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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 |
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added:
barcode_splitter.xml test-data/barcode_splitter1.fastq test-data/barcode_splitter_barcodes.txt test-data/barcode_splitter_barcodes_dual.txt test-data/barcode_splitter_index.fastq test-data/barcode_splitter_index_2.fastq test-data/test_1_BC1-read-1.out test-data/test_1_BC2-read-1.out test-data/test_1_BC3-read-1.out test-data/test_1_BC4-read-1.out test-data/test_1_error.out test-data/test_1_multimatched-read-1.out test-data/test_1_summary.out test-data/test_1_unmatched-read-1.out test-data/test_2_BC1-read-1.fastq test-data/test_2_BC1_index1.fastq test-data/test_2_BC1_index2.fastq test-data/test_2_BC2-read-1.fastq test-data/test_2_BC2_index1.fastq test-data/test_2_BC2_index2.fastq test-data/test_2_BC3-read-1.fastq test-data/test_2_BC3_index1.fastq test-data/test_2_BC3_index2.fastq test-data/test_2_BC4-read-1.fastq test-data/test_2_BC4_index1.fastq test-data/test_2_BC4_index2.fastq test-data/test_2_multimatched-read-1.fastq test-data/test_2_multimatched_index1.fastq test-data/test_2_multimatched_index2.fastq test-data/test_2_summary.out test-data/test_2_unmatched-read-1.fastq test-data/test_2_unmatched_index1.fastq test-data/test_2_unmatched_index2.fastq test-data/test_3_BC1-forward.fastq test-data/test_3_BC1-reverse.fastq test-data/test_3_BC2-forward.fastq test-data/test_3_BC2-reverse.fastq test-data/test_3_BC3-forward.fastq test-data/test_3_BC3-reverse.fastq test-data/test_3_BC4-forward.fastq test-data/test_3_BC4-reverse.fastq test-data/test_3_multimatched-forward.fastq test-data/test_3_multimatched-reverse.fastq test-data/test_3_unmatched-forward.fastq test-data/test_3_unmatched-reverse.fastq test-data/test_5_BC4-read-1.out test-data/test_5_summary.out test-data/test_5_unmatched-read-1.out test-data/test_6_BC1_index2.fastq test-data/test_6_BC1_read1.fastq test-data/test_6_BC1_read2.fastq test-data/test_6_BC2_index2.fastq test-data/test_6_BC2_read1.fastq test-data/test_6_BC2_read2.fastq test-data/test_6_BC3_index2.fastq test-data/test_6_BC3_read1.fastq test-data/test_6_BC3_read2.fastq test-data/test_6_BC4_index2.fastq test-data/test_6_BC4_read1.fastq test-data/test_6_BC4_read2.fastq test-data/test_6_multimatched_index2.fastq test-data/test_6_multimatched_read1.fastq test-data/test_6_multimatched_read2.fastq test-data/test_6_summary.out test-data/test_6_unmatched_index2.fastq test-data/test_6_unmatched_read1.fastq test-data/test_6_unmatched_read2.fastq |
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| diff -r 000000000000 -r ff12d2c1f5d6 barcode_splitter.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/barcode_splitter.xml Wed May 29 10:24:27 2019 -0400 |
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| b'@@ -0,0 +1,795 @@\n+<tool id="barcode_splitter" name="Barcode Splitter" version="0.18.4.0">\n+ <description>Split sequence files using multiple sets of barcodes</description>\n+ <requirements>\n+ <requirement type="package" version="0.18.4">barcode_splitter</requirement>\n+ </requirements>\n+ <version_command>barcode_splitter --version</version_command>\n+ <command detect_errors="exit_code">\n+ <![CDATA[\n+ mkdir split &&\n+ barcode_splitter\n+\n+ --bcfile \'$bcfile\' --mismatches \'$mismatches\' --galaxy $barcodes_at_end --prefix \'split/\'\n+\n+ #set $auto_split_all = $split_all\n+ #set $format = ""\n+ #set $paired_match = "0"\n+ #set $num_index_files = 0\n+\n+ #if str($runinterface.run_type) == "flexible":\n+\n+ ## Determine the format based on the first input file\'s extension\n+ ## #for $indf in $runinterface.seqfiles\n+ ## #set $format = $indf.input.extension\n+ ## #break\n+ ## #end for\n+ #set $format = $runinterface.seqfiles[0].input.extension\n+\n+ ## Add the sequence files, count the number of forward, reverse, and other non-index read names, and auto-set split_all\n+ #set $numforwards = 0\n+ #set $numreverses = 0\n+ #for $sf in $runinterface.seqfiles\n+ #if str($sf.nameinterface.readtype) == "forward" or str($sf.nameinterface.readtype) == "forwardindex":\n+ #set $numforwards += 1\n+ #elif str($sf.nameinterface.readtype) == "reverse" or str($sf.nameinterface.readtype) == "reverseindex":\n+ #set $numreverses += 1\n+ #end if\n+ #if str($sf.nameinterface.readtype) == "singleindex" or str($sf.nameinterface.readtype) == "forwardindex" or str($sf.nameinterface.readtype) == "reverseindex":\n+ #set $auto_split_all = "--split_all"\n+ #end if\n+ \'${sf.input}\'\n+ #end for\n+\n+ ## Determine whether valid paired-end data exists\n+ #if $numforwards == 1 and $numreverses == 1:\n+ #set $paired_match = "1"\n+ #end if\n+\n+ ##Add the relative file argument positions of the index files in the list included above\n+ --idxread\n+ #set $n = 0\n+ #for $sf in $runinterface.seqfiles\n+ #set $n += 1\n+ #if str($sf.nameinterface.readtype) == \'index\' or str($sf.nameinterface.readtype) == "singleindex" or str($sf.nameinterface.readtype) == "forwardindex" or str($sf.nameinterface.readtype) == "reverseindex":\n+ #set $num_index_files += 1\n+ \'${n}\'\n+ #end if\n+ #end for\n+\n+ #elif str($runinterface.run_type) == "single":\n+\n+ #set $format = $runinterface.snglinput.extension\n+\n+ ## Add the sequence files\n+ \'${runinterface.snglinput}\'\n+ #for $sf in $runinterface.idxfiles\n+ \'${sf.idxinput}\'\n+ #end for\n+\n+ ##Add the relative file argument positions of the index files\n+ --idxread\n+ #set $n = 1\n+ #for $sf in $runinterface.idxfiles\n+ #set $num_index_files += 1\n+ #set $n += 1\n+ \'${n}\'\n+ #end for\n+\n+ #elif str($runinterface.run_type) == "paired":\n+\n+ #set $format = $runinterface.fwdinput.extension\n+ #set $paired_match = "1"\n+\n+ ## Add the sequence files\n+ \'${runinterface.fwdinput}\' \'${runinterface.revinput}\'\n+ #for $sf in $runinterface.idxfiles\n+ \'${sf.idxinput}\'\n+ #'..b'ntified. Ignoring multimatched and error states for the moment, the following 4 rows are possible, but only those with counts greater than 0 will be included in the summary table:\n+\n+ unmatched\tunmatched\tunmatched\t1\n+ unmatched\tmatched\tunmatched\t2\n+ unmatched\tunmatched\tmatched\t3\n+ unmatched\tmatched\tmatched\t4\n+\n+The first column is the ID, which is \'unmatched\' in all cases (except the error row). Here\'s what each row means in the above example:\n+\n+ 1. For 1 read group, neither of the index sequences matched any barcodes in either barcode column.\n+ 2. For 2 read groups, a barcode in the first barcode column matched but none from the second were matched.\n+ 3. For 3 read groups, no barcodes in the first column matched but a barcode in the second barcode column did match.\n+ 4. For 4 read groups, a barcode from each column matched, but they were not in the same row.\n+\n+If you encounter large counts in case 4, then barcodes are likely not paired correctly in the barcodes file.\n+\n+Two other states can also be reported: multimatched & error. Read groups with \'multimatch\' in one or more columns means that with the allowed number of mismatches, the affected index read can match multiple barcodes in the corresponding column. A multimatch will only be reported if the number of mismatches in the 2 matched barcodes are the same. If they are different, barcode_splitter will assign the read group to the better match. If you have any multimatch barcodes or barcode collision warnings, then the barcode design should be improved. The number of differences between any pair of barcodes in a single column should be greater than double the number of allowed mismatches, or else you may end up with numerous multimatch scenarios. A match in another barcode column will not resolve a multimatch in a different column.