| Previous changeset 6:604fa75232a2 (2014-01-16) Next changeset 8:88fcac97c2a0 (2014-12-23) |
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Commit message:
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modified:
cuffdiff_wrapper.xml test-data/cuffdiff_out1.txt test-data/cuffdiff_out10.txt test-data/cuffdiff_out2.txt test-data/cuffdiff_out3.txt test-data/cuffdiff_out5.txt test-data/cuffdiff_out6.txt test-data/cuffdiff_out7.txt test-data/cuffdiff_out9.txt tool_dependencies.xml |
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added:
cuff_macros.xml |
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| diff -r 604fa75232a2 -r 8da0eade1f59 cuff_macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/cuff_macros.xml Fri Dec 19 11:57:43 2014 -0500 |
| [ |
| @@ -0,0 +1,91 @@ +<macros> + <token name="@VERSION@">2.2.1</token> + <xml name="requirements"> + <requirements> + <requirement type="package" version="2.2.1">cufflinks</requirement> + <yield /> + </requirements> + </xml> + <xml name="stdio"> + <stdio> + <exit_code range="1:" /> + <exit_code range=":-1" /> + <regex match="Error:" /> + <regex match="Exception:" /> + </stdio> + </xml> + <xml name="condition_inputs"> + <!-- DEFAULT : use BAM/SAM files --> + <conditional name="in_type"> + <param name="set_in_type" type="select" label="Input data type" + help="CuffNorm supports either CXB (from cuffquant) or SAM/BAM input files. Mixing is not supported. Default: SAM/BAM"> + <option value="BAM">SAM/BAM</option> + <option value="CXB">Cuffquant (CXB)</option> + <option value="CONDITION_LIST">List of single replicate conditions</option> + <option value="CONDITION_REPLICATE_LIST">List of multiple replicate conditions</option> + </param> + <when value="BAM"> + <repeat name="conditions" title="Condition" min="2"> + <param name="name" title="Condition name" type="text" label="Name"/> + <param name="samples" label="Replicates" type="data" format="sam,bam" multiple="true"/> + </repeat> + </when> + <when value="CXB"> + <repeat name="conditions" title="Condition" min="2"> + <param name="name" title="Condition name" type="text" label="Name"/> + <param name="samples" label="Replicates" type="data" format="cxb" multiple="true"/> + </repeat> + </when> + <when value="CONDITION_LIST"> + <param name="conditions" title="List of Conditions" type="data_collection" collection_type="list" /> + </when> + <when value="CONDITION_REPLICATE_LIST"> + <param name="conditions" title="List of Conditions" type="data_collection" collection_type="list:list" /> + </when> + </conditional> + </xml> + <token name="@CONDITION_SAMPLES@"> + #if $in_type.set_in_type in ['BAM', 'CXB'] + #for $condition in $in_type.conditions: + #set samples = ','.join( [ str( $sample ) for $sample in $condition.samples ] ) + $samples + #end for + #elif $in_type.set_in_type == 'CONDITION_LIST' + #for $sample in $in_type.conditions: + $sample + #end for + #elif $in_type.set_in_type == 'CONDITION_REPLICATE_LIST' + #for $condition_list in $in_type.conditions: + #set samples = ','.join( [ str( $sample ) for $sample in $condition_list ] ) + $samples + #end for + #end if + </token> + <token name="@CONDITION_LABELS@"> + #import re + #if $in_type.set_in_type in ['BAM', 'CXB'] + #set labels = '\'' + '\',\''.join( [ str( $condition.name ) for $condition in $in_type.conditions ] ) + '\'' + #elif $in_type.set_in_type in ['CONDITION_LIST', 'CONDITION_REPLICATE_LIST'] + #set labels = '\'' + '\',\''.join( map(lambda x: re.sub('[^\w\-_]', '_', x), $in_type.conditions.keys() ) ) + '\'' + #end if + --labels $labels + </token> + <xml name="cufflinks_gtf_inputs"> + <param format="gtf" name="inputs" type="data" label="GTF file(s) produced by Cufflinks" help="" multiple="true" /> + <repeat name="additional_inputs" title="Additional GTF Inputs (Lists)"> + <param format="gtf" name="additional_inputs" type="data_collection" label="GTF file(s) produced by Cufflinks" help="" /> + </repeat> + </xml> + <token name="@CUFFLINKS_GTF_INPUTS@"> + ## Inputs. + #for $input_file in $inputs: + "${input_file}" + #end for + #for $additional_input in $additional_inputs: + #for $input_file in $additional_input.additional_inputs: + "${input_file}" + #end for + #end for + </token> + <token name="@HAS_MULTIPLE_INPUTS@">getattr(inputs, "__len__", [].__len__)() >= 2</token> +</macros> \ No newline at end of file |
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| diff -r 604fa75232a2 -r 8da0eade1f59 cuffdiff_wrapper.xml --- a/cuffdiff_wrapper.xml Thu Jan 16 13:13:52 2014 -0500 +++ b/cuffdiff_wrapper.xml Fri Dec 19 11:57:43 2014 -0500 |
| [ |
| b'@@ -1,9 +1,10 @@\n-<tool id="cuffdiff" name="Cuffdiff" version="0.0.7">\n- <!-- Wrapper supports Cuffdiff versions 2.1.0-2.1.1 -->\n+<tool id="cuffdiff" name="Cuffdiff" version="@VERSION@.0">\n <description>find significant changes in transcript expression, splicing, and promoter use</description>\n- <requirements>\n- <requirement type="package" version="2.1.1">cufflinks</requirement>\n- </requirements>\n+ <expand macro="requirements" />\n+ <expand macro="stdio" />\n+ <macros>\n+ <import>cuff_macros.xml</import>\n+ </macros>\n <version_command>cuffdiff 2>&1 | head -n 1</version_command>\n <command>\n cuffdiff\n@@ -14,15 +15,15 @@\n --library-norm-method=$library_norm_method\n --dispersion-method=$dispersion_method\n \n- ## Set advanced data parameters?\n+ ## Set advanced SE data parameters?\n #if $additional.sAdditional == "Yes":\n -m $additional.frag_mean_len\n -s $additional.frag_len_std_dev\n #end if\n \n ## Multi-read correct?\n- #if str($multiread_correct) == "Yes":\n- -u\n+ #if $multiread_correct :\n+ -u\n #end if\n \n ## Bias correction?\n@@ -33,30 +34,40 @@\n $bias_correction.seq_source.ref_file\n #else:\n ## Built-in genome.\n- ${__get_data_table_entry__(\'fasta_indexes\', \'value\', $gtf_input.dbkey, \'path\')}\n+ "${ bias_correction.seq_source.index.fields.path }"\n #end if\n #end if\n \n- #set labels = \'\\\'\' + \'\\\',\\\'\'.join( [ str( $condition.name ) for $condition in $conditions ] ) + \'\\\'\'\n- --labels $labels\n+ @CONDITION_LABELS@\n+\n+ $length_correction\n \n+ ## Set advanced parameters for cufflinks\n+ #if $advanced_settings.sAdvanced == "Yes":\n+ #if str($advanced_settings.library_type) != \'auto\':\n+ --library-type=$advanced_settings.library_type\n+ #end if\n+ #if $advanced_settings.mask_file:\n+ --mask-file=$advanced_settings.mask_file\n+ #end if\n+ #if $advanced_settings.time_series:\n+ --time-series\n+ #end if\n+ --max-mle-iterations=$advanced_settings.max_mle_iterations\n+ $advanced_settings.hits_norm\n+ --max-bundle-frags=$advanced_settings.max_bundle_frags\n+ --num-frag-count-draws=$advanced_settings.num_frag_count_draws\n+ --num-frag-assign-draws=$advanced_settings.num_frag_assign_draws\n+ --min-reps-for-js-test=$advanced_settings.min_reps_for_js_test\n+ #end if\n ## Inputs.\n $gtf_input\n- #for $condition in $conditions:\n- #set samples = \',\'.join( [ str( $sample.sample ) for $sample in $condition.samples ] )\n- $samples\n- #end for\n+\n+ @CONDITION_SAMPLES@\n </command>\n <inputs>\n <param format="gtf,gff3" name="gtf_input" type="data" label="Transcripts" help="A transcript GFF3 or GTF file produced by cufflinks, cuffcompare, or other source."/>\n-\n- <repeat name="conditions" title="Condition" min="2">\n- <param name="name" title="Condition name" type="text" label="Name"/>\n- <repeat name="samples" title="Replicate" min="1">\n- <param name="sample" label="Add replicate" type="data" format="sam,bam"/>\n- </repeat>\n- </repeat>\n-\n+ <expand macro="condition_inputs" />\n <param name="library_norm_method" type="select" label="Library normalization method">\n <option value="geometric" selected="True">geometric</option>\n <option value="classic-fpkm">classic-fpkm</option>\n@@ -67,19 +78,18 @@\n <option value='..b'00\n- -s INT Fragment legnth standard deviation; default 80\n+ -m INT Average fragment length (SE reads); default 200\n+ -s INT Fragment legnth standard deviation (SE reads); default 80\n -c INT The minimum number of alignments in a locus for needed to conduct significance testing on changes in that locus observed between samples. If no testing is performed, changes in the locus are deemed not significant, and the locus\' observed changes don\'t contribute to correction for multiple testing. The default is 1,000 fragment alignments (up to 2,000 paired reads).\n --FDR FLOAT The allowed false discovery rate. The default is 0.05.\n- --num-importance-samples INT Sets the number of importance samples generated for each locus during abundance estimation. Default: 1000\n --max-mle-iterations INT Sets the number of iterations allowed during maximum likelihood estimation of abundances. Default: 5000\n- -N With this option, Cufflinks excludes the contribution of the top 25 percent most highly expressed genes from the number of mapped fragments used in the FPKM denominator. This can improve robustness of differential expression calls for less abundant genes and transcripts.