGGAACAAATCTGCAAACTCTTAGCCGAAAATGGCTTTGCCGTCATAACNGGAGGAGGAGCTGGGGCCATCGNNNNNGGTAGAN\n++2242:2:1101:1532:1981/2\n+^a_cccaZJQbe[beghihigbJ[bX^^deffffYe\\f_a`dRZU_aa\\bGLT\\T_bZ_bd^`Z^ZX\\ZTTX^[[RYGS]Y]_^R_Y]]bbBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@2242:2:1101:1908:1977/2\n+GGGATGTCGGCTGATACCCCCTCACCCTCTCCCTCTCCCTCTCCCACCCAGGGGGACGGGGGTTTTAGACCAAATCCTTACTCCGAGCTTACCTTTTGCCTTTTTTTTTTNTTCANTTTCCAATATATAGTTCGCTTTNNNNNCAGATNN\n++2242:2:1101:1908:1977/2\n+\\a_e\\cacYHOQ_YY`a^Rb___YH^bBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@2242:2:1101:2236:1971/2\n+TATACTTAATACAATGATTGGTATATCGAATACAGCGGCTGCATGATAGCAAGGCCGATAAAGCCGATTAACAAACCGGCAATAATAATGGAAGCCGGTTCAATCATACCNAGCANCTNGCGCCATCTTAANTCCAGCNNNNNTTNATNN\n++2242:2:1101:2236:1971/2\n+^^Wac`ceeWeegaafffffffhh^ef_egbgefccfa`ced_fhhchS\\\\egf^efUY\\^aVZZX`ac^_]RY^X[__a_aGY]R]]`bGY]R^`_[OTW_bcbbBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@2242:2:1101:2574:1974/2\n+AAGAACTGGACAACTTGCGGTTGACGGCAAAAAACTCAAAACAGTACCTCGCCAACCTGGAAAAACAGGAGCGAGAGCGTACGGGCATAAAGTCGTTGAAAGTCGGCTATNATCANGCCTTTGGCTACTATATTGAGGNNNNNAATGCNN\n++2242:2:1101:2574:1974/2\n+_a_cccccceeggfd]adafegdgXbcOcegfiiUbfgh[ehficgX_Z_Z`aa`aabccccbZ^aa^`a[aaL[[[[a_^accaV_[b_b_G]_[Xb^b]__]^TT^aGBJQWQBJGJJGYSRGGY^b`c]``bbBBBBBBBBBBBBBB\n+@2242:2:1101:2599:1978/2\n+CTCCCATGGAACGAAGACGTCGTCGAAAACCATGTAGGAGTCGCAGCTCCCCGCGTTGAAGCCCTTGGGGAAGCGCTTCCGATCCCGGTAGTTGTGCGCGGTAACCAGCTNTTTCNGCCCGTCCCCATCCCCCGGAATNNNNNAGGCGAN\n++2242:2:1101:2599:1978/2\n+bbbeeeeegggggiihiiiiiiihiiiiiiiieihhhihdbffhiighggdgeccaccccccccccbcccaca^aaaaccccccac_aX[]`cbb^baaaca_cccc^a_BGQWWBJJW[^TWT[GRX^`^_BBBBBBBBBBBBBBBBBB\n+@2242:2:1101:3233:1997/2\n+TAAAGGATGGCGACTATGTCCAGAATAGTGAAGCAGGGTATAGACCTCTCTCTGCTTCTTTGTCATGGACAGAAAGGCATCGAGCTCACTCAGCATATACTCTTTCTTCTCGTCCAGAAAGCCATCCACTTGCATGAGGNGGTTCAGACT\n++2242:2:1101:3233:1997/2\n+bbbeeeeegggggiiihiiiiiihiifgghfhfhiiih^cefhiiiiihihhiiiiiiiiihiiiiiigggegeede\\_`bbccccccbc`bccccbbcccccbcccc]`_[a_c^`bRYbGWXbX^bbcbbbGS]b`^BJWGJ[``__]\n+@2242:2:1101:3494:1987/2\n+CCGTTGAATTCGCGAACTTGCCGGCCGGGCTGAAGTTCCAGGTGTAGACCGTCCGGGCCACCCGATAAAAATAGTTCGGGGACATGATATCATATTTCAGGAACTGATAGCTCAAGTAGAAATCGACGAAGGCGAAATCNNNNATGACAN\n++2242:2:1101:3494:1987/2\n+___`ccccce[eeddf`bddffY_egfgehff_VV^d_\\MM^VZ_ab