\n+\n+**Barcode file Format**\n+\n+Barcode files are simple text files.\n+Each line should contain an identifier (descriptive name for the barcode), and at least 1 barcode, separated by TAB characters. Multiple columns of barcodes are supported (each corresponding to a separate barcoded read file), though there\'s usually just 1. An example of the usage of multiple sets of barcodes could be the first set of barcodes can denote user and the second set can be each user\'s sample barcodes.\n+Example::\n+\n+ #This line is a comment (starts with a \'number\' sign)\n+ BC1\tGATCT\tTTGCAT\n+ BC2\tATCGT\tGCGCAT\n+ BC3\tGTGAT\tAGGTCA\n+ BC4\tTGTCT\tCTTTGG\n+\n+For each barcode, a new FASTQ file will be created (with the barcodes\' identifier as part of the file name).\n+Sequences matching the barcodes in a row will be stored in the appropriate file.\n+\n+The first sequence file submitted must contain sequences with the barcodes in the first column of the barcode file. The second sequence file must contain sequences with the barcodes in the second column, and so on. The Number of Index Files supplied must match the number of actual columns in the barcode file and the order in which they are supplied must match the order of the barcode columns as well.\n+\n+As many as 2 additional FASTQ output files will be created for each read/index file: the \'unmatched\' file and the \'multimatched\' file, where sequences not matching any barcode or matching more than 1 barcode (when mismatches are taken into account) will be stored.\n+\n+The output of this tool is a summary table displaying the split counts for each barcode identifier and the percentage of the total reads those represent.\n+In addition, each FASTQ file produced will be loaded into the galaxy history as part of a collection list.\n+ ]]>\n+ </help>\n+ <citations>\n+ <citation type="bibtex">\n+ @misc{paired_sequence_utils,\n+ title = {{Barcode}-{Splitter}},\n+ url = {https://bitbucket.org/princeton_genomics/barcode_splitter/},\n+ author = "Parsons, Lance and Leach, Robert"\n+ }\n+ </citation>\n+ </citations>\n+</tool>\n' |
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| diff -r 000000000000 -r ff12d2c1f5d6 test-data/barcode_splitter1.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/barcode_splitter1.fastq Wed May 29 10:24:27 2019 -0400 |
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| @@ -0,0 +1,168 @@ +@CSHL_3_FC042AGLLWW:1:2:7:203 +GATCTAGTAGTAGTAGA ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +GATCTAGTAGTAGTAGA ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +GATCTAGTAGTAGTAGA ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +GATCTAGTAGTAGTAGA ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +GATCTAGTAGTAGTAGA ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGTCTAGTAGTAGTAGA ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGTCTTCTCTATGTACA ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGTCTGAGTATACACAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGTATTCTCTATGTACA ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGTATTCTCTATGTACA ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGTATTCTCTATGTACA ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGTACGAGTATACACAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGTACTCTCTATGTACA ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGTACGAGTATACACAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +ATCGTTCTCTATGTACA ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +ATCGTGAGTATACACAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +ATCGTTCTCTATGTACA ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +ATCGTGAGTATACACAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +ATCTTTCTCTATGTACA ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +ATCTTGAGTATACACAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +ATCTTGAGTATACACAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +ATCTTTCTCTATGTACA ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +ATCTCGAGTATACACAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +ATCTCGAGTATACACAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +ATCTCTCTCTATGTACA ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +ATCTCGAGTATACACAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGAATGAGTATACACAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGAATTCTCTATGTACA ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGAATGAGTATACACAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGAATTCTCTATGTACA ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGAATGAGTATACACAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGAATTCTCTATGTACA ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGAATGAGTATACACAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGAATTCTCTATGTACA ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGAATGAGTATACACAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +TAGTTGAGTATACACAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +TAGTTGAGTATACACAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +TAGTTTCTCTATGTACA ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +TAGTTTCTCTATGTACA ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +TAGTTGAGTATACACAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203/1 +TAGTTTCTCTATGTACA ++CSHL_3_FC042AGLLWW:1:2:7:203/1 +aab^V^aU]`aa^aZaa +@HWI-X00000:2:000000000-XXXXX:1:1117:19643:1028 1:N:0: +TGTCTGAGTATACACAT ++HWI-X00000:2:000000000-XXXXX:1:1117:19643:1028 1:N:0: +aab^V^aU]`aa^aZaa |
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| diff -r 000000000000 -r ff12d2c1f5d6 test-data/barcode_splitter_barcodes.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/barcode_splitter_barcodes.txt Wed May 29 10:24:27 2019 -0400 |
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| @@ -0,0 +1,4 @@ +BC1 GATCT +BC2 ATCGT +BC3 GTGAT +BC4 TGTCT \ No newline at end of file |
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| diff -r 000000000000 -r ff12d2c1f5d6 test-data/barcode_splitter_barcodes_dual.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/barcode_splitter_barcodes_dual.txt Wed May 29 10:24:27 2019 -0400 |
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| @@ -0,0 +1,4 @@ +BC1 GATCT GATC +BC2 ATCGT ATCG +BC3 GTGAT GTGA +BC4 TGTCT TGTC |
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| diff -r 000000000000 -r ff12d2c1f5d6 test-data/barcode_splitter_index.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/barcode_splitter_index.fastq Wed May 29 10:24:27 2019 -0400 |
| b |