\n- \n+ --library-norm-method Library Normalization method : Geometric (default), classic-fpkm, quartile\n+ --dispersion-method Dispersion estimation method : Pooled (default), per-condition, blind, poisson\n+ -u Multi read correction tells Cufflinks to do an initial estimation procedure to more accurately weight reads mapping to multiple locations in the genome.\n+ -b ref.fasta bias correction. Bias detection and correction can significantly improve accuracy of transcript abundance estimates.\n+ --no-effective-length-correction Use standard length correction\n+ --no-length-correction Disable all length correction.\n+ --library-type ff-firststrand,ff-secondstrand,ff-unstranded,fr-firstrand,fr-secondstrand,fr-unstranded,transfrags\n+ --mask-file (gff3/gtf) Ignore all alignment within transcripts in this file\n+ --time-series Treat provided sam files as time series\n+ --compatible-hits-norm With this option, Cufflinks counts only those fragments compatible with some reference transcript towards the number of mapped fragments used in the FPKM denominator. Using this mode is generally recommended in Cuffdiff to reduce certain types of bias caused by differential amounts of ribosomal reads which can create the impression of falsely differentially expressed genes.\n+ --total-hits-norm With this option, Cufflinks counts all fragments, including those not compatible with any reference transcript, towards the number of mapped fragments used in the FPKM denominator \n+ --max-bundle-frags Sets the maximum number of fragments a locus may have before being skipped. Skipped loci are listed in skipped.gtf.\n+ --num-frag-count-draws Cuffdiff will make this many draws from each transcript\'s predicted negative binomial random numbder generator. Each draw is a number of fragments that will be probabilistically assigned to the transcripts in the transcriptome. Used to estimate the variance-covariance matrix on assigned fragment counts.\n+ --num-frag-assign-draws For each fragment drawn from a transcript, Cuffdiff will assign it this many times (probabilistically), thus estimating the assignment uncertainty for each transcript. Used to estimate the variance-covariance matrix on assigned fragment counts.\n+ --min-reps-for-js-test Cuffdiff won\'t test genes for differential regulation unless the conditions in question have at least this many replicates.\n </help>\n+ <citations>\n+ <citation type="doi">10.1038/nbt.1621</citation>\n+ </citations>\n </tool>\n' |
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| diff -r 604fa75232a2 -r 8da0eade1f59 test-data/cuffdiff_out1.txt --- a/test-data/cuffdiff_out1.txt Thu Jan 16 13:13:52 2014 -0500 +++ b/test-data/cuffdiff_out1.txt Fri Dec 19 11:57:43 2014 -0500 |
| b |
| b'@@ -1,32 +1,32 @@\n test_id\tgene_id\tgene\tlocus\tsample_1\tsample_2\tstatus\tvalue_1\tvalue_2\tlog2(fold_change)\ttest_stat\tp_value\tq_value\tsignificant\n-TCONS_00000001\tXLOC_000001\tXkr4\tchr1:3204754-3204833\tq1\tq2\tOK\t0\t8.3103e+06\t1.79769e+308\t1.79769e+308\t0.0786496\t0.150149\tno\n-TCONS_00000002\tXLOC_000002\t-\tchr1:3111449-3111490\tq1\tq2\tOK\t0\t2.1403e+08\t1.79769e+308\t1.79769e+308\t0.158655\t0.158655\tno\n+TCONS_00000001\tXLOC_000001\tXkr4\tchr1:3204754-3204833\tq1\tq2\tOK\t0\t9.45986e+06\tinf\t-nan\t0.01975\t0.101571\tno\n+TCONS_00000002\tXLOC_000002\t-\tchr1:3111449-3111490\tq1\tq2\tOK\t0\t2.43637e+08\tinf\t-nan\t0.12465\t0.186975\tno\n TCONS_00000003\tXLOC_000003\t-\tchr1:3111545-3111576\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n-TCONS_00000009\tXLOC_000011\t-\tchr1:3192441-3192494\tq1\tq2\tOK\t0\t5.68095e+07\t1.79769e+308\t1.79769e+308\t0.0786496\t0.150149\tno\n-TCONS_00000010\tXLOC_000012\t-\tchr1:3192550-3192629\tq1\tq2\tOK\t0\t4.15515e+06\t1.79769e+308\t1.79769e+308\t0.158655\t0.158655\tno\n+TCONS_00000009\tXLOC_000011\t-\tchr1:3192441-3192494\tq1\tq2\tOK\t0\t9.7002e+07\tinf\t-nan\t0.07975\t0.186975\tno\n+TCONS_00000010\tXLOC_000012\t-\tchr1:3192550-3192629\tq1\tq2\tOK\t0\t4.72993e+06\tinf\t-nan\t0.12465\t0.186975\tno\n TCONS_00000011\tXLOC_000014\t-\tchr1:3192731-3192811\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n-TCONS_00000012\tXLOC_000015\t-\tchr1:3192940-3193042\tq1\tq2\tOK\t0\t6.02976e+06\t1.79769e+308\t1.79769e+308\t0.0512352\t0.150149\tno\n-TCONS_00000013\tXLOC_000016\t-\tchr1:3194185-3194226\tq1\tq2\tOK\t0\t2.1403e+08\t1.79769e+308\t1.79769e+308\t0.158655\t0.158655\tno\n+TCONS_00000012\tXLOC_000015\t-\tchr1:3192940-3193042\tq1\tq2\tOK\t0\t6.86386e+06\tinf\t-nan\t0.0612\t0.186975\tno\n+TCONS_00000013\tXLOC_000016\t-\tchr1:3194185-3194226\tq1\tq2\tOK\t0\t2.43637e+08\tinf\t-nan\t0.12465\t0.186975\tno\n TCONS_00000014\tXLOC_000017\t-\tchr1:3194302-3194329\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n TCONS_00000015\tXLOC_000019\t-\tchr1:3195083-3195110\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n TCONS_00000016\tXLOC_000020\t-\tchr1:3195450-3195477\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n TCONS_00000017\tXLOC_000021\t-\tchr1:3197089-3197116\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n TCONS_00000018\tXLOC_000022\t-\tchr1:3197246-3197273\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n TCONS_00000019\tXLOC_000023\t-\tchr1:3197346-3197373\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n-TCONS_00000020\tXLOC_000025\t-\tchr1:3200022-3200191\tq1\tq2\tNOTEST\t959058\t705514\t-0.442943\t0.376027\t0.706897\t1\tno\n+TCONS_00000020\tXLOC_000025\t-\tchr1:3200022-3200191\tq1\tq2\tOK\t826392\t803108\t-0.0412311\t-0.0180163\t0.8625\t0.887143\tno\n TCONS_00000021\tXLOC_000026\t-\tchr1:3200325-3200352\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n-TCONS_00000022\tXLOC_000029\t-\tchr1:3201077-3201481\tq1\tq2\tNOTEST\t77513.9\t285108\t1.87898\t-1.76152\t0.0781506\t1\tno\n+TCONS_00000022\tXLOC_000029\t-\tchr1:3201077-3201481\tq1\tq2\tOK\t66791.3\t324548\t2.2807\t1.1905\t0.3026\t0.380545\tno\n TCONS_00000023\tXLOC_000031\t-\tchr1:3201672-3201699\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n-TCONS_00000024\tXLOC_000034\tXkr4\tchr1:3212213-3212292\tq1\tq2\tOK\t0\t8.3103e+06\t1.79769e+308\t1.79769e+308\t0.0786496\t0.150149\tno\n-TCONS_00000025\tXLOC_000035\tXkr4\tchr1:3212367-3212439\tq1\tq2\tOK\t0\t2.4671e+07\t1.79769e+308\t1.79769e+308\t0.0512352\t0.150149\tno\n-TCONS_00000026\tXLOC_000037\tXkr4\tchr1:3213095-3213242\tq1\tq2\tNOTEST\t3.99739e+06\t1.82908e+06\t-1.12794\t0.781831\t0.434314\t1\tno\n-TCONS_00000027\tXLOC_000040\tXkr4\tchr1:3242633-3242923\tq1\tq2\tNOTEST\t56312.4\t372827\t2.72698\t-1.67622\t0.0936947\t1\tno\n-TCONS_00000028\tXLOC_000042\tXkr4\tchr1:3243018-3243079\tq1\tq2\tOK\t0\t2.66226e+07\t1.79769e+308\t1.79769e+308\t0.0786496\t0.150149\tno\n-TCONS_00000029\tXLOC_000044\tXkr4\tchr1:3243347-3243401\tq1\tq2\tOK\t0\t5.0951e+07\t1.79769e+308\t1.79769e+308\t0.0786496\t0.150149\tno\n-TCONS_00000030\tXLOC_000046\tXkr4\tchr1:3256974-3257011\tq1\tq2\tOK\t0\t2.06814e+09\t1.79769e+308\t1.79769e+308\t0.0786496\t0.150149\tno\n+TCONS_00000024\tXLOC_000034\tXkr4\tchr1:3212213-3212292\tq1\tq2\tOK\t0\t9.45986e+06\tinf\t-nan\t0.01975\t0.101571\tno\n+TCONS_00000025\tXLOC_000035\tXkr4\tchr1:3212367-3212439\tq1\tq2\tOK\t0\t2.80837e+07\tinf\t-nan\t0.0612\t0.186975\tno\n+TCONS_00000026\tXLOC_000037\tXkr4\tchr1:3213095-3213242\tq1\tq2\tOK\t4.24463e+06\t2.08209e+06\t-1.0276\t-0.36063\t0.3844\t0.435206\tno\n+TCONS_00000027\tXLOC_000040\tXkr4\tchr1:3242633-3242923\tq1\tq2\tOK\t48522.7\t424400\t3.'