`_ZRRXW\\_NVT[W[TTTLW[bbc[Y`S]`WTTXTEWYGJ]``BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@2242:2:1101:3624:1977/2\n+CTACGCTAATTGTTGAAAAAATTAAAGGAGGTCAATGAAAATGGATATAGGAACGATAATTATCATAGTGATTCTGGCAATTGTGGTACTAGTTACTCTTAAAAAGTCGGNAACCNTTATCCGCCAGGCCGAGAAGGGNNNNNTGGAGNN\n++2242:2:1101:3624:1977/2\n+___cecececgggiidgfdh]_ffeeffhfdbeegadgfbfffgbghhhh_fhiiihfhhhhiggcge`dd__ceeedcdcbdcccZT``cc__bc_bbbccb_]abb[]BJJJWBJQWO[`V^aa]^acVOXX_bBBBBBBBBBBBBBB\n+@2242:2:1101:4155:1969/2\n+GGTAAGATTCCATATCAGCCAGCTGTCCACTGTTCCGAACAGCAGGTCGCCCCTCCGGGCGCGTTCCTGTCCGTCCGGGGTGGTATTCAGTAGCCAGCGAATCTTTTTTGNTGAGNAGNAGGCAGCTATAANTAGACCNNNNNTGNGGNN\n++2242:2:1101:4155:1969/2\n+a_YaccZcgacggde]aeXecY[gcggfdg`eggI^^OWbeghdfaOX^UZ_e^_`Z`daBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@2242:2:1101:4098:1976/2\n+ATTGGTCTGCCGGACAAGCAATTCCTGGCGAACTTTCAACGCTGCTTGAAGCGCATTCAAGGAGTCTGTCCAAATAATTGGATTCAGCAAAATGAAAATTGTAAAGAATCNTGCCNCAAATCTGGCTGTTTGTCCGACNNNNNATCTCNN\n++2242:2:1101:4098:1976/2\n+___cacececgggdgadgffhfgfbghiihgchicgbaeghhiiihfhddgec^`a`dddcc`abbccccccbccbcddcb_b`_`bcbX^bccbbbcc`bbbbccb`b]BJW^_BJWGWWbbcb`^^GY_bcbbBBBBBBBBBBBBBBB\n+@2242:2:1101:4632:1974/2\n+CCCGCCGGGGCCCTGCAGCACCAGCTCACCCTGGAGCCGGCCAGCCTGCCCCCCCTGGCCGAAGCCCCCGCCGCCACCCCCTCGCTGGGCAGGCTGGTTCCGGATCTGGANCGGCNCATCCTCTACGCCGTGCTGTACNNNNNTGATCNN\n++2242:2:1101:4632:1974/2\n+bbbeeeeegggggiiihiiiiiiiiiihiiihhhghfhhfeecccccccc^acccc_accaZacaccccccca]a[[acccT[X]WT[^[GX_XW[]^bY_BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@2242:2:1101:4557:1998/2\n+TTGAATACCATGAGTACTCGCGGACCCTTCTCGCTTC'..b'cQWZaccccaccabG]bbbcbbbcb_]bY_acaac[W`YSSGJ]]_`Y]GJY`_[`bb`c_`ba`JGQQ^aBBBBBBBBBBB\n+@2242:2:1101:5322:2499/2\n+TTTTGTTGGTGGGTTGGTTGTTGCAAAGTATACATCGTAGGTGACGGTGTCACCTGCATCTGGGTCTCCTCCAATCCAGCTGAGATCAGTGTTGATTGACACATCCGTTGCACCATCTGGTGGGAGAGGGGCATGCGGTTCATACGGTGG\n++2242:2:1101:5322:2499/2\n+abbeeceeg`eggbeghegiiihhfhiiegihihihhiiii^eghihfffdghggegdggdceebddbbddcb^bcccccbbcccbcccbcb_^bbcbbbbbX`bcaGSW_`bc[Y^bbb]XOEQWOW^aETTX[___OM[bYY_^^BBB\n+@2242:2:1101:5578:2289/2\n+ACACGAGACCCCGCCGCAGATTCTTATCCATGAGGTCGCCGAGGATGATCCCGAGTACCAGGGGAGCCATCGGATATTTCATCTGTCGGCGGATGTACCCGATGATCGCGAAACCGATCATCACGTAGCTGTCGAAGAGCGTGCTGCTAA\n++2242:2:1101:5578:2289/2\n+\\WY``WOH[QbZ_H[dOOYYXIOOOIX^adbacR\\HWFae_`[`c_]T_ZTKZFKGGT]`Y[T[a_aWXRRWHW^TSR]_BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@2242:2:1101:5564:2297/2\n+ATGCAGCTGACGTCCGTCGCCCAGCTCGTACCACGCCCCCGCGAAGGGAAACGCCGGCCGATCGACTTCCCGCAGGCCAAGCACCTCTCCGTAGAAACGCTTCGATCGGGCGATGTCTCTGACGCAGACCGCGACGTGATGGAGCGAGGG\n++2242:2:1101:5564:2297/2\n+___eeeeegfgggiiiegfiiihiiiiigghiiihhiiiiigecacccccccccccaccca_ca_acccccaca_accaaa^^^```_^]TQ[^^b`]VXW^[[acaOX_XMETXW_`bb]Y_X]][_^BBBBBBBBBBBBBBBBBBBBB\n+@2242:2:1101:5670:2333/2\n+CCGAAAGGGTGCGCTCGTCGCCGATGGAGAACTGCTCGGCCTGGGGCTGGGGAGCTTTGGCGTCATGGTAGCCGCCGGGCGAGGTGCGCGATCCGGCACTGATCTGTGCGACGCCCAGGGCCATCAACTCGTTTCTCAACCGCGGCCCTT\n++2242:2:1101:5670:2333/2\n+^_^acc^caQ`ccehhidfb[eghhhffdghcggdffdfgN\\`aac_bc_PZ\\WRX`bbb`[TZT^]bY`bbcBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@2242:2:1101:5665:2357/2\n+CTTTGTAGAGCTCGTAGGCCAGGTCGATGATAGAGGACTCCGCCTGCTCGGCCAGGCTGTCGTTTCTCCCCTTGACCGAAAGATACTCCTTGTAGGCCTCAATGGCTTCTTCCTCATGGCCCTTCCGCCGGGTCAGACACTCCTCCCTGT\n++2242:2:1101:5665:2357/2\n+a__eecdegggcgdddghhhiii`eghffihihiiihiffhhhifhiiihffgihggdgaeedccddbdcab^b_bbcY][acbccc_^`Y`b]_`]b_abbbbbcXPXY`bcRYJSJY[`a[RGXTT^BBBBBBBBBBBBBBBBBBBBB\n+@2242:2:1101:5703:2367/2\n+GATACCCGTCAGCTCAACTACCTTAAAGATAGTGACCGACTGTCTCGCCATCTTCAGTTCGTTGATTACACGCGTAATCCTGCCGTAAACCTAGTTCCCCTCGTTGCTGACCATCTTTTCTTCGTCTCGCAATTCAGGGCAAACACACTG\n++2242:2:1101:5703:2367/2\n+_\\^c^cccbcg_JQQ`]aYe]fd]e_d_a[bbPY^^bf_cegWafbaZZZeV\\_ZVMHVVGL^HUZad]_Z\\FRRQ^_RZbY_BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@2242:2:1101:5687:2369/2\n+TTGTACAAGCGCACCACCTGAGGCATCATCTTCTTGGTCACCGTGCCTGAGACAATCATCACGTCTGCCTGGCGGGGGCTTGGTCGCATCACTTCCATGCCGAAACGGGAGAAATCGAAACGGCTGGCGCCGCGCGGGATCATCTCCCAG\n++2242:2:1101:5687:2369/2\n+^ZZ`accaegeecfhhaggdeffbf[acafcgfffhhac_ccaaaffd_fgZ_cdfddghhfddgeeeebabdcc[X_c[^aa]`[aaa_R]S]_`YYY`b]MX][^_aacaccBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@2242:2:1101:5649:2379/2\n+TCCTCACTGGCCCGCTGATGTTGGTGATCATGCTAACGGTAATGGCGATGCTTGGCGGAGGAGACCTTGGATTGCTCAGTCCAGACCTGTTGCTAAACATGCTCACCTACTTGGGCATTCCGTTAGGAGCAATAGTCTTCTTGATCATTC\n++2242:2:1101:5649:2379/2\n+bbbeeeeegggggiiiihhighii^effhihhiiiiiii^egghiiihihfhhhgggccccaaaacccccccbbccccccbcccbcabbbccccY_`bb`bbccbbccbbbb_YQ[b[Y_b`b`aabbbacbbbb]bcc]S]YbRY]Y]Y\n+@2242:2:1101:5633