| @@ -0,0 +1,168 @@ +@CSHL_3_FC042AGLLWW:1:2:7:203 +GATCT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +GATCT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +GATCT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +GATCT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +GATCT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGTCT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGTCT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGTCT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGTAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGTAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGTAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGTAC ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGTAC ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGTAC ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +ATCGT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +ATCGT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +ATCGT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +ATCGT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +ATCTT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +ATCTT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +ATCTT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +ATCTT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +ATCTC ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +ATCTC ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +ATCTC ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +ATCTC ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGAAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGAAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGAAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGAAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGAAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGAAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGAAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGAAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGAAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +TAGTT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +TAGTT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +TAGTT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +TAGTT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +TAGTT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203/2 +TAGTT ++CSHL_3_FC042AGLLWW:1:2:7:203/2 +aab^V +@HWI-X00000:2:000000000-XXXXX:1:1117:19643:1028 3:N:0: +TGTCT ++HWI-X00000:2:000000000-XXXXX:1:1117:19643:1028 3:N:0: +aab^V |
| b |
| diff -r 000000000000 -r ff12d2c1f5d6 test-data/barcode_splitter_index_2.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/barcode_splitter_index_2.fastq Wed May 29 10:24:27 2019 -0400 |
| b |
| @@ -0,0 +1,168 @@ +@CSHL_3_FC042AGLLWW:1:2:7:203 +GATCT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +GATCT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +GATCT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +GATCT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +GATCT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGTCT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGTCT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGTCT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGTAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGTAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGTAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGTAC ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGTAC ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGTAC ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +ATCGT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +ATCGT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +ATCGT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +ATCGT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +ATCTT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +ATCTT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +ATCTT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +ATCTT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +ATCTC ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +ATCTC ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +ATCTC ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +ATCTC ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGAAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGAAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGAAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGAAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGAAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGAAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGAAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGAAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGAAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +TAGTT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +TAGTT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +TAGTT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +TAGTT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +TAGTT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203/2 +TAGTT ++CSHL_3_FC042AGLLWW:1:2:7:203/2 +aab^V +@HWI-X00000:2:000000000-XXXXX:1:1117:19643:1028 4:N:0: +TGTCT ++HWI-X00000:2:000000000-XXXXX:1:1117:19643:1028 4:N:0: +aab^V |
| b |
| diff -r 000000000000 -r ff12d2c1f5d6 test-data/test_1_BC1-read-1.out --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_1_BC1-read-1.out Wed May 29 10:24:27 2019 -0400 |
| b |
| @@ -0,0 +1,20 @@ +@CSHL_3_FC042AGLLWW:1:2:7:203 +GATCTAGTAGTAGTAGA ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +GATCTAGTAGTAGTAGA ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +GATCTAGTAGTAGTAGA ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +GATCTAGTAGTAGTAGA ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +GATCTAGTAGTAGTAGA ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa |
| b |
| diff -r 000000000000 -r ff12d2c1f5d6 test-data/test_1_BC2-read-1.out --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_1_BC2-read-1.out Wed May 29 10:24:27 2019 -0400 |
| b |
| @@ -0,0 +1,48 @@ +@CSHL_3_FC042AGLLWW:1:2:7:203 +ATCGTTCTCTATGTACA ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +ATCGTGAGTATACACAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +ATCGTTCTCTATGTACA ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +ATCGTGAGTATACACAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +ATCTTTCTCTATGTACA ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +ATCTTGAGTATACACAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +ATCTTGAGTATACACAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +ATCTTTCTCTATGTACA ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +ATCTCGAGTATACACAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +ATCTCGAGTATACACAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +ATCTCTCTCTATGTACA ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +ATCTCGAGTATACACAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa |
| b |
| diff -r 000000000000 -r ff12d2c1f5d6 test-data/test_1_BC3-read-1.out --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_1_BC3-read-1.out Wed May 29 10:24:27 2019 -0400 |
| b |
| @@ -0,0 +1,36 @@ +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGAATGAGTATACACAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGAATTCTCTATGTACA ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGAATGAGTATACACAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGAATTCTCTATGTACA ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGAATGAGTATACACAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGAATTCTCTATGTACA ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGAATGAGTATACACAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGAATTCTCTATGTACA ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGAATGAGTATACACAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa |
| b |
| diff -r 000000000000 -r ff12d2c1f5d6 test-data/test_1_error.out --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_1_error.out Wed May 29 10:24:27 2019 -0400 |
| b |
| @@ -0,0 +1,6 @@ +WARNING: More than one barcode matches @CSHL_3_FC042AGLLWW:1:2:7:203, moving to multimatched category +WARNING: More than one barcode matches @CSHL_3_FC042AGLLWW:1:2:7:203, moving to multimatched category +WARNING: More than one barcode matches @CSHL_3_FC042AGLLWW:1:2:7:203, moving to multimatched category +WARNING: More than one barcode matches @CSHL_3_FC042AGLLWW:1:2:7:203, moving to multimatched category +WARNING: More than one barcode matches @CSHL_3_FC042AGLLWW:1:2:7:203, moving to multimatched category +WARNING: More than one barcode matches @CSHL_3_FC042AGLLWW:1:2:7:203, moving to multimatched category |
| b |
| diff -r 000000000000 -r ff12d2c1f5d6 test-data/test_1_multimatched-read-1.out --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_1_multimatched-read-1.out Wed May 29 10:24:27 2019 -0400 |
| b |
| @@ -0,0 +1,24 @@ +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGTCTAGTAGTAGTAGA ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGTCTTCTCTATGTACA ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGTCTGAGTATACACAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGTATTCTCTATGTACA ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGTATTCTCTATGTACA ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGTATTCTCTATGTACA ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa |
| b |
| diff -r 000000000000 -r ff12d2c1f5d6 test-data/test_1_summary.out --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_1_summary.out Wed May 29 10:24:27 2019 -0400 |
| b |
| @@ -0,0 +1,8 @@ +Sample Barcode1 Count Percent Files +BC1 GATCT 5 11.90% split/BC1-read-*.fastq +BC2 ATCGT 12 28.57% split/BC2-read-*.fastq +BC3 GTGAT 9 21.43% split/BC3-read-*.fastq +BC4 TGTCT 0 0.00% split/BC4-read-*.fastq +multimatched multimatched 6 14.29% split/multimatched-read-*.fastq +unmatched unmatched 8 19.05% split/unmatched-read-*.fastq +ERRORS NA 2 4.76% STDERR |
| b |
| diff -r 000000000000 -r ff12d2c1f5d6 test-data/test_1_unmatched-read-1.out --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_1_unmatched-read-1.out Wed May 29 10:24:27 2019 -0400 |
| b |
| @@ -0,0 +1,32 @@ +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGTACGAGTATACACAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGTACTCTCTATGTACA ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGTACGAGTATACACAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +TAGTTGAGTATACACAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +TAGTTGAGTATACACAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +TAGTTTCTCTATGTACA ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +TAGTTTCTCTATGTACA ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +TAGTTGAGTATACACAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa |
| b |
| diff -r 000000000000 -r ff12d2c1f5d6 test-data/test_2_BC1-read-1.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_2_BC1-read-1.fastq Wed May 29 10:24:27 2019 -0400 |
| b |
| @@ -0,0 +1,20 @@ +@CSHL_3_FC042AGLLWW:1:2:7:203 +GATCTAGTAGTAGTAGA ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +GATCTAGTAGTAGTAGA ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +GATCTAGTAGTAGTAGA ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +GATCTAGTAGTAGTAGA ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +GATCTAGTAGTAGTAGA ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa |
| b |
| diff -r 000000000000 -r ff12d2c1f5d6 test-data/test_2_BC1_index1.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_2_BC1_index1.fastq Wed May 29 10:24:27 2019 -0400 |
| b |
| @@ -0,0 +1,20 @@ +@CSHL_3_FC042AGLLWW:1:2:7:203 +GATCT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +GATCT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +GATCT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +GATCT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +GATCT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V |
| b |
| diff -r 000000000000 -r ff12d2c1f5d6 test-data/test_2_BC1_index2.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_2_BC1_index2.fastq Wed May 29 10:24:27 2019 -0400 |
| b |
| @@ -0,0 +1,20 @@ +@CSHL_3_FC042AGLLWW:1:2:7:203 +GATCT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +GATCT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +GATCT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +GATCT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +GATCT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V |
| b |
| diff -r 000000000000 -r ff12d2c1f5d6 test-data/test_2_BC2-read-1.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_2_BC2-read-1.fastq Wed May 29 10:24:27 2019 -0400 |
| b |
| @@ -0,0 +1,48 @@ +@CSHL_3_FC042AGLLWW:1:2:7:203 +ATCGTTCTCTATGTACA ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +ATCGTGAGTATACACAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +ATCGTTCTCTATGTACA ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +ATCGTGAGTATACACAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +ATCTTTCTCTATGTACA ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +ATCTTGAGTATACACAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +ATCTTGAGTATACACAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +ATCTTTCTCTATGTACA ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +ATCTCGAGTATACACAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +ATCTCGAGTATACACAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +ATCTCTCTCTATGTACA ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +ATCTCGAGTATACACAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa |
| b |
| diff -r 000000000000 -r ff12d2c1f5d6 test-data/test_2_BC2_index1.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_2_BC2_index1.fastq Wed May 29 10:24:27 2019 -0400 |
| b |
| @@ -0,0 +1,48 @@ +@CSHL_3_FC042AGLLWW:1:2:7:203 +ATCGT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +ATCGT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +ATCGT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +ATCGT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +ATCTT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +ATCTT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +ATCTT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +ATCTT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +ATCTC ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +ATCTC ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +ATCTC ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +ATCTC ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V |
| b |
| diff -r 000000000000 -r ff12d2c1f5d6 test-data/test_2_BC2_index2.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_2_BC2_index2.fastq Wed May 29 10:24:27 2019 -0400 |
| b |