..b'0000070\tXLOC_000038\tXkr4\tchr1:3240606-3240633\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n TCONS_00000071\tXLOC_000039\tXkr4\tchr1:3242479-3242512\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n TCONS_00000072\tXLOC_000041\tXkr4\tchr1:3242924-3243005\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n-TCONS_00000073\tXLOC_000043\tXkr4\tchr1:3243108-3243154\tq1\tq2\tOK\t9.99919e+07\t0\t-1.79769e+308\t-1.79769e+308\t0.158655\t0.158655\tno\n+TCONS_00000073\tXLOC_000043\tXkr4\tchr1:3243108-3243154\tq1\tq2\tOK\t8.616e+07\t0\t-inf\t-nan\t0.12165\t0.186975\tno\n TCONS_00000074\tXLOC_000045\tXkr4\tchr1:3254079-3254106\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n TCONS_00000075\tXLOC_000047\tXkr4\tchr1:3277155-3277182\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n-TCONS_00000076\tXLOC_000049\tXkr4\tchr1:3277913-3278390\tq1\tq2\tNOTEST\t265614\t41870.3\t-2.66534\t2.48499\t0.0129556\t1\tno\n+TCONS_00000076\tXLOC_000049\tXkr4\tchr1:3277913-3278390\tq1\tq2\tOK\t228872\t47662.2\t-2.26362\t-1.16262\t0.30655\t0.380545\tno\n TCONS_00000077\tXLOC_000050\tXkr4\tchr1:3280117-3280144\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n TCONS_00000078\tXLOC_000051\tXkr4\tchr1:3280498-3280525\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n TCONS_00000079\tXLOC_000053\tXkr4\tchr1:3282504-3282531\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n TCONS_00000080\tXLOC_000054\tXkr4\tchr1:3282650-3282677\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n TCONS_00000081\tXLOC_000055\tXkr4\tchr1:3282760-3282832\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n TCONS_00000082\tXLOC_000056\tXkr4\tchr1:3284966-3284993\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n-TCONS_00000083\tXLOC_000058\tXkr4\tchr1:3290798-3290859\tq1\tq2\tOK\t1.8095e+07\t0\t-1.79769e+308\t-1.79769e+308\t0.158655\t0.158655\tno\n-TCONS_00000084\tXLOC_000059\tXkr4\tchr1:3290919-3291273\tq1\tq2\tNOTEST\t342218\t75524\t-2.17991\t1.96162\t0.049807\t1\tno\n-TCONS_00000085\tXLOC_000060\tXkr4\tchr1:3299443-3299664\tq1\tq2\tNOTEST\t937403\t137917\t-2.76487\t1.66807\t0.0953024\t1\tno\n+TCONS_00000083\tXLOC_000058\tXkr4\tchr1:3290798-3290859\tq1\tq2\tOK\t1.55919e+07\t0\t-inf\t-nan\t0.12165\t0.186975\tno\n+TCONS_00000084\tXLOC_000059\tXkr4\tchr1:3290919-3291273\tq1\tq2\tOK\t294879\t85971.3\t-1.7782\t-0.902752\t0.36915\t0.435206\tno\n+TCONS_00000085\tXLOC_000060\tXkr4\tchr1:3299443-3299664\tq1\tq2\tOK\t807732\t156995\t-2.36316\t-0.933704\t0.4205\t0.458727\tno\n TCONS_00000086\tXLOC_000061\tXkr4\tchr1:3299691-3299733\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n TCONS_00000087\tXLOC_000063\tXkr4\tchr1:3307748-3307775\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n TCONS_00000088\tXLOC_000064\tXkr4\tchr1:3318620-3318647\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n TCONS_00000089\tXLOC_000066\tXkr4\tchr1:3330527-3330554\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n-TCONS_00000090\tXLOC_000067\tXkr4\tchr1:3351240-3351311\tq1\tq2\tOK\t8.91489e+06\t0\t-1.79769e+308\t-1.79769e+308\t0.158655\t0.158655\tno\n-TCONS_00000091\tXLOC_000068\tXkr4\tchr1:3355887-3356119\tq1\tq2\tNOTEST\t585828\t0\t-1.79769e+308\t-1.79769e+308\t0.0512352\t1\tno\n-TCONS_00000092\tXLOC_000069\tXkr4\tchr1:3356180-3356225\tq1\tq2\tOK\t1.19208e+08\t0\t-1.79769e+308\t-1.79769e+308\t0.158655\t0.158655\tno\n-TCONS_00000093\tXLOC_000070\tXkr4\tchr1:3363076-3363176\tq1\tq2\tNOTEST\t4.42166e+06\t0\t-1.79769e+308\t-1.79769e+308\t0.0786496\t1\tno\n-TCONS_00000094\tXLOC_000072\tXkr4\tchr1:3363387-3363446\tq1\tq2\tOK\t4.28358e+07\t0\t-1.79769e+308\t-1.79769e+308\t0.0786496\t0.150149\tno\n-TCONS_00000095\tXLOC_000074\tXkr4\tchr1:3364871-3364919\tq1\tq2\tOK\t7.29939e+07\t0\t-1.79769e+308\t-1.79769e+308\t0.158655\t0.158655\tno\n+TCONS_00000090\tXLOC_000067\tXkr4\tchr1:3351240-3351311\tq1\tq2\tOK\t7.68169e+06\t0\t-inf\t-nan\t0.12165\t0.186975\tno\n+TCONS_00000091\tXLOC_000068\tXkr4\tchr1:3355887-3356119\tq1\tq2\tOK\t504790\t0\t-inf\t-nan\t0.05945\t0.186975\tno\n+TCONS_00000092\tXLOC_000069\tXkr4\tchr1:3356180-3356225\tq1\tq2\tOK\t1.02717e+08\t0\t-inf\t-nan\t0.12165\t0.186975\tno\n+TCONS_00000093\tXLOC_000070\tXkr4\tchr1:3363076-3363176\tq1\tq2\tOK\t3.81001e+06\t0\t-inf\t-nan\t0.0148\t0.101571\tno\n+TCONS_00000094\tXLOC_000072\tXkr4\tchr1:3363387-3363446\tq1\tq2\tOK\t5.53654e+07\t0\t-inf\t-nan\t0.0773\t0.186975\tno\n+TCONS_00000095\tXLOC_000074\tXkr4\tchr1:3364871-3364919\tq1\tq2\tOK\t6.28966e+07\t0\t-inf\t-nan\t0.12165\t0.186975\tno\n TCONS_00000096\tXLOC_000076\tXkr4\tchr1:3367210-3367237\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n TCONS_00000097\tXLOC_000078\tXkr4\tchr1:3369580-3369607\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n TCONS_00000098\tXLOC_000079\tXkr4\tchr1:3375001-3375028\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n' |
| b |
| diff -r 604fa75232a2 -r 8da0eade1f59 test-data/cuffdiff_out10.txt --- a/test-data/cuffdiff_out10.txt Thu Jan 16 13:13:52 2014 -0500 +++ b/test-data/cuffdiff_out10.txt Fri Dec 19 11:57:43 2014 -0500 |
| b |
| b'@@ -1,88 +1,88 @@\n test_id\tgene_id\tgene\tlocus\tsample_1\tsample_2\tstatus\tvalue_1\tvalue_2\tsqrt(JS)\ttest_stat\tp_value\tq_value\tsignificant\n XLOC_000001\tXLOC_000001\tXkr4\tchr1:3204754-3204833\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n XLOC_000002\tXLOC_000002\t-\tchr1:3111449-3111490\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n-XLOC_000003\tXLOC_000003\t-\tchr1:3111545-3111576\tq1\tq2\tLOWDATA\t0\t0\t0\t0\t0\t1\tno\n-XLOC_000004\tXLOC_000004\t-\tchr1:3174765-3174792\tq1\tq2\tLOWDATA\t0\t0\t0\t0\t0\t1\tno\n-XLOC_000005\tXLOC_000005\t-\tchr1:3187401-3187428\tq1\tq2\tLOWDATA\t0\t0\t0\t0\t0\t1\tno\n-XLOC_000006\tXLOC_000006\t-\tchr1:3188521-3188548\tq1\tq2\tLOWDATA\t0\t0\t0\t0\t0\t1\tno\n+XLOC_000003\tXLOC_000003\t-\tchr1:3111545-3111576\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n+XLOC_000004\tXLOC_000004\t-\tchr1:3174765-3174792\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n+XLOC_000005\tXLOC_000005\t-\tchr1:3187401-3187428\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n+XLOC_000006\tXLOC_000006\t-\tchr1:3188521-3188548\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n XLOC_000007\tXLOC_000007\t-\tchr1:3189810-3190789\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n XLOC_000008\tXLOC_000008\t-\tchr1:3190858-3191434\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n XLOC_000009\tXLOC_000009\t-\tchr1:3191512-3192077\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n XLOC_000010\tXLOC_000010\t-\tchr1:3192250-3192336\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n XLOC_000011\tXLOC_000011\t-\tchr1:3192441-3192494\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n XLOC_000012\tXLOC_000012\t-\tchr1:3192550-3192629\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n-XLOC_000013\tXLOC_000013\t-\tchr1:3192649-3192676\tq1\tq2\tLOWDATA\t0\t0\t0\t0\t0\t1\tno\n-XLOC_000014\tXLOC_000014\t-\tchr1:3192731-3192811\tq1\tq2\tLOWDATA\t0\t0\t0\t0\t0\t1\tno\n+XLOC_000013\tXLOC_000013\t-\tchr1:3192649-3192676\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n+XLOC_000014\tXLOC_000014\t-\tchr1:3192731-3192811\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n XLOC_000015\tXLOC_000015\t-\tchr1:3192940-3193042\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n XLOC_000016\tXLOC_000016\t-\tchr1:3194185-3194226\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n-XLOC_000017\tXLOC_000017\t-\tchr1:3194302-3194329\tq1\tq2\tLOWDATA\t0\t0\t0\t0\t0\t1\tno\n-XLOC_000018\tXLOC_000018\t-\tchr1:3194706-3194733\tq1\tq2\tLOWDATA\t0\t0\t0\t0\t0\t1\tno\n-XLOC_000019\tXLOC_000019\t-\tchr1:3195083-3195110\tq1\tq2\tLOWDATA\t0\t0\t0\t0\t0\t1\tno\n-XLOC_000020\tXLOC_000020\t-\tchr1:3195450-3195477\tq1\tq2\tLOWDATA\t0\t0\t0\t0\t0\t1\tno\n-XLOC_000021\tXLOC_000021\t-\tchr1:3197089-3197116\tq1\tq2\tLOWDATA\t0\t0\t0\t0\t0\t1\tno\n-XLOC_000022\tXLOC_000022\t-\tchr1:3197246-3197273\tq1\tq2\tLOWDATA\t0\t0\t0\t0\t0\t1\tno\n-XLOC_000023\tXLOC_000023\t-\tchr1:3197346-3197373\tq1\tq2\tLOWDATA\t0\t0\t0\t0\t0\t1\tno\n-XLOC_000024\tXLOC_000024\t-\tchr1:3197425-3197452\tq1\tq2\tLOWDATA\t0\t0\t0\t0\t0\t1\tno\n+XLOC_000017\tXLOC_000017\t-\tchr1:3194302-3194329\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n+XLOC_000018\tXLOC_000018\t-\tchr1:3194706-3194733\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n+XLOC_000019\tXLOC_000019\t-\tchr1:3195083-3195110\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n+XLOC_000020\tXLOC_000020\t-\tchr1:3195450-3195477\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n+XLOC_000021\tXLOC_000021\t-\tchr1:3197089-3197116\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n+XLOC_000022\tXLOC_000022\t-\tchr1:3197246-3197273\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n+XLOC_000023\tXLOC_000023\t-\tchr1:3197346-3197373\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n+XLOC_000024\tXLOC_000024\t-\tchr1:3197425-3197452\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n XLOC_000025\tXLOC_000025\t-\tchr1:3200022-3200191\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n-XLOC_000026\tXLOC_000026\t-\tchr1:3200325-3200352\tq1\tq2\tLOWDATA\t0\t0\t0\t0\t0\t1\tno\n-XLOC_000027\tXLOC_000027\t-\tchr1:3200430-3200457\tq1\tq2\tLOWDATA\t0\t0\t0\t0\t0\t1\tno\n-XLOC_000028\tXLOC_000028\t-\tchr1:3201007-3201039\tq1\tq2\tLOWDATA\t0\t0\t0\t0\t0\t1\tno\n+XLOC_000026\tXLOC_000026\t-\tchr1:3200325-3200352\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n+XLOC_000027\tXLOC_000027\t-\tchr1:3200430-3200457\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n+XLOC_000028\tXLOC_000028\t-\tchr1:3201007-3201039\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n XLOC_000029\tXLOC_000029\t-\tchr1:3201077-3201481\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n XLOC_000030\tXLOC_000030\t-\tchr1:3201596-3201666\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n-XLOC_000031\tXLOC_000031\t-\tchr1:3201672-3201699\tq1\tq2\tLOWDATA\t0\t0\t0\t0\t0\t1\tno\n+XLOC_000031\tXLOC_000031\t-\tchr1:3201672-3201699\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n