:2394/2\n+CGCATCGCCGCCGAACTGGGACTACGCATCGAAGACGATACCGAAGAGCTTATCCGCCGGTACAGCCGGCTGGTAACGACCGTCGCCGGCGAACGGGCAAGGGGAGAGCGGCAGCGGCTGCGCGCCGTCCCCCCCGCCGGCCGCCGCCGC\n++2242:2:1101:5633:2394/2\n+ZZZacc^c``egcfh`R^cebf_ZeGVcZ`fXHT_a_TZZ\\aaab_BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@2242:2:1101:5545:2405/2\n+AAGCCAGCATTTTCAGTATATCCTGTCTTTATCCCTTTTATAAATTCATATTCCAATAGTTTATTGGTATTCTCAAGAGGAATAATTTCATCATCTAATATTATATTATCAGATTTTGTACCGACTATTTCCCTAAAAAGGCTGTTTTCC\n++2242:2:1101:5545:2405/2\n+_bbcceeeeggggihighfiihihhegiiihfffhhiiihiihiiiiiiiiiiihihfhhiiiihhhegiiiiiihifdgghhfhhfggggggeeeeeeebdeecbbdd`ccbcbbc_`cbb__]a]b_`_bbbcX]b]a^`]`[b`X_R\n+@2242:2:1101:5710:2454/2\n+GAATGAGTTCGAGGGTGGGAGTGCTCAAGGGTTTGCTCCTTCAAACGTATGGTAGGCGGGCATCCCGATGCCCACTGCTGGCGCATGGGGATGCGCCCGCTACCGCGACAGAAGCCAAAATATCGGCAAAGACCGGACAGTGGGATCCGA\n++2242:2:1101:5710:2454/2\n+abbeeeedgggggih`fgiehdfghhiihih^fgiiiiihighhiiibggfhhgfffgecZ_bccccccaabbba`bbb]_^_c]a^aac^O[aa__ccaX]acacccac_bRXX[^X`^_bbbV][[Xa``GGET[aX^JSRJQY_XPW\n' |
| b |
| diff -r 000000000000 -r a5f56370e870 tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Thu Nov 12 07:05:48 2015 -0500 |
| b |
| @@ -0,0 +1,29 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="zlib" version="1.2.8"> + <repository changeset_revision="63a4a902cda2" name="package_zlib_1_2_8" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> + <package name="sickle" version="1.33"> + <install version="1.0"> + <actions> + <action target_filename="sickle-1.33.tar.gz" type="download_by_url">https://github.com/najoshi/sickle/archive/v1.33.tar.gz</action> + <action type="set_environment_for_install"> + <repository changeset_revision="63a4a902cda2" name="package_zlib_1_2_8" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu"> + <package name="zlib" version="1.2.8" /> + </repository> + </action> + <action type="shell_command">make</action> + <action type="move_file"> + <source>sickle</source> + <destination>$INSTALL_DIR/bin</destination> + </action> + <action type="set_environment"> + <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable> + </action> + </actions> + </install> + <readme> +Sickle is a windowed adaptive trimming tool for FASTQ files using quality. + </readme> + </package> +</tool_dependency> |