| @@ -0,0 +1,48 @@ +@CSHL_3_FC042AGLLWW:1:2:7:203 +ATCGT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +ATCGT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +ATCGT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +ATCGT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +ATCTT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +ATCTT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +ATCTT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +ATCTT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +ATCTC ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +ATCTC ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +ATCTC ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +ATCTC ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V |
| b |
| diff -r 000000000000 -r ff12d2c1f5d6 test-data/test_2_BC3-read-1.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_2_BC3-read-1.fastq Wed May 29 10:24:27 2019 -0400 |
| b |
| @@ -0,0 +1,36 @@ +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGAATGAGTATACACAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGAATTCTCTATGTACA ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGAATGAGTATACACAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGAATTCTCTATGTACA ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGAATGAGTATACACAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGAATTCTCTATGTACA ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGAATGAGTATACACAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGAATTCTCTATGTACA ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGAATGAGTATACACAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa |
| b |
| diff -r 000000000000 -r ff12d2c1f5d6 test-data/test_2_BC3_index1.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_2_BC3_index1.fastq Wed May 29 10:24:27 2019 -0400 |
| b |
| @@ -0,0 +1,36 @@ +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGAAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGAAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGAAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGAAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGAAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGAAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGAAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGAAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGAAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V |
| b |
| diff -r 000000000000 -r ff12d2c1f5d6 test-data/test_2_BC3_index2.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_2_BC3_index2.fastq Wed May 29 10:24:27 2019 -0400 |
| b |
| @@ -0,0 +1,36 @@ +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGAAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGAAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGAAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGAAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGAAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGAAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGAAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGAAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGAAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V |
| b |
| diff -r 000000000000 -r ff12d2c1f5d6 test-data/test_2_multimatched-read-1.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_2_multimatched-read-1.fastq Wed May 29 10:24:27 2019 -0400 |
| b |
| @@ -0,0 +1,24 @@ +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGTCTAGTAGTAGTAGA ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGTCTTCTCTATGTACA ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGTCTGAGTATACACAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGTATTCTCTATGTACA ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGTATTCTCTATGTACA ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGTATTCTCTATGTACA ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa |
| b |
| diff -r 000000000000 -r ff12d2c1f5d6 test-data/test_2_multimatched_index1.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_2_multimatched_index1.fastq Wed May 29 10:24:27 2019 -0400 |
| b |
| @@ -0,0 +1,24 @@ +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGTCT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGTCT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGTCT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGTAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGTAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGTAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V |
| b |
| diff -r 000000000000 -r ff12d2c1f5d6 test-data/test_2_multimatched_index2.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_2_multimatched_index2.fastq Wed May 29 10:24:27 2019 -0400 |
| b |
| @@ -0,0 +1,24 @@ +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGTCT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGTCT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGTCT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGTAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGTAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGTAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V |
| b |
| diff -r 000000000000 -r ff12d2c1f5d6 test-data/test_2_summary.out --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_2_summary.out Wed May 29 10:24:27 2019 -0400 |
| b |
| @@ -0,0 +1,9 @@ +Sample Barcode1 Barcode2 Count Percent Files +BC1 GATCT GATC 5 11.90% split/BC1-read-*.fastq +BC2 ATCGT ATCG 12 28.57% split/BC2-read-*.fastq +BC3 GTGAT GTGA 9 21.43% split/BC3-read-*.fastq +BC4 TGTCT TGTC 0 0.00% split/BC4-read-*.fastq +multimatched multimatched multimatched 6 14.29% split/multimatched-read-*.fastq +unmatched unmatched matched 3 7.14% split/unmatched-read-*.fastq +unmatched unmatched unmatched 5 11.90% split/unmatched-read-*.fastq +ERRORS NA NA 2 4.76% STDERR |
| b |
| diff -r 000000000000 -r ff12d2c1f5d6 test-data/test_2_unmatched-read-1.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_2_unmatched-read-1.fastq Wed May 29 10:24:27 2019 -0400 |
| b |
| @@ -0,0 +1,32 @@ +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGTACGAGTATACACAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGTACTCTCTATGTACA ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGTACGAGTATACACAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +TAGTTGAGTATACACAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +TAGTTGAGTATACACAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +TAGTTTCTCTATGTACA ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +TAGTTTCTCTATGTACA ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +TAGTTGAGTATACACAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa |
| b |
| diff -r 000000000000 -r ff12d2c1f5d6 test-data/test_2_unmatched_index1.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_2_unmatched_index1.fastq Wed May 29 10:24:27 2019 -0400 |
| b |
| @@ -0,0 +1,32 @@ +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGTAC ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGTAC ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGTAC ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +TAGTT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +TAGTT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +TAGTT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +TAGTT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +TAGTT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V |
| b |
| diff -r 000000000000 -r ff12d2c1f5d6 test-data/test_2_unmatched_index2.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_2_unmatched_index2.fastq Wed May 29 10:24:27 2019 -0400 |
| b |