XLOC_000032\tXLOC_000032\t-\tchr1:3201725-3201809\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n-XLOC_000033\tXLOC_000033\tXkr4\tchr1:3211521-3'..b'q1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n XLOC_000059\tXLOC_000059\tXkr4\tchr1:3290919-3291273\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n XLOC_000060\tXLOC_000060\tXkr4\tchr1:3299443-3299664\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n-XLOC_000061\tXLOC_000061\tXkr4\tchr1:3299691-3299733\tq1\tq2\tLOWDATA\t0\t0\t0\t0\t0\t1\tno\n-XLOC_000062\tXLOC_000062\tXkr4\tchr1:3300051-3300078\tq1\tq2\tLOWDATA\t0\t0\t0\t0\t0\t1\tno\n-XLOC_000063\tXLOC_000063\tXkr4\tchr1:3307748-3307775\tq1\tq2\tLOWDATA\t0\t0\t0\t0\t0\t1\tno\n-XLOC_000064\tXLOC_000064\tXkr4\tchr1:3318620-3318647\tq1\tq2\tLOWDATA\t0\t0\t0\t0\t0\t1\tno\n-XLOC_000065\tXLOC_000065\tXkr4\tchr1:3318999-3319051\tq1\tq2\tLOWDATA\t0\t0\t0\t0\t0\t1\tno\n-XLOC_000066\tXLOC_000066\tXkr4\tchr1:3330527-3330554\tq1\tq2\tLOWDATA\t0\t0\t0\t0\t0\t1\tno\n+XLOC_000061\tXLOC_000061\tXkr4\tchr1:3299691-3299733\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n+XLOC_000062\tXLOC_000062\tXkr4\tchr1:3300051-3300078\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n+XLOC_000063\tXLOC_000063\tXkr4\tchr1:3307748-3307775\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n+XLOC_000064\tXLOC_000064\tXkr4\tchr1:3318620-3318647\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n+XLOC_000065\tXLOC_000065\tXkr4\tchr1:3318999-3319051\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n+XLOC_000066\tXLOC_000066\tXkr4\tchr1:3330527-3330554\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n XLOC_000067\tXLOC_000067\tXkr4\tchr1:3351240-3351311\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n XLOC_000068\tXLOC_000068\tXkr4\tchr1:3355887-3356119\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n XLOC_000069\tXLOC_000069\tXkr4\tchr1:3356180-3356225\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n XLOC_000070\tXLOC_000070\tXkr4\tchr1:3363076-3363176\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n-XLOC_000071\tXLOC_000071\tXkr4\tchr1:3363214-3363278\tq1\tq2\tLOWDATA\t0\t0\t0\t0\t0\t1\tno\n+XLOC_000071\tXLOC_000071\tXkr4\tchr1:3363214-3363278\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n XLOC_000072\tXLOC_000072\tXkr4\tchr1:3363387-3363446\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n-XLOC_000073\tXLOC_000073\tXkr4\tchr1:3363753-3363849\tq1\tq2\tLOWDATA\t0\t0\t0\t0\t0\t1\tno\n+XLOC_000073\tXLOC_000073\tXkr4\tchr1:3363753-3363849\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n XLOC_000074\tXLOC_000074\tXkr4\tchr1:3364871-3364919\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n-XLOC_000075\tXLOC_000075\tXkr4\tchr1:3367135-3367162\tq1\tq2\tLOWDATA\t0\t0\t0\t0\t0\t1\tno\n-XLOC_000076\tXLOC_000076\tXkr4\tchr1:3367210-3367237\tq1\tq2\tLOWDATA\t0\t0\t0\t0\t0\t1\tno\n-XLOC_000077\tXLOC_000077\tXkr4\tchr1:3367333-3367382\tq1\tq2\tLOWDATA\t0\t0\t0\t0\t0\t1\tno\n-XLOC_000078\tXLOC_000078\tXkr4\tchr1:3369580-3369607\tq1\tq2\tLOWDATA\t0\t0\t0\t0\t0\t1\tno\n-XLOC_000079\tXLOC_000079\tXkr4\tchr1:3375001-3375028\tq1\tq2\tLOWDATA\t0\t0\t0\t0\t0\t1\tno\n-XLOC_000080\tXLOC_000080\tXkr4\tchr1:3377211-3377262\tq1\tq2\tLOWDATA\t0\t0\t0\t0\t0\t1\tno\n-XLOC_000081\tXLOC_000081\tXkr4\tchr1:3379888-3379915\tq1\tq2\tLOWDATA\t0\t0\t0\t0\t0\t1\tno\n-XLOC_000082\tXLOC_000082\tXkr4\tchr1:3386739-3386836\tq1\tq2\tLOWDATA\t0\t0\t0\t0\t0\t1\tno\n-XLOC_000083\tXLOC_000083\tXkr4\tchr1:3391325-3391352\tq1\tq2\tLOWDATA\t0\t0\t0\t0\t0\t1\tno\n-XLOC_000084\tXLOC_000084\tXkr4\tchr1:3435841-3435880\tq1\tq2\tLOWDATA\t0\t0\t0\t0\t0\t1\tno\n-XLOC_000085\tXLOC_000085\tXkr4\tchr1:3447761-3447788\tq1\tq2\tLOWDATA\t0\t0\t0\t0\t0\t1\tno\n-XLOC_000086\tXLOC_000086\tXkr4\tchr1:3450906-3450965\tq1\tq2\tLOWDATA\t0\t0\t0\t0\t0\t1\tno\n-XLOC_000087\tXLOC_000087\tXkr4\tchr1:3451051-3451109\tq1\tq2\tLOWDATA\t0\t0\t0\t0\t0\t1\tno\n+XLOC_000075\tXLOC_000075\tXkr4\tchr1:3367135-3367162\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n+XLOC_000076\tXLOC_000076\tXkr4\tchr1:3367210-3367237\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n+XLOC_000077\tXLOC_000077\tXkr4\tchr1:3367333-3367382\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n+XLOC_000078\tXLOC_000078\tXkr4\tchr1:3369580-3369607\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n+XLOC_000079\tXLOC_000079\tXkr4\tchr1:3375001-3375028\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n+XLOC_000080\tXLOC_000080\tXkr4\tchr1:3377211-3377262\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n+XLOC_000081\tXLOC_000081\tXkr4\tchr1:3379888-3379915\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n+XLOC_000082\tXLOC_000082\tXkr4\tchr1:3386739-3386836\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n+XLOC_000083\tXLOC_000083\tXkr4\tchr1:3391325-3391352\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n+XLOC_000084\tXLOC_000084\tXkr4\tchr1:3435841-3435880\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n+XLOC_000085\tXLOC_000085\tXkr4\tchr1:3447761-3447788\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n+XLOC_000086\tXLOC_000086\tXkr4\tchr1:3450906-3450965\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n+XLOC_000087\tXLOC_000087\tXkr4\tchr1:3451051-3451109\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n' |
| b |
| diff -r 604fa75232a2 -r 8da0eade1f59 test-data/cuffdiff_out2.txt --- a/test-data/cuffdiff_out2.txt Thu Jan 16 13:13:52 2014 -0500 +++ b/test-data/cuffdiff_out2.txt Fri Dec 19 11:57:43 2014 -0500 |
| b |
| b'@@ -1,20 +1,20 @@\n test_id\tgene_id\tgene\tlocus\tsample_1\tsample_2\tstatus\tvalue_1\tvalue_2\tlog2(fold_change)\ttest_stat\tp_value\tq_value\tsignificant\n-XLOC_000001\tXLOC_000001\tXkr4\tchr1:3204754-3204833\tq1\tq2\tOK\t0\t8.3103e+06\t1.79769e+308\t1.79769e+308\t0.0786496\t0.157299\tno\n-XLOC_000002\tXLOC_000002\t-\tchr1:3111449-3111490\tq1\tq2\tOK\t0\t2.1403e+08\t1.79769e+308\t1.79769e+308\t0.158655\t0.16621\tno\n+XLOC_000001\tXLOC_000001\tXkr4\tchr1:3204754-3204833\tq1\tq2\tOK\t0\t9.45986e+06\tinf\t-nan\t0.01975\t0.09875\tno\n+XLOC_000002\tXLOC_000002\t-\tchr1:3111449-3111490\tq1\tq2\tOK\t0\t2.43637e+08\tinf\t-nan\t0.12465\t0.181781\tno\n XLOC_000003\tXLOC_000003\t-\tchr1:3111545-3111576\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n XLOC_000004\tXLOC_000004\t-\tchr1:3174765-3174792\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n XLOC_000005\tXLOC_000005\t-\tchr1:3187401-3187428\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n XLOC_000006\tXLOC_000006\t-\tchr1:3188521-3188548\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n-XLOC_000007\tXLOC_000007\t-\tchr1:3189810-3190789\tq1\tq2\tNOTEST\t368900\t429265\t0.21864\t-0.483034\t0.629072\t1\tno\n-XLOC_000008\tXLOC_000008\t-\tchr1:3190858-3191434\tq1\tq2\tNOTEST\t404373\t338500\t-0.25653\t0.342922\t0.731657\t1\tno\n-XLOC_000009\tXLOC_000009\t-\tchr1:3191512-3192077\tq1\tq2\tNOTEST\t402276\t686974\t0.772069\t-1.24554\t0.212932\t1\tno\n-XLOC_000010\tXLOC_000010\t-\tchr1:3192250-3192336\tq1\tq2\tNOTEST\t3.994e+06\t2.93812e+06\t-0.442943\t0.217099\t0.828131\t1\tno\n-XLOC_000011\tXLOC_000011\t-\tchr1:3192441-3192494\tq1\tq2\tOK\t0\t5.68095e+07\t1.79769e+308\t1.79769e+308\t0.0786496\t0.157299\tno\n-XLOC_000012\tXLOC_000012\t-\tchr1:3192550-3192629\tq1\tq2\tOK\t0\t4.15515e+06\t1.79769e+308\t1.79769e+308\t0.158655\t0.16621\tno\n+XLOC_000007\tXLOC_000007\t-\tchr1:3189810-3190789\tq1\tq2\tOK\t358326\t522345\t0.543731\t1.1445\t0.1952\t0.27328\tno\n+XLOC_000008\tXLOC_000008\t-\tchr1:3190858-3191434\tq1\tq2\tOK\t408511\t420354\t0.0412311\t0.0469899\t0.96715\t0.96715\tno\n+XLOC_000009\tXLOC_000009\t-\tchr1:3191512-3192077\tq1\tq2\tOK\t433286\t842157\t0.958769\t1.27887\t0.20385\t0.274413\tno\n+XLOC_000010\tXLOC_000010\t-\tchr1:3192250-3192336\tq1\tq2\tOK\t3.44151e+06\t3.34455e+06\t-0.0412311\t-0.014084\t0.67715\t0.718189\tno\n+XLOC_000011\tXLOC_000011\t-\tchr1:3192441-3192494\tq1\tq2\tOK\t0\t9.7002e+07\tinf\t-nan\t0.07975\t0.181781\tno\n+XLOC_000012\tXLOC_000012\t-\tchr1:3192550-3192629\tq1\tq2\tOK\t0\t4.72993e+06\tinf\t-nan\t0.12465\t0.181781\tno\n XLOC_000013\tXLOC_000013\t-\tchr1:3192649-3192676\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n XLOC_000014\tXLOC_000014\t-\tchr1:3192731-3192811\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n-XLOC_000015\tXLOC_000015\t-\tchr1:3192940-3193042\tq1\tq2\tOK\t0\t6.02976e+06\t1.79769e+308\t1.79769e+308\t0.0512352\t0.157299\tno\n-XLOC_000016\tXLOC_000016\t-\tchr1:3194185-3194226\tq1\tq2\tOK\t0\t2.1403e+08\t1.79769e+308\t1.79769e+308\t0.158655\t0.16621\tno\n+XLOC_000015\tXLOC_000015\t-\tchr1:3192940-3193042\tq1\tq2\tOK\t0\t6.86386e+06\tinf\t-nan\t0.0612\t0.181781\tno\n+XLOC_000016\tXLOC_000016\t-\tchr1:3194185-3194226\tq1\tq2\tOK\t0\t2.43637e+08\tinf\t-nan\t0.12465\t0.181781\tno\n XLOC_000017\tXLOC_000017\t-\tchr1:3194302-3194329\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n XLOC_000018\tXLOC_000018\t-\tchr1:3194706-3194733\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n XLOC_000019\tXLOC_000019\t-\tchr1:3195083-3195110\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n@@ -23,56 +23,56 @@\n XLOC_000022\tXLOC_000022\t-\tchr1:3197246-3197273\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n XLOC_000023\tXLOC_000023\t-\tchr1:3197346-3197373\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n XLOC_000024\tXLOC_000024\t-\tchr1:3197425-3197452\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n-XLOC_000025\tXLOC_000025\t-\tchr1:3200022-3200191\tq1\tq2\tNOTEST\t959058\t705514\t-0.442943\t0.376027\t0.706897\t1\tno\n+XLOC_000025\tXLOC_000025\t-\tchr1:3200022-3200191\tq1\tq2\tOK\t826392\t803108\t-0.0412311\t-0.0180163\t0.8625\t0.887868\tno\n XLOC_000026\tXLOC_000026\t-\tchr1:3200325-3200352\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n XLOC_000027\tXLOC_000027\t-\tchr1:3200430-3200457\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n XLOC_000028\tXLOC_000028\t-\tchr1:3201007-3201039\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n-XLOC_000029\tXLOC_000029\t-\tchr1:3201077-3201481\tq1\tq2\tNOTEST\t77513.9\t285108\t1.87898\t-1.76152\t0.0781506\t1\tno\n-XLOC_000030\tXLOC_000030\t-\tchr1:3201596-3201666\tq1\tq2\tOK\t1.89853e+07\t0\t-1.79769e+308\t-1.79769e+308\t0.0786496\t0.157299\tno\n+XLOC_000029\tXLOC_000029\t-\tchr1:3201077-3201481\tq1\tq2\tOK\t'..b'\tXkr4\tchr1:3277913-3278390\tq1\tq2\tNOTEST\t265614\t41870.3\t-2.66534\t2.48499\t0.0129556\t1\tno\n+XLOC_000049\tXLOC_000049\tXkr4\tchr1:3277913-3278390\tq1\tq2\tOK\t228872\t47662.2\t-2.26362\t-1.16262\t0.30655\t0.383188\tno\n XLOC_000050\tXLOC_000050\tXkr4\tchr1:3280117-3280144\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n XLOC_000051\tXLOC_000051\tXkr4\tchr1:3280498-3280525\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n-XLOC_000052\tXLOC_000052\tXkr4\tchr1:3280686-3280741\tq1\tq2\tOK\t0\t2.29576e+07\t1.79769e+308\t1.79769e+308\t0.158655\t0.16621\tno\n+XLOC_000052\tXLOC_000052\tXkr4\tchr1:3280686-3280741\tq1\tq2\tOK\t0\t2.61334e+07\tinf\t-nan\t0.12465\t0.181781\tno\n XLOC_000053\tXLOC_000053\tXkr4\tchr1:3282504-3282531\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n XLOC_000054\tXLOC_000054\tXkr4\tchr1:3282650-3282677\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n XLOC_000055\tXLOC_000055\tXkr4\tchr1:3282760-3282832\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n XLOC_000056\tXLOC_000056\tXkr4\tchr1:3284966-3284993\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n-XLOC_000057\tXLOC_000057\tXkr4\tchr1:3290488-3290553\tq1\tq2\tOK\t0\t9.79535e+06\t1.79769e+308\t1.79769e+308\t0.158655\t0.16621\tno\n-XLOC_000058\tXLOC_000058\tXkr4\tchr1:3290798-3290859\tq1\tq2\tOK\t1.8095e+07\t0\t-1.79769e+308\t-1.79769e+308\t0.158655\t0.16621\tno\n-XLOC_000059\tXLOC_000059\tXkr4\tchr1:3290919-3291273\tq1\tq2\tNOTEST\t342218\t75524\t-2.17991\t1.96162\t0.049807\t1\tno\n-XLOC_000060\tXLOC_000060\tXkr4\tchr1:3299443-3299664\tq1\tq2\tNOTEST\t937403\t137917\t-2.76487\t1.66807\t0.0953024\t1\tno\n+XLOC_000057\tXLOC_000057\tXkr4\tchr1:3290488-3290553\tq1\tq2\tOK\t0\t1.11503e+07\tinf\t-nan\t0.12465\t0.181781\tno\n+XLOC_000058\tXLOC_000058\tXkr4\tchr1:3290798-3290859\tq1\tq2\tOK\t1.55919e+07\t0\t-inf\t-nan\t0.12165\t0.181781\tno\n+XLOC_000059\tXLOC_000059\tXkr4\tchr1:3290919-3291273\tq1\tq2\tOK\t294879\t85971.3\t-1.7782\t-0.902752\t0.36915\t0.445526\tno\n+XLOC_000060\tXLOC_000060\tXkr4\tchr1:3299443-3299664\tq1\tq2\tOK\t807732\t156995\t-2.36316\t-0.89463\t0.3993\t0.450823\tno\n XLOC_000061\tXLOC_000061\tXkr4\tchr1:3299691-3299733\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n XLOC_000062\tXLOC_000062\tXkr4\tchr1:3300051-3300078\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n XLOC_000063\tXLOC_000063\tXkr4\tchr1:3307748-3307775\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n XLOC_000064\tXLOC_000064\tXkr4\tchr1:3318620-3318647\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n XLOC_000065\tXLOC_000065\tXkr4\tchr1:3318999-3319051\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n XLOC_000066\tXLOC_000066\tXkr4\tchr1:3330527-3330554\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n-XLOC_000067\tXLOC_000067\tXkr4\tchr1:3351240-3351311\tq1\tq2\tOK\t8.91489e+06\t0\t-1.79769e+308\t-1.79769e+308\t0.158655\t0.16621\tno\n-XLOC_000068\tXLOC_000068\tXkr4\tchr1:3355887-3356119\tq1\tq2\tNOTEST\t585828\t0\t-1.79769e+308\t-1.79769e+308\t0.0512352\t1\tno\n-XLOC_000069\tXLOC_000069\tXkr4\tchr1:3356180-3356225\tq1\tq2\tOK\t1.19208e+08\t0\t-1.79769e+308\t-1.79769e+308\t0.158655\t0.16621\tno\n-XLOC_000070\tXLOC_000070\tXkr4\tchr1:3363076-3363176\tq1\tq2\tNOTEST\t4.42166e+06\t0\t-1.79769e+308\t-1.79769e+308\t0.0786496\t1\tno\n+XLOC_000067\tXLOC_000067\tXkr4\tchr1:3351240-3351311\tq1\tq2\tOK\t7.68169e+06\t0\t-inf\t-nan\t0.12165\t0.181781\tno\n+XLOC_000068\tXLOC_000068\tXkr4\tchr1:3355887-3356119\tq1\tq2\tOK\t504790\t0\t-inf\t-nan\t0.04565\t0.181781\tno\n+XLOC_000069\tXLOC_000069\tXkr4\tchr1:3356180-3356225\tq1\tq2\tOK\t1.02717e+08\t0\t-inf\t-nan\t0.12165\t0.181781\tno\n+XLOC_000070\tXLOC_000070\tXkr4\tchr1:3363076-3363176\tq1\tq2\tOK\t3.81001e+06\t0\t-inf\t-nan\t0.0148\t0.09875\tno\n XLOC_000071\tXLOC_000071\tXkr4\tchr1:3363214-3363278\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n-XLOC_000072\tXLOC_000072\tXkr4\tchr1:3363387-3363446\tq1\tq2\tOK\t4.28358e+07\t0\t-1.79769e+308\t-1.79769e+308\t0.0786496\t0.157299\tno\n+XLOC_000072\tXLOC_000072\tXkr4\tchr1:3363387-3363446\tq1\tq2\tOK\t5.53654e+07\t0\t-inf\t-nan\t0.0773\t0.181781\tno\n XLOC_000073\tXLOC_000073\tXkr4\tchr1:3363753-3363849\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n-XLOC_000074\tXLOC_000074\tXkr4\tchr1:3364871-3364919\tq1\tq2\tOK\t7.29939e+07\t0\t-1.79769e+308\t-1.79769e+308\t0.158655\t0.16621\tno\n+XLOC_000074\tXLOC_000074\tXkr4\tchr1:3364871-3364919\tq1\tq2\tOK\t6.28966e+07\t0\t-inf\t-nan\t0.12165\t0.181781\tno\n XLOC_000075\tXLOC_000075\tXkr4\tchr1:3367135-3367162\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n XLOC_000076\tXLOC_000076\tXkr4\tchr1:3367210-3367237\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n XLOC_000077\tXLOC_000077\tXkr4\tchr1:3367333-3367382\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n' |
| b |
| diff -r 604fa75232a2 -r 8da0eade1f59 test-data/cuffdiff_out3.txt --- a/test-data/cuffdiff_out3.txt Thu Jan 16 13:13:52 2014 -0500 +++ b/test-data/cuffdiff_out3.txt Fri Dec 19 11:57:43 2014 -0500 |
| b |
| b'@@ -1,91 +1,89 @@\n test_id\tgene_id\tgene\tlocus\tsample_1\tsample_2\tstatus\tvalue_1\tvalue_2\tlog2(fold_change)\ttest_stat\tp_value\tq_value\tsignificant\n-TSS1\tXLOC_000001\tXkr4\tchr1:3204754-3204833\tq1\tq2\tOK\t0\t8.3103e+06\t1.79769e+308\t1.79769e+308\t0.0786496\t0.150149\tno\n-TSS11\tXLOC_000008\t-\tchr1:3190858-3191434\tq1\tq2\tNOTEST\t404373\t338500\t-0.25653\t0.342922\t0.731657\t1\tno\n-TSS12\tXLOC_000009\t-\tchr1:3191512-3192077\tq1\tq2\tNOTEST\t402276\t686974\t0.772069\t-1.24554\t0.212932\t1\tno\n-TSS15\tXLOC_000010\t-\tchr1:3192250-3192336\tq1\tq2\tNOTEST\t3.994e+06\t2.93812e+06\t-0.442943\t0.217099\t0.828131\t1\tno\n-TSS16\tXLOC_000011\t-\tchr1:3192441-3192494\tq1\tq2\tOK\t0\t5.68095e+07\t1.79769e+308\t1.79769e+308\t0.0786496\t0.150149\tno\n-TSS17\tXLOC_000012\t-\tchr1:3192550-3192629\tq1\tq2\tOK\t0\t4.15515e+06\t1.79769e+308\t1.79769e+308\t0.158655\t0.158655\tno\n-TSS18\tXLOC_000013\t-\tchr1:3192649-3192676\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n-TSS19\tXLOC_000014\t-\tchr1:3192731-3192811\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n-TSS2\tXLOC_000002\t-\tchr1:3111449-3111490\tq1\tq2\tOK\t0\t2.1403e+08\t1.79769e+308\t1.79769e+308\t0.158655\t0.158655\tno\n-TSS20\tXLOC_000015\t-\tchr1:3192940-3193042\tq1\tq2\tOK\t0\t6.02976e+06\t1.79769e+308\t1.79769e+308\t0.0512352\t0.150149\tno\n-TSS21\tXLOC_000016\t-\tchr1:3194185-3194226\tq1\tq2\tOK\t0\t2.1403e+08\t1.79769e+308\t1.79769e+308\t0.158655\t0.158655\tno\n-TSS22\tXLOC_000017\t-\tchr1:3194302-3194329\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n-TSS23\tXLOC_000018\t-\tchr1:3194706-3194733\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n-TSS24\tXLOC_000019\t-\tchr1:3195083-3195110\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n-TSS25\tXLOC_000020\t-\tchr1:3195450-3195477\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n-TSS26\tXLOC_000021\t-\tchr1:3197089-3197116\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n-TSS27\tXLOC_000022\t-\tchr1:3197246-3197273\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n-TSS28\tXLOC_000023\t-\tchr1:3197346-3197373\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n-TSS29\tXLOC_000024\t-\tchr1:3197425-3197452\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