| @@ -0,0 +1,32 @@ +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGTAC ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGTAC ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGTAC ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +TAGTT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +TAGTT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +TAGTT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +TAGTT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +TAGTT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V |
| b |
| diff -r 000000000000 -r ff12d2c1f5d6 test-data/test_3_BC1-forward.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_3_BC1-forward.fastq Wed May 29 10:24:27 2019 -0400 |
| b |
| @@ -0,0 +1,20 @@ +@CSHL_3_FC042AGLLWW:1:2:7:203 +GATCTAGTAGTAGTAGA ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +GATCTAGTAGTAGTAGA ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +GATCTAGTAGTAGTAGA ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +GATCTAGTAGTAGTAGA ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +GATCTAGTAGTAGTAGA ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa |
| b |
| diff -r 000000000000 -r ff12d2c1f5d6 test-data/test_3_BC1-reverse.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_3_BC1-reverse.fastq Wed May 29 10:24:27 2019 -0400 |
| b |
| @@ -0,0 +1,20 @@ +@CSHL_3_FC042AGLLWW:1:2:7:203 +GATCT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +GATCT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +GATCT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +GATCT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +GATCT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V |
| b |
| diff -r 000000000000 -r ff12d2c1f5d6 test-data/test_3_BC2-forward.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_3_BC2-forward.fastq Wed May 29 10:24:27 2019 -0400 |
| b |
| @@ -0,0 +1,48 @@ +@CSHL_3_FC042AGLLWW:1:2:7:203 +ATCGTTCTCTATGTACA ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +ATCGTGAGTATACACAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +ATCGTTCTCTATGTACA ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +ATCGTGAGTATACACAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +ATCTTTCTCTATGTACA ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +ATCTTGAGTATACACAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +ATCTTGAGTATACACAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +ATCTTTCTCTATGTACA ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +ATCTCGAGTATACACAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +ATCTCGAGTATACACAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +ATCTCTCTCTATGTACA ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +ATCTCGAGTATACACAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa |
| b |
| diff -r 000000000000 -r ff12d2c1f5d6 test-data/test_3_BC2-reverse.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_3_BC2-reverse.fastq Wed May 29 10:24:27 2019 -0400 |
| b |
| @@ -0,0 +1,48 @@ +@CSHL_3_FC042AGLLWW:1:2:7:203 +ATCGT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +ATCGT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +ATCGT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +ATCGT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +ATCTT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +ATCTT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +ATCTT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +ATCTT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +ATCTC ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +ATCTC ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +ATCTC ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +ATCTC ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V |
| b |
| diff -r 000000000000 -r ff12d2c1f5d6 test-data/test_3_BC3-forward.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_3_BC3-forward.fastq Wed May 29 10:24:27 2019 -0400 |
| b |
| @@ -0,0 +1,36 @@ +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGAATGAGTATACACAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGAATTCTCTATGTACA ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGAATGAGTATACACAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGAATTCTCTATGTACA ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGAATGAGTATACACAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGAATTCTCTATGTACA ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGAATGAGTATACACAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGAATTCTCTATGTACA ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGAATGAGTATACACAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa |
| b |
| diff -r 000000000000 -r ff12d2c1f5d6 test-data/test_3_BC3-reverse.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_3_BC3-reverse.fastq Wed May 29 10:24:27 2019 -0400 |
| b |
| @@ -0,0 +1,36 @@ +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGAAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGAAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGAAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGAAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGAAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGAAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGAAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGAAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGAAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V |
| b |
| diff -r 000000000000 -r ff12d2c1f5d6 test-data/test_3_multimatched-forward.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_3_multimatched-forward.fastq Wed May 29 10:24:27 2019 -0400 |
| b |
| @@ -0,0 +1,24 @@ +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGTCTAGTAGTAGTAGA ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGTCTTCTCTATGTACA ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGTCTGAGTATACACAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGTATTCTCTATGTACA ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGTATTCTCTATGTACA ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGTATTCTCTATGTACA ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa |
| b |
| diff -r 000000000000 -r ff12d2c1f5d6 test-data/test_3_multimatched-reverse.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_3_multimatched-reverse.fastq Wed May 29 10:24:27 2019 -0400 |
| b |
| @@ -0,0 +1,24 @@ +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGTCT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGTCT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGTCT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGTAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGTAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGTAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V |
| b |
| diff -r 000000000000 -r ff12d2c1f5d6 test-data/test_3_unmatched-forward.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_3_unmatched-forward.fastq Wed May 29 10:24:27 2019 -0400 |
| b |
| @@ -0,0 +1,32 @@ +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGTACGAGTATACACAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGTACTCTCTATGTACA ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGTACGAGTATACACAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +TAGTTGAGTATACACAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +TAGTTGAGTATACACAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +TAGTTTCTCTATGTACA ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +TAGTTTCTCTATGTACA ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +TAGTTGAGTATACACAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa |
| b |
| diff -r 000000000000 -r ff12d2c1f5d6 test-data/test_3_unmatched-reverse.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_3_unmatched-reverse.fastq Wed May 29 10:24:27 2019 -0400 |
| b |
| @@ -0,0 +1,32 @@ +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGTAC ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGTAC ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGTAC ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +TAGTT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +TAGTT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +TAGTT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +TAGTT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +TAGTT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V |
| b |
| diff -r 000000000000 -r ff12d2c1f5d6 test-data/test_5_BC4-read-1.out --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_5_BC4-read-1.out Wed May 29 10:24:27 2019 -0400 |
| b |
| @@ -0,0 +1,4 @@ +@HWI-X00000:2:000000000-XXXXX:1:1117:19643:1028 1:N:0: +TGTCTGAGTATACACAT ++HWI-X00000:2:000000000-XXXXX:1:1117:19643:1028 1:N:0: +aab^V^aU]`aa^aZaa |
| b |
| diff -r 000000000000 -r ff12d2c1f5d6 test-data/test_5_summary.out --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_5_summary.out Wed May 29 10:24:27 2019 -0400 |
| b |
| @@ -0,0 +1,7 @@ +Sample Barcode1 Count Percent Files +BC1 GATCT 5 11.90% split/BC1-read-*.fastq +BC2 ATCGT 12 28.57% split/BC2-read-*.fastq +BC3 GTGAT 9 21.43% split/BC3-read-*.fastq +BC4 TGTCT 1 2.38% split/BC4-read-*.fastq +multimatched multimatched 6 14.29% split/multimatched-read-*.fastq +unmatched unmatched 9 21.43% split/unmatched-read-*.fastq |
| b |
| diff -r 000000000000 -r ff12d2c1f5d6 test-data/test_5_unmatched-read-1.out --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_5_unmatched-read-1.out Wed May 29 10:24:27 2019 -0400 |
| b |
| @@ -0,0 +1,36 @@ +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGTACGAGTATACACAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGTACTCTCTATGTACA ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGTACGAGTATACACAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +TAGTTGAGTATACACAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +TAGTTGAGTATACACAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +TAGTTTCTCTATGTACA ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +TAGTTTCTCTATGTACA ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +TAGTTGAGTATACACAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203/1 +TAGTTTCTCTATGTACA ++CSHL_3_FC042AGLLWW:1:2:7:203/1 +aab^V^aU]`aa^aZaa |
| b |
| diff -r 000000000000 -r ff12d2c1f5d6 test-data/test_6_BC1_index2.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_6_BC1_index2.fastq Wed May 29 10:24:27 2019 -0400 |
| b |
| @@ -0,0 +1,20 @@ +@CSHL_3_FC042AGLLWW:1:2:7:203 +GATCT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +GATCT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +GATCT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +GATCT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +GATCT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V |
| b |
| diff -r 000000000000 -r ff12d2c1f5d6 test-data/test_6_BC1_read1.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_6_BC1_read1.fastq Wed May 29 10:24:27 2019 -0400 |
| b |
| @@ -0,0 +1,20 @@ +@CSHL_3_FC042AGLLWW:1:2:7:203 +GATCTAGTAGTAGTAGA ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +GATCTAGTAGTAGTAGA ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +GATCTAGTAGTAGTAGA ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +GATCTAGTAGTAGTAGA ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +GATCTAGTAGTAGTAGA ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa |
| b |
| diff -r 000000000000 -r ff12d2c1f5d6 test-data/test_6_BC1_read2.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_6_BC1_read2.fastq Wed May 29 10:24:27 2019 -0400 |
| b |
| @@ -0,0 +1,20 @@ +@CSHL_3_FC042AGLLWW:1:2:7:203 +GATCT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +GATCT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +GATCT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +GATCT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +GATCT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V |
| b |
| diff -r 000000000000 -r ff12d2c1f5d6 test-data/test_6_BC2_index2.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_6_BC2_index2.fastq Wed May 29 10:24:27 2019 -0400 |
| b |
| @@ -0,0 +1,48 @@ +@CSHL_3_FC042AGLLWW:1:2:7:203 +ATCGT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +ATCGT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +ATCGT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +ATCGT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +ATCTT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +ATCTT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +ATCTT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +ATCTT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +ATCTC ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +ATCTC ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +ATCTC ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +ATCTC ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V |
| b |
| diff -r 000000000000 -r ff12d2c1f5d6 test-data/test_6_BC2_read1.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_6_BC2_read1.fastq Wed May 29 10:24:27 2019 -0400 |
| b |
| @@ -0,0 +1,48 @@ +@CSHL_3_FC042AGLLWW:1:2:7:203 +ATCGTTCTCTATGTACA ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +ATCGTGAGTATACACAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +ATCGTTCTCTATGTACA ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +ATCGTGAGTATACACAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +ATCTTTCTCTATGTACA ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +ATCTTGAGTATACACAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +ATCTTGAGTATACACAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +ATCTTTCTCTATGTACA ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +ATCTCGAGTATACACAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +ATCTCGAGTATACACAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +ATCTCTCTCTATGTACA ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +ATCTCGAGTATACACAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa |
| b |
| diff -r 000000000000 -r ff12d2c1f5d6 test-data/test_6_BC2_read2.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_6_BC2_read2.fastq Wed May 29 10:24:27 2019 -0400 |
| b |
| @@ -0,0 +1,48 @@ +@CSHL_3_FC042AGLLWW:1:2:7:203 +ATCGT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +ATCGT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +ATCGT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +ATCGT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +ATCTT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +ATCTT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +ATCTT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +ATCTT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +ATCTC ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +ATCTC ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +ATCTC ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +ATCTC ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V |
| b |