n+TSS1\tXLOC_000001\tXkr4\tchr1:3204754-3204833\tq1\tq2\tOK\t0\t9.45986e+06\tinf\t-nan\t0.01975\t0.09875\tno\n+TSS10\tXLOC_000008\t-\tchr1:3190858-3191434\tq1\tq2\tOK\t408511\t420354\t0.0412311\t0.0469899\t0.96715\t0.96715\tno\n+TSS11\tXLOC_000009\t-\tchr1:3191512-3192077\tq1\tq2\tOK\t433286\t842157\t0.958769\t1.27887\t0.20385\t0.274413\tno\n+TSS13\tXLOC_000010\t-\tchr1:3192250-3192336\tq1\tq2\tOK\t3.44151e+06\t3.34455e+06\t-0.0412311\t-0.014084\t0.67715\t0.718189\tno\n+TSS14\tXLOC_000011\t-\tchr1:3192441-3192494\tq1\tq2\tOK\t0\t9.7002e+07\tinf\t-nan\t0.07975\t0.181781\tno\n+TSS15\tXLOC_000012\t-\tchr1:3192550-3192629\tq1\tq2\tOK\t0\t4.72993e+06\tinf\t-nan\t0.12465\t0.181781\tno\n+TSS16\tXLOC_000013\t-\tchr1:3192649-3192676\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n+TSS17\tXLOC_000014\t-\tchr1:3192731-3192811\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n+TSS18\tXLOC_000015\t-\tchr1:3192940-3193042\tq1\tq2\tOK\t0\t6.86386e+06\tinf\t-nan\t0.0612\t0.181781\tno\n+TSS19\tXLOC_000016\t-\tchr1:3194185-3194226\tq1\tq2\tOK\t0\t2.43637e+08\tinf\t-nan\t0.12465\t0.181781\tno\n+TSS2\tXLOC_000002\t-\tchr1:3111449-3111490\tq1\tq2\tOK\t0\t2.43637e+08\tinf\t-nan\t0.12465\t0.181781\tno\n+TSS20\tXLOC_000017\t-\tchr1:3194302-3194329\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n+TSS21\tXLOC_000018\t-\tchr1:3194706-3194733\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n+TSS22\tXLOC_000019\t-\tchr1:3195083-3195110\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n+TSS23\tXLOC_000020\t-\tchr1:3195450-3195477\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n+TSS24\tXLOC_000021\t-\tchr1:3197089-3197116\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n+TSS25\tXLOC_000022\t-\tchr1:3197246-3197273\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n+TSS26\tXLOC_000023\t-\tchr1:3197346-3197373\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n+TSS27\tXLOC_000024\t-\tchr1:3197425-3197452\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n+TSS28\tXLOC_000025\t-\tchr1:3200022-3200191\tq1\tq2\tOK\t826392\t803108\t-0.0412311\t-0.0180163\t0.8625\t0.887868\tno\n+TSS29\tXLOC_000026\t-\tchr1:3200325-3200352\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n TSS3\tXLOC_000003\t-\tchr1:3111545-3111576\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n-TSS30\tXLOC_000025\t-\tchr1:3200022-3200191\tq1\tq2\tNOTEST\t959058\t705514\t-0.442943\t0.376027\t0.706897\t1\tno\n-TSS32\tXLOC_000026\t-\tchr1:3200325-3200352\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n-TSS33\tXLOC_000027\t-\tchr1:3200430-3200457\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n-TSS34\tXLOC_000028\t-\tchr1:3201007-3201039\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n-TSS35\tXLOC_000029\t-\tchr1:3201'..b'\tchr1:3363387-3363446\tq1\tq2\tOK\t4.28358e+07\t0\t-1.79769e+308\t-1.79769e+308\t0.0786496\t0.150149\tno\n-TSS85\tXLOC_000073\tXkr4\tchr1:3363753-3363849\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n-TSS86\tXLOC_000074\tXkr4\tchr1:3364871-3364919\tq1\tq2\tOK\t7.29939e+07\t0\t-1.79769e+308\t-1.79769e+308\t0.158655\t0.158655\tno\n-TSS87\tXLOC_000075\tXkr4\tchr1:3367135-3367162\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n-TSS88\tXLOC_000076\tXkr4\tchr1:3367210-3367237\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n-TSS89\tXLOC_000077\tXkr4\tchr1:3367333-3367382\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n-TSS90\tXLOC_000078\tXkr4\tchr1:3369580-3369607\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n-TSS91\tXLOC_000079\tXkr4\tchr1:3375001-3375028\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n-TSS92\tXLOC_000080\tXkr4\tchr1:3377211-3377262\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n-TSS93\tXLOC_000081\tXkr4\tchr1:3379888-3379915\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n-TSS94\tXLOC_000082\tXkr4\tchr1:3386739-3386836\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n-TSS95\tXLOC_000083\tXkr4\tchr1:3391325-3391352\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n-TSS96\tXLOC_000084\tXkr4\tchr1:3435841-3435880\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n-TSS97\tXLOC_000085\tXkr4\tchr1:3447761-3447788\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n-TSS98\tXLOC_000086\tXkr4\tchr1:3450906-3450965\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n-TSS99\tXLOC_000087\tXkr4\tchr1:3451051-3451109\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n+TSS60\tXLOC_000056\tXkr4\tchr1:3284966-3284993\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n+TSS61\tXLOC_000057\tXkr4\tchr1:3290488-3290553\tq1\tq2\tOK\t0\t1.11503e+07\tinf\t-nan\t0.12465\t0.181781\tno\n+TSS62\tXLOC_000058\tXkr4\tchr1:3290798-3290859\tq1\tq2\tOK\t1.55919e+07\t0\t-inf\t-nan\t0.12165\t0.181781\tno\n+TSS63\tXLOC_000059\tXkr4\tchr1:3290919-3291273\tq1\tq2\tOK\t294879\t85971.3\t-1.7782\t-0.902752\t0.36915\t0.445526\tno\n+TSS65\tXLOC_000060\tXkr4\tchr1:3299443-3299664\tq1\tq2\tOK\t807732\t156995\t-2.36316\t-0.933704\t0.4205\t0.474758\tno\n+TSS66\tXLOC_000060\tXkr4\tchr1:3299443-3299664\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n+TSS67\tXLOC_000061\tXkr4\tchr1:3299691-3299733\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n+TSS68\tXLOC_000062\tXkr4\tchr1:3300051-3300078\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n+TSS69\tXLOC_000063\tXkr4\tchr1:3307748-3307775\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n+TSS7\tXLOC_000007\t-\tchr1:3189810-3190789\tq1\tq2\tOK\t358326\t522345\t0.543731\t1.1445\t0.1952\t0.27328\tno\n+TSS70\tXLOC_000064\tXkr4\tchr1:3318620-3318647\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n+TSS71\tXLOC_000065\tXkr4\tchr1:3318999-3319051\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n+TSS72\tXLOC_000066\tXkr4\tchr1:3330527-3330554\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n+TSS73\tXLOC_000067\tXkr4\tchr1:3351240-3351311\tq1\tq2\tOK\t7.68169e+06\t0\t-inf\t-nan\t0.12165\t0.181781\tno\n+TSS74\tXLOC_000068\tXkr4\tchr1:3355887-3356119\tq1\tq2\tOK\t504790\t0\t-inf\t-nan\t0.04565\t0.181781\tno\n+TSS75\tXLOC_000069\tXkr4\tchr1:3356180-3356225\tq1\tq2\tOK\t1.02717e+08\t0\t-inf\t-nan\t0.12165\t0.181781\tno\n+TSS76\tXLOC_000070\tXkr4\tchr1:3363076-3363176\tq1\tq2\tOK\t3.81001e+06\t0\t-inf\t-nan\t0.0148\t0.09875\tno\n+TSS77\tXLOC_000071\tXkr4\tchr1:3363214-3363278\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n+TSS78\tXLOC_000072\tXkr4\tchr1:3363387-3363446\tq1\tq2\tOK\t5.53654e+07\t0\t-inf\t-nan\t0.0773\t0.181781\tno\n+TSS79\tXLOC_000073\tXkr4\tchr1:3363753-3363849\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n+TSS80\tXLOC_000074\tXkr4\tchr1:3364871-3364919\tq1\tq2\tOK\t6.28966e+07\t0\t-inf\t-nan\t0.12165\t0.181781\tno\n+TSS81\tXLOC_000075\tXkr4\tchr1:3367135-3367162\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n+TSS82\tXLOC_000076\tXkr4\tchr1:3367210-3367237\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n+TSS83\tXLOC_000077\tXkr4\tchr1:3367333-3367382\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n+TSS84\tXLOC_000078\tXkr4\tchr1:3369580-3369607\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n+TSS85\tXLOC_000079\tXkr4\tchr1:3375001-3375028\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n+TSS86\tXLOC_000080\tXkr4\tchr1:3377211-3377262\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n+TSS87\tXLOC_000081\tXkr4\tchr1:3379888-3379915\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n+TSS88\tXLOC_000082\tXkr4\tchr1:3386739-3386836\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n+TSS89\tXLOC_000083\tXkr4\tchr1:3391325-3391352\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n+TSS90\tXLOC_000084\tXkr4\tchr1:3435841-3435880\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n+TSS91\tXLOC_000085\tXkr4\tchr1:3447761-3447788\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n+TSS92\tXLOC_000086\tXkr4\tchr1:3450906-3450965\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n+TSS93\tXLOC_000087\tXkr4\tchr1:3451051-3451109\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n' |
| b |
| diff -r 604fa75232a2 -r 8da0eade1f59 test-data/cuffdiff_out5.txt --- a/test-data/cuffdiff_out5.txt Thu Jan 16 13:13:52 2014 -0500 +++ b/test-data/cuffdiff_out5.txt Fri Dec 19 11:57:43 2014 -0500 |
| b |
| b'@@ -1,91 +1,91 @@\n tracking_id\tclass_code\tnearest_ref_id\tgene_id\tgene_short_name\ttss_id\tlocus\tlength\tcoverage\tq1_FPKM\tq1_conf_lo\tq1_conf_hi\tq1_status\tq2_FPKM\tq2_conf_lo\tq2_conf_hi\tq2_status\n-TCONS_00000001\tc\tXkr4\tXLOC_000001\tXkr4\tTSS1\tchr1:3204754-3204833\t79\t-\t0\t0\t0\tOK\t8.3103e+06\t0\t2.00628e+07\tOK\n-TCONS_00000002\t-\t-\tXLOC_000002\t-\tTSS2\tchr1:3111449-3111490\t41\t-\t0\t0\t0\tOK\t2.1403e+08\t0\t6.42089e+08\tOK\n+TCONS_00000001\tc\tXkr4\tXLOC_000001\tXkr4\tTSS1\tchr1:3204754-3204833\t79\t-\t0\t0\t0\tOK\t9.45986e+06\t0\t3.33035e+07\tOK\n+TCONS_00000002\t-\t-\tXLOC_000002\t-\tTSS2\tchr1:3111449-3111490\t41\t-\t0\t0\t0\tOK\t2.43637e+08\t0\t9.52723e+08\tOK\n TCONS_00000003\t-\t-\tXLOC_000003\t-\tTSS3\tchr1:3111545-3111576\t31\t-\t0\t0\t0\tOK\t0\t0\t0\tOK\n-TCONS_00000009\t-\t-\tXLOC_000011\t-\tTSS16\tchr1:3192441-3192494\t53\t-\t0\t0\t0\tOK\t5.68095e+07\t0\t1.3715e+08\tOK\n-TCONS_00000010\t-\t-\tXLOC_000012\t-\tTSS17\tchr1:3192550-3192629\t79\t-\t0\t0\t0\tOK\t4.15515e+06\t0\t1.24654e+07\tOK\n-TCONS_00000011\t-\t-\tXLOC_000014\t-\tTSS19\tchr1:3192731-3192811\t80\t-\t0\t0\t0\tOK\t0\t0\t0\tOK\n-TCONS_00000012\t-\t-\tXLOC_000015\t-\tTSS20\tchr1:3192940-3193042\t102\t-\t0\t0\t0\tOK\t6.02976e+06\t0\t1.34147e+07\tOK\n-TCONS_00000013\t-\t-\tXLOC_000016\t-\tTSS21\tchr1:3194185-3194226\t41\t-\t0\t0\t0\tOK\t2.1403e+08\t0\t6.42089e+08\tOK\n-TCONS_00000014\t-\t-\tXLOC_000017\t-\tTSS22\tchr1:3194302-3194329\t27\t-\t0\t0\t0\tOK\t0\t0\t0\tOK\n-TCONS_00000015\t-\t-\tXLOC_000019\t-\tTSS24\tchr1:3195083-3195110\t27\t-\t0\t0\t0\tOK\t0\t0\t0\tOK\n-TCONS_00000016\t-\t-\tXLOC_000020\t-\tTSS25\tchr1:3195450-3195477\t27\t-\t0\t0\t0\tOK\t0\t0\t0\tOK\n-TCONS_00000017\t-\t-\tXLOC_000021\t-\tTSS26\tchr1:3197089-3197116\t27\t-\t0\t0\t0\tOK\t0\t0\t0\tOK\n-TCONS_00000018\t-\t-\tXLOC_000022\t-\tTSS27\tchr1:3197246-3197273\t27\t-\t0\t0\t0\tOK\t0\t0\t0\tOK\n-TCONS_00000019\t-\t-\tXLOC_000023\t-\tTSS28\tchr1:3197346-3197373\t27\t-\t0\t0\t0\tOK\t0\t0\t0\tOK\n-TCONS_00000020\t-\t-\tXLOC_000025\t-\tTSS30\tchr1:3200022-3200191\t169\t-\t959058\t0\t2.06648e+06\tOK\t705514\t0\t1.52017e+06\tOK\n-TCONS_00000021\t-\t-\tXLOC_000026\t-\tTSS32\tchr1:3200325-3200352\t27\t-\t0\t0\t0\tOK\t0\t0\t0\tOK\n-TCONS_00000022\t-\t-\tXLOC_000029\t-\tTSS35\tchr1:3201077-3201481\t404\t-\t77513.9\t0\t167019\tOK\t285108\t21736.5\t548480\tOK\n-TCONS_00000023\t-\t-\tXLOC_000031\t-\tTSS38\tchr1:3201672-3201699\t27\t-\t0\t0\t0\tOK\t0\t0\t0\tOK\n-TCONS_00000024\ti\tXkr4\tXLOC_000034\tXkr4\tTSS41\tchr1:3212213-3212292\t79\t-\t0\t0\t0\tOK\t8.3103e+06\t0\t2.00628e+07\tOK\n-TCONS_00000025\ti\tXkr4\tXLOC_000035\tXkr4\tTSS42\tchr1:3212367-3212439\t72\t-\t0\t0\t0\tOK\t2.4671e+07\t0\t5.48867e+07\tOK\n-TCONS_00000026\ti\tXkr4\tXLOC_000037\tXkr4\tTSS44\tchr1:3213095-3213242\t97\t-\t3.99739e+06\t3.99339e+06\t4.00139e+06\tLOWDATA\t1.82908e+06\t0\t5.48723e+06\tOK\n-TCONS_00000027\ti\tXkr4\tXLOC_000040\tXkr4\tTSS48\tchr1:3242633-3242923\t290\t-\t56312.4\t0\t168937\tOK\t372827\t0\t761430\tOK\n-TCONS_00000028\ti\tXkr4\tXLOC_000042\tXkr4\tTSS50\tchr1:3243018-3243079\t61\t-\t0\t0\t0\tOK\t2.66226e+07\t0\t6.42725e+07\tOK\n-TCONS_00000029\ti\tXkr4\tXLOC_000044\tXkr4\tTSS52\tchr1:3243347-3243401\t54\t-\t0\t0\t0\tOK\t5.0951e+07\t0\t1.23007e+08\tOK\n-TCONS_00000030\ti\tXkr4\tXLOC_000046\tXkr4\tTSS54\tchr1:3256974-3257011\t37\t-\t0\t0\t0\tOK\t2.06814e+09\t0\t4.99293e+09\tOK\n-TCONS_00000031\ti\tXkr4\tXLOC_000048\tXkr4\tTSS56\tchr1:3277190-3277218\t28\t-\t0\t0\t0\tOK\t0\t0\t0\tOK\n-TCONS_00000033\ti\tXkr4\tXLOC_000052\tXkr4\tTSS61\tchr1:3280686-3280741\t55\t-\t0\t0\t0\tOK\t2.29576e+07\t0\t6.88728e+07\tOK\n-TCONS_00000034\ti\tXkr4\tXLOC_000057\tXkr4\tTSS66\tchr1:3290488-3290553\t65\t-\t0\t0\t0\tOK\t9.79535e+06\t0\t2.9386e+07\tOK\n-TCONS_00000037\ti\tXkr4\tXLOC_000060\tXkr4\tTSS71\tchr1:3299443-3299664\t55\t-\t0\t0\t0\tOK\t0\t0\t0\tOK\n-TCONS_00000038\ti\tXkr4\tXLOC_000062\tXkr4\tTSS73\tchr1:3300051-3300078\t27\t-\t0\t0\t0\tOK\t0\t0\t0\tOK\n-TCONS_00000039\ti\tXkr4\tXLOC_000065\tXkr4\tTSS76\tchr1:3318999-3319051\t52\t-\t0\t0\t0\tOK\t0\t0\t0\tOK\n-TCONS_00000040\ti\tXkr4\tXLOC_000068\tXkr4\tTSS79\tchr1:3355887-3356119\t27\t-\t0\t0\t0\tOK\t0\t0\t0\tOK\n-TCONS_00000041\ti\tXkr4\tXLOC_000071\tXkr4\tTSS83\tchr1:3363214-3363278\t64\t-\t0\t0\t0\tOK\t0\t0\t0\tOK\n-TCONS_00000042\ti\tXkr4\tXLOC_000073\tXkr4\tTSS85\tchr1:3363753-3363849\t96\t-\t0\t0\t0\tOK\t0\t0\t0\tOK\n-TCONS_00000043\ti\tXkr4\tXLOC_000075\tXkr4\tTSS87\tchr1:3367135-3367162\t27\t-\t0\t0\t0\tOK\t0\t0\t0\tOK\n-TCONS_00000044\ti\tXkr4\tXLOC_000077\tXkr4\tTSS89\tchr1:3367333-3367382\t49\t-\t0\t0\t0\tOK\t0\t0\t0\tOK\n-TCONS_00000045\ti\tXkr4\tXLOC_000080\tXkr4\tTSS92\tchr1:3377211-3377262\t51\t-\t0'..b'6\t0\t1.31756e+07\tOK\t3.34455e+06\t0\t1.30786e+07\tOK\n+TCONS_00000058\t-\t-\tXLOC_000013\t-\tTSS16\tchr1:3192649-3192676\t27\t-\t0\t0\t0\tOK\t0\t0\t0\tOK\n+TCONS_00000059\t-\t-\tXLOC_000018\t-\tTSS21\tchr1:3194706-3194733\t27\t-\t0\t0\t0\tOK\t0\t0\t0\tOK\n+TCONS_00000060\t-\t-\tXLOC_000024\t-\tTSS27\tchr1:3197425-3197452\t27\t-\t0\t0\t0\tOK\t0\t0\t0\tOK\n+TCONS_00000062\t-\t-\tXLOC_000027\t-\tTSS30\tchr1:3200430-3200457\t27\t-\t0\t0\t0\tOK\t0\t0\t0\tOK\n+TCONS_00000063\t-\t-\tXLOC_000028\t-\tTSS31\tchr1:3201007-3201039\t32\t-\t0\t0\t0\tOK\t0\t0\t0\tOK\n+TCONS_00000065\t-\t-\tXLOC_000030\t-\tTSS33\tchr1:3201596-3201666\t70\t-\t1.6359e+07\t0\t5.96409e+07\tOK\t0\t0\t0\tOK\n+TCONS_00000066\t-\t-\tXLOC_000032\t-\tTSS35\tchr1:3201725-3201809\t84\t-\t1.5136e+07\t0\t4.63396e+07\tOK\t0\t0\t0\tOK\n+TCONS_00000067\ti\tXkr4\tXLOC_000033\tXkr4\tTSS36\tchr1:3211521-3211561\t40\t-\t0\t0\t0\tOK\t0\t0\t0\tOK\n+TCONS_00000068\ti\tXkr4\tXLOC_000036\tXkr4\tTSS39\tchr1:3212717-3212801\t84\t-\t3.784e+06\t0\t1.44868e+07\tOK\t0\t0\t0\tOK\n+TCONS_00000069\ti\tXkr4\tXLOC_000037\tXkr4\tTSS40\tchr1:3213095-3213242\t124\t-\t863189\t0\t4.25222e+06\tOK\t0\t0\t72384.9\tOK\n+TCONS_00000070\ti\tXkr4\tXLOC_000038\tXkr4\tTSS41\tchr1:3240606-3240633\t27\t-\t0\t0\t0\tOK\t0\t0\t0\tOK\n+TCONS_00000071\ti\tXkr4\tXLOC_000039\tXkr4\tTSS42\tchr1:3242479-3242512\t33\t-\t0\t0\t0\tOK\t0\t0\t0\tOK\n+TCONS_00000072\ti\tXkr4\tXLOC_000041\tXkr4\tTSS44\tchr1:3242924-3243005\t81\t-\t0\t0\t0\tOK\t0\t0\t0\tOK\n+TCONS_00000073\ti\tXkr4\tXLOC_000043\tXkr4\tTSS46\tchr1:3243108-3243154\t46\t-\t8.616e+07\t0\t3.29857e+08\tOK\t0\t0\t0\tOK\n+TCONS_00000074\ti\tXkr4\tXLOC_000045\tXkr4\tTSS48\tchr1:3254079-3254106\t27\t-\t0\t0\t0\tOK\t0\t0\t0\tOK\n+TCONS_00000075\ti\tXkr4\tXLOC_000047\tXkr4\tTSS50\tchr1:3277155-3277182\t27\t-\t0\t0\t0\tOK\t0\t0\t0\tOK\n+TCONS_00000076\ti\tXkr4\tXLOC_000049\tXkr4\tTSS52\tchr1:3277913-3278390\t477\t-\t228872\t0\t561229\tOK\t47662.2\t0\t156103\tOK\n+TCONS_00000077\ti\tXkr4\tXLOC_000050\tXkr4\tTSS54\tchr1:3280117-3280144\t27\t-\t0\t0\t0\tOK\t0\t0\t0\tOK\n+TCONS_00000078\ti\tXkr4\tXLOC_000051\tXkr4\tTSS55\tchr1:3280498-3280525\t27\t-\t0\t0\t0\tOK\t0\t0\t0\tOK\n+TCONS_00000079\ti\tXkr4\tXLOC_000053\tXkr4\tTSS57\tchr1:3282504-3282531\t27\t-\t0\t0\t0\tOK\t0\t0\t0\tOK\n+TCONS_00000080\ti\tXkr4\tXLOC_000054\tXkr4\tTSS58\tchr1:3282650-3282677\t27\t-\t0\t0\t0\tOK\t0\t0\t0\tOK\n+TCONS_00000081\ti\tXkr4\tXLOC_000055\tXkr4\tTSS59\tchr1:3282760-3282832\t72\t-\t0\t0\t0\tOK\t0\t0\t0\tOK\n+TCONS_00000082\ti\tXkr4\tXLOC_000056\tXkr4\tTSS60\tchr1:3284966-3284993\t27\t-\t0\t0\t0\tOK\t0\t0\t0\tOK\n+TCONS_00000083\ti\tXkr4\tXLOC_000058\tXkr4\tTSS62\tchr1:3290798-3290859\t61\t-\t1.55919e+07\t0\t5.96926e+07\tOK\t0\t0\t0\tOK\n+TCONS_00000084\ti\tXkr4\tXLOC_000059\tXkr4\tTSS63\tchr1:3290919-3291273\t354\t-\t294879\t0\t740137\tOK\t85971.3\t0\t281572\tOK\n+TCONS_00000085\ti\tXkr4\tXLOC_000060\tXkr4\tTSS65\tchr1:3299443-3299664\t197\t-\t807732\t0\t2.39056e+06\tOK\t156995\t0\t613917\tOK\n+TCONS_00000086\ti\tXkr4\tXLOC_000061\tXkr4\tTSS67\tchr1:3299691-3299733\t42\t-\t0\t0\t0\tOK\t0\t0\t0\tOK\n+TCONS_00000087\ti\tXkr4\tXLOC_000063\tXkr4\tTSS69\tchr1:3307748-3307775\t27\t-\t0\t0\t0\tOK\t0\t0\t0\tOK\n+TCONS_00000088\ti\tXkr4\tXLOC_000064\tXkr4\tTSS70\tchr1:3318620-3318647\t27\t-\t0\t0\t0\tOK\t0\t0\t0\tOK\n+TCONS_00000089\ti\tXkr4\tXLOC_000066\tXkr4\tTSS72\tchr1:3330527-3330554\t27\t-\t0\t0\t0\tOK\t0\t0\t0\tOK\n+TCONS_00000090\ti\tXkr4\tXLOC_000067\tXkr4\tTSS73\tchr1:3351240-3351311\t71\t-\t7.68169e+06\t0\t2.94088e+07\tOK\t0\t0\t0\tOK\n+TCONS_00000091\ti\tXkr4\tXLOC_000068\tXkr4\tTSS74\tchr1:3355887-3356119\t212\t-\t504790\t0\t1.54544e+06\tOK\t0\t0\t0\tOK\n+TCONS_00000092\ti\tXkr4\tXLOC_000069\tXkr4\tTSS75\tchr1:3356180-3356225\t45\t-\t1.02717e+08\t0\t3.93246e+08\tOK\t0\t0\t0\tOK\n+TCONS_00000093\ti\tXkr4\tXLOC_000070\tXkr4\tTSS76\tchr1:3363076-3363176\t100\t-\t3.81001e+06\t0\t1.38903e+07\tOK\t0\t0\t0\tOK\n+TCONS_00000094\ti\tXkr4\tXLOC_000072\tXkr4\tTSS78\tchr1:3363387-3363446\t59\t-\t5.53654e+07\t0\t1.77783e+08\tOK\t0\t0\t0\tOK\n+TCONS_00000095\ti\tXkr4\tXLOC_000074\tXkr4\tTSS80\tchr1:3364871-3364919\t48\t-\t6.28966e+07\t0\t2.40795e+08\tOK\t0\t0\t0\tOK\n+TCONS_00000096\ti\tXkr4\tXLOC_000076\tXkr4\tTSS82\tchr1:3367210-3367237\t27\t-\t0\t0\t0\tOK\t0\t0\t0\tOK\n+TCONS_00000097\ti\tXkr4\tXLOC_000078\tXkr4\tTSS84\tchr1:3369580-3369607\t27\t-\t0\t0\t0\tOK\t0\t0\t0\tOK\n+TCONS_00000098\ti\tXkr4\tXLOC_000079\tXkr4\tTSS85\tchr1:3375001-3375028\t27\t-\t0\t0\t0\tOK\t0\t0\t0\tOK\n+TCONS_00000099\ti\tXkr4\tXLOC_000081\tXkr4\tTSS87\tchr1:3379888-3379915\t27\t-\t0\t0\t0\tOK\t0\t0\t0\tOK\n+TCONS_00000100\ti\tXkr4\tXLOC_000082\tXkr4\tTSS88\tchr1:3386739-3386836\t97\t-\t0\t0\t0\tOK\t0\t0\t0\tOK\n' |