| diff -r 000000000000 -r ff12d2c1f5d6 test-data/test_6_BC3_index2.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_6_BC3_index2.fastq Wed May 29 10:24:27 2019 -0400 |
| b |
| @@ -0,0 +1,36 @@ +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGAAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGAAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGAAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGAAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGAAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGAAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGAAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGAAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGAAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V |
| b |
| diff -r 000000000000 -r ff12d2c1f5d6 test-data/test_6_BC3_read1.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_6_BC3_read1.fastq Wed May 29 10:24:27 2019 -0400 |
| b |
| @@ -0,0 +1,36 @@ +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGAATGAGTATACACAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGAATTCTCTATGTACA ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGAATGAGTATACACAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGAATTCTCTATGTACA ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGAATGAGTATACACAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGAATTCTCTATGTACA ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGAATGAGTATACACAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGAATTCTCTATGTACA ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGAATGAGTATACACAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa |
| b |
| diff -r 000000000000 -r ff12d2c1f5d6 test-data/test_6_BC3_read2.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_6_BC3_read2.fastq Wed May 29 10:24:27 2019 -0400 |
| b |
| @@ -0,0 +1,36 @@ +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGAAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGAAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGAAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGAAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGAAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGAAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGAAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGAAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGAAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V |
| b |
| diff -r 000000000000 -r ff12d2c1f5d6 test-data/test_6_multimatched_index2.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_6_multimatched_index2.fastq Wed May 29 10:24:27 2019 -0400 |
| b |
| @@ -0,0 +1,24 @@ +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGTCT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGTCT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGTCT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGTAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGTAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGTAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V |
| b |
| diff -r 000000000000 -r ff12d2c1f5d6 test-data/test_6_multimatched_read1.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_6_multimatched_read1.fastq Wed May 29 10:24:27 2019 -0400 |
| b |
| @@ -0,0 +1,24 @@ +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGTCTAGTAGTAGTAGA ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGTCTTCTCTATGTACA ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGTCTGAGTATACACAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGTATTCTCTATGTACA ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGTATTCTCTATGTACA ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGTATTCTCTATGTACA ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa |
| b |
| diff -r 000000000000 -r ff12d2c1f5d6 test-data/test_6_multimatched_read2.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_6_multimatched_read2.fastq Wed May 29 10:24:27 2019 -0400 |
| b |
| @@ -0,0 +1,24 @@ +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGTCT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGTCT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGTCT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGTAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGTAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGTAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V |
| b |
| diff -r 000000000000 -r ff12d2c1f5d6 test-data/test_6_summary.out --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_6_summary.out Wed May 29 10:24:27 2019 -0400 |
| b |
| @@ -0,0 +1,9 @@ +Sample Barcode1 Barcode2 Count Percent Files +BC1 GATCT GATC 5 11.90% split/BC1-read-*.fastq +BC2 ATCGT ATCG 12 28.57% split/BC2-read-*.fastq +BC3 GTGAT GTGA 9 21.43% split/BC3-read-*.fastq +BC4 TGTCT TGTC 0 0.00% split/BC4-read-*.fastq +multimatched multimatched multimatched 6 14.29% split/multimatched-read-*.fastq +unmatched unmatched matched 3 7.14% split/unmatched-read-*.fastq +unmatched unmatched unmatched 5 11.90% split/unmatched-read-*.fastq +ERRORS NA NA 2 4.76% STDERR |
| b |
| diff -r 000000000000 -r ff12d2c1f5d6 test-data/test_6_unmatched_index2.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_6_unmatched_index2.fastq Wed May 29 10:24:27 2019 -0400 |
| b |
| @@ -0,0 +1,32 @@ +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGTAC ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGTAC ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGTAC ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +TAGTT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +TAGTT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +TAGTT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +TAGTT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +TAGTT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V |
| b |
| diff -r 000000000000 -r ff12d2c1f5d6 test-data/test_6_unmatched_read1.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_6_unmatched_read1.fastq Wed May 29 10:24:27 2019 -0400 |
| b |
| @@ -0,0 +1,32 @@ +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGTACGAGTATACACAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGTACTCTCTATGTACA ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGTACGAGTATACACAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +TAGTTGAGTATACACAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +TAGTTGAGTATACACAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +TAGTTTCTCTATGTACA ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +TAGTTTCTCTATGTACA ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +TAGTTGAGTATACACAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa |
| b |
| diff -r 000000000000 -r ff12d2c1f5d6 test-data/test_6_unmatched_read2.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_6_unmatched_read2.fastq Wed May 29 10:24:27 2019 -0400 |
| b |
| @@ -0,0 +1,32 @@ +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGTAC ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGTAC ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGTAC ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +TAGTT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +TAGTT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +TAGTT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +TAGTT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +TAGTT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V |