| b |
| diff -r 604fa75232a2 -r 8da0eade1f59 test-data/cuffdiff_out6.txt --- a/test-data/cuffdiff_out6.txt Thu Jan 16 13:13:52 2014 -0500 +++ b/test-data/cuffdiff_out6.txt Fri Dec 19 11:57:43 2014 -0500 |
| b |
| b'@@ -1,88 +1,88 @@\n tracking_id\tclass_code\tnearest_ref_id\tgene_id\tgene_short_name\ttss_id\tlocus\tlength\tcoverage\tq1_FPKM\tq1_conf_lo\tq1_conf_hi\tq1_status\tq2_FPKM\tq2_conf_lo\tq2_conf_hi\tq2_status\n-XLOC_000001\t-\t-\tXLOC_000001\tXkr4\tTSS1\tchr1:3204754-3204833\t-\t-\t0\t0\t0\tOK\t8.3103e+06\t0\t2.00628e+07\tOK\n-XLOC_000002\t-\t-\tXLOC_000002\t-\tTSS2\tchr1:3111449-3111490\t-\t-\t0\t0\t0\tOK\t2.1403e+08\t0\t6.42089e+08\tOK\n+XLOC_000001\t-\t-\tXLOC_000001\tXkr4\tTSS1\tchr1:3204754-3204833\t-\t-\t0\t0\t0\tOK\t9.45986e+06\t0\t3.33035e+07\tOK\n+XLOC_000002\t-\t-\tXLOC_000002\t-\tTSS2\tchr1:3111449-3111490\t-\t-\t0\t0\t0\tOK\t2.43637e+08\t0\t9.52723e+08\tOK\n XLOC_000003\t-\t-\tXLOC_000003\t-\tTSS3\tchr1:3111545-3111576\t-\t-\t0\t0\t0\tOK\t0\t0\t0\tOK\n XLOC_000004\t-\t-\tXLOC_000004\t-\tTSS4\tchr1:3174765-3174792\t-\t-\t0\t0\t0\tOK\t0\t0\t0\tOK\n XLOC_000005\t-\t-\tXLOC_000005\t-\tTSS5\tchr1:3187401-3187428\t-\t-\t0\t0\t0\tOK\t0\t0\t0\tOK\n XLOC_000006\t-\t-\tXLOC_000006\t-\tTSS6\tchr1:3188521-3188548\t-\t-\t0\t0\t0\tOK\t0\t0\t0\tOK\n-XLOC_000007\t-\t-\tXLOC_000007\t-\tTSS7\tchr1:3189810-3190789\t-\t-\t368900\t151353\t586447\tOK\t429265\t337221\t521309\tOK\n-XLOC_000008\t-\t-\tXLOC_000008\t-\tTSS11\tchr1:3190858-3191434\t-\t-\t404373\t101434\t707312\tOK\t338500\t95761.5\t581239\tOK\n-XLOC_000009\t-\t-\tXLOC_000009\t-\tTSS12\tchr1:3191512-3192077\t-\t-\t402276\t96829.4\t707722\tOK\t686974\t410563\t963384\tOK\n-XLOC_000010\t-\t-\tXLOC_000010\t-\tTSS15\tchr1:3192250-3192336\t-\t-\t3.994e+06\t0\t1.1982e+07\tOK\t2.93812e+06\t0\t8.81435e+06\tOK\n-XLOC_000011\t-\t-\tXLOC_000011\t-\tTSS16\tchr1:3192441-3192494\t-\t-\t0\t0\t0\tOK\t5.68095e+07\t0\t1.3715e+08\tOK\n-XLOC_000012\t-\t-\tXLOC_000012\t-\tTSS17\tchr1:3192550-3192629\t-\t-\t0\t0\t0\tOK\t4.15515e+06\t0\t1.24654e+07\tOK\n-XLOC_000013\t-\t-\tXLOC_000013\t-\tTSS18\tchr1:3192649-3192676\t-\t-\t0\t0\t0\tOK\t0\t0\t0\tOK\n-XLOC_000014\t-\t-\tXLOC_000014\t-\tTSS19\tchr1:3192731-3192811\t-\t-\t0\t0\t0\tOK\t0\t0\t0\tOK\n-XLOC_000015\t-\t-\tXLOC_000015\t-\tTSS20\tchr1:3192940-3193042\t-\t-\t0\t0\t0\tOK\t6.02976e+06\t0\t1.34147e+07\tOK\n-XLOC_000016\t-\t-\tXLOC_000016\t-\tTSS21\tchr1:3194185-3194226\t-\t-\t0\t0\t0\tOK\t2.1403e+08\t0\t6.42089e+08\tOK\n-XLOC_000017\t-\t-\tXLOC_000017\t-\tTSS22\tchr1:3194302-3194329\t-\t-\t0\t0\t0\tOK\t0\t0\t0\tOK\n-XLOC_000018\t-\t-\tXLOC_000018\t-\tTSS23\tchr1:3194706-3194733\t-\t-\t0\t0\t0\tOK\t0\t0\t0\tOK\n-XLOC_000019\t-\t-\tXLOC_000019\t-\tTSS24\tchr1:3195083-3195110\t-\t-\t0\t0\t0\tOK\t0\t0\t0\tOK\n-XLOC_000020\t-\t-\tXLOC_000020\t-\tTSS25\tchr1:3195450-3195477\t-\t-\t0\t0\t0\tOK\t0\t0\t0\tOK\n-XLOC_000021\t-\t-\tXLOC_000021\t-\tTSS26\tchr1:3197089-3197116\t-\t-\t0\t0\t0\tOK\t0\t0\t0\tOK\n-XLOC_000022\t-\t-\tXLOC_000022\t-\tTSS27\tchr1:3197246-3197273\t-\t-\t0\t0\t0\tOK\t0\t0\t0\tOK\n-XLOC_000023\t-\t-\tXLOC_000023\t-\tTSS28\tchr1:3197346-3197373\t-\t-\t0\t0\t0\tOK\t0\t0\t0\tOK\n-XLOC_000024\t-\t-\tXLOC_000024\t-\tTSS29\tchr1:3197425-3197452\t-\t-\t0\t0\t0\tOK\t0\t0\t0\tOK\n-XLOC_000025\t-\t-\tXLOC_000025\t-\tTSS30\tchr1:3200022-3200191\t-\t-\t959058\t0\t2.06648e+06\tOK\t705514\t0\t1.52017e+06\tOK\n-XLOC_000026\t-\t-\tXLOC_000026\t-\tTSS32\tchr1:3200325-3200352\t-\t-\t0\t0\t0\tOK\t0\t0\t0\tOK\n-XLOC_000027\t-\t-\tXLOC_000027\t-\tTSS33\tchr1:3200430-3200457\t-\t-\t0\t0\t0\tOK\t0\t0\t0\tOK\n-XLOC_000028\t-\t-\tXLOC_000028\t-\tTSS34\tchr1:3201007-3201039\t-\t-\t0\t0\t0\tOK\t0\t0\t0\tOK\n-XLOC_000029\t-\t-\tXLOC_000029\t-\tTSS35\tchr1:3201077-3201481\t-\t-\t77513.9\t0\t167019\tOK\t285108\t21736.5\t548480\tOK\n-XLOC_000030\t-\t-\tXLOC_000030\t-\tTSS37\tchr1:3201596-3201666\t-\t-\t1.89853e+07\t0\t4.58345e+07\tOK\t0\t0\t0\tOK\n-XLOC_000031\t-\t-\tXLOC_000031\t-\tTSS38\tchr1:3201672-3201699\t-\t-\t0\t0\t0\tOK\t0\t0\t0\tOK\n-XLOC_000032\t-\t-\tXLOC_000032\t-\tTSS39\tchr1:3201725-3201809\t-\t-\t1.31744e+07\t0\t2.83869e+07\tOK\t0\t0\t0\tOK\n-XLOC_000033\t-\t-\tXLOC_000033\tXkr4\tTSS40\tchr1:3211521-3211561\t-\t-\t0\t0\t0\tOK\t0\t0\t0\tOK\n-XLOC_000034\t-\t-\tXLOC_000034\tXkr4\tTSS41\tchr1:3212213-3212292\t-\t-\t0\t0\t0\tOK\t8.3103e+06\t0\t2.00628e+07\tOK\n-XLOC_000035\t-\t-\tXLOC_000035\tXkr4\tTSS42\tchr1:3212367-3212439\t-\t-\t0\t0\t0\tOK\t2.4671e+07\t0\t5.48867e+07\tOK\n-XLOC_000036\t-\t-\tXLOC_000036\tXkr4\tTSS43\tchr1:3212717-3212801\t-\t-\t4.39147e+06\t0\t1.31744e+07\tOK\t0\t0\t0\tOK\n-XLOC_000037\t-\t-\tXLOC_000037\tXkr4\tTSS44,TSS45\tchr1:3213095-3213242\t-\t-\t5.3664e+06\t0\t1.39795e+07\tLOWDATA\t1.82908e+06\t0\t5.48723e+06\tOK\n-XLOC_000038\t-\t-\tXLOC_000038\tXkr4\tTSS46\tchr1:3240606-3240633\t-\t-\t0\t0\t0\tOK\t0\t0\t0\tOK\n-XLOC_000039\t-\t-\tXLOC_000039\tXkr4\tTSS47\tchr1:3242479-3242512\t-\t-\t0\t0\t0\tOK\t0\t0\t0\tOK\n-XLOC_000040\t-\t-\tXLOC'..b'r1:3243108-3243154\t-\t-\t8.616e+07\t0\t3.29857e+08\tOK\t0\t0\t0\tOK\n+XLOC_000044\t-\t-\tXLOC_000044\tXkr4\tTSS47\tchr1:3243347-3243401\t-\t-\t0\t0\t0\tOK\t5.79991e+07\t0\t2.04186e+08\tOK\n+XLOC_000045\t-\t-\tXLOC_000045\tXkr4\tTSS48\tchr1:3254079-3254106\t-\t-\t0\t0\t0\tOK\t0\t0\t0\tOK\n+XLOC_000046\t-\t-\tXLOC_000046\tXkr4\tTSS49\tchr1:3256974-3257011\t-\t-\t0\t0\t0\tOK\t2.35423e+09\t0\t8.28806e+09\tOK\n+XLOC_000047\t-\t-\tXLOC_000047\tXkr4\tTSS50\tchr1:3277155-3277182\t-\t-\t0\t0\t0\tOK\t0\t0\t0\tOK\n+XLOC_000048\t-\t-\tXLOC_000048\tXkr4\tTSS51\tchr1:3277190-3277218\t-\t-\t0\t0\t0\tOK\t0\t0\t0\tOK\n+XLOC_000049\t-\t-\tXLOC_000049\tXkr4\tTSS52\tchr1:3277913-3278390\t-\t-\t228872\t0\t561229\tOK\t47662.2\t0\t156103\tOK\n+XLOC_000050\t-\t-\tXLOC_000050\tXkr4\tTSS54\tchr1:3280117-3280144\t-\t-\t0\t0\t0\tOK\t0\t0\t0\tOK\n+XLOC_000051\t-\t-\tXLOC_000051\tXkr4\tTSS55\tchr1:3280498-3280525\t-\t-\t0\t0\t0\tOK\t0\t0\t0\tOK\n+XLOC_000052\t-\t-\tXLOC_000052\tXkr4\tTSS56\tchr1:3280686-3280741\t-\t-\t0\t0\t0\tOK\t2.61334e+07\t0\t1.02193e+08\tOK\n+XLOC_000053\t-\t-\tXLOC_000053\tXkr4\tTSS57\tchr1:3282504-3282531\t-\t-\t0\t0\t0\tOK\t0\t0\t0\tOK\n+XLOC_000054\t-\t-\tXLOC_000054\tXkr4\tTSS58\tchr1:3282650-3282677\t-\t-\t0\t0\t0\tOK\t0\t0\t0\tOK\n+XLOC_000055\t-\t-\tXLOC_000055\tXkr4\tTSS59\tchr1:3282760-3282832\t-\t-\t0\t0\t0\tOK\t0\t0\t0\tOK\n+XLOC_000056\t-\t-\tXLOC_000056\tXkr4\tTSS60\tchr1:3284966-3284993\t-\t-\t0\t0\t0\tOK\t0\t0\t0\tOK\n+XLOC_000057\t-\t-\tXLOC_000057\tXkr4\tTSS61\tchr1:3290488-3290553\t-\t-\t0\t0\t0\tOK\t1.11503e+07\t0\t4.36026e+07\tOK\n+XLOC_000058\t-\t-\tXLOC_000058\tXkr4\tTSS62\tchr1:3290798-3290859\t-\t-\t1.55919e+07\t0\t5.96926e+07\tOK\t0\t0\t0\tOK\n+XLOC_000059\t-\t-\tXLOC_000059\tXkr4\tTSS63\tchr1:3290919-3291273\t-\t-\t294879\t0\t740137\tOK\t85971.3\t0\t281572\tOK\n+XLOC_000060\t-\t-\tXLOC_000060\tXkr4\tTSS65,TSS66\tchr1:3299443-3299664\t-\t-\t807732\t0\t2.39786e+06\tOK\t156995\t0\t641748\tOK\n+XLOC_000061\t-\t-\tXLOC_000061\tXkr4\tTSS67\tchr1:3299691-3299733\t-\t-\t0\t0\t0\tOK\t0\t0\t0\tOK\n+XLOC_000062\t-\t-\tXLOC_000062\tXkr4\tTSS68\tchr1:3300051-3300078\t-\t-\t0\t0\t0\tOK\t0\t0\t0\tOK\n+XLOC_000063\t-\t-\tXLOC_000063\tXkr4\tTSS69\tchr1:3307748-3307775\t-\t-\t0\t0\t0\tOK\t0\t0\t0\tOK\n+XLOC_000064\t-\t-\tXLOC_000064\tXkr4\tTSS70\tchr1:3318620-3318647\t-\t-\t0\t0\t0\tOK\t0\t0\t0\tOK\n+XLOC_000065\t-\t-\tXLOC_000065\tXkr4\tTSS71\tchr1:3318999-3319051\t-\t-\t0\t0\t0\tOK\t0\t0\t0\tOK\n+XLOC_000066\t-\t-\tXLOC_000066\tXkr4\tTSS72\tchr1:3330527-3330554\t-\t-\t0\t0\t0\tOK\t0\t0\t0\tOK\n+XLOC_000067\t-\t-\tXLOC_000067\tXkr4\tTSS73\tchr1:3351240-3351311\t-\t-\t7.68169e+06\t0\t2.94088e+07\tOK\t0\t0\t0\tOK\n+XLOC_000068\t-\t-\tXLOC_000068\tXkr4\tTSS74\tchr1:3355887-3356119\t-\t-\t504790\t0\t1.59712e+06\tOK\t0\t0\t0\tOK\n+XLOC_000069\t-\t-\tXLOC_000069\tXkr4\tTSS75\tchr1:3356180-3356225\t-\t-\t1.02717e+08\t0\t3.93246e+08\tOK\t0\t0\t0\tOK\n+XLOC_000070\t-\t-\tXLOC_000070\tXkr4\tTSS76\tchr1:3363076-3363176\t-\t-\t3.81001e+06\t0\t1.38903e+07\tOK\t0\t0\t0\tOK\n+XLOC_000071\t-\t-\tXLOC_000071\tXkr4\tTSS77\tchr1:3363214-3363278\t-\t-\t0\t0\t0\tOK\t0\t0\t0\tOK\n+XLOC_000072\t-\t-\tXLOC_000072\tXkr4\tTSS78\tchr1:3363387-3363446\t-\t-\t5.53654e+07\t0\t1.77783e+08\tOK\t0\t0\t0\tOK\n+XLOC_000073\t-\t-\tXLOC_000073\tXkr4\tTSS79\tchr1:3363753-3363849\t-\t-\t0\t0\t0\tOK\t0\t0\t0\tOK\n+XLOC_000074\t-\t-\tXLOC_000074\tXkr4\tTSS80\tchr1:3364871-3364919\t-\t-\t6.28966e+07\t0\t2.40795e+08\tOK\t0\t0\t0\tOK\n+XLOC_000075\t-\t-\tXLOC_000075\tXkr4\tTSS81\tchr1:3367135-3367162\t-\t-\t0\t0\t0\tOK\t0\t0\t0\tOK\n+XLOC_000076\t-\t-\tXLOC_000076\tXkr4\tTSS82\tchr1:3367210-3367237\t-\t-\t0\t0\t0\tOK\t0\t0\t0\tOK\n+XLOC_000077\t-\t-\tXLOC_000077\tXkr4\tTSS83\tchr1:3367333-3367382\t-\t-\t0\t0\t0\tOK\t0\t0\t0\tOK\n+XLOC_000078\t-\t-\tXLOC_000078\tXkr4\tTSS84\tchr1:3369580-3369607\t-\t-\t0\t0\t0\tOK\t0\t0\t0\tOK\n+XLOC_000079\t-\t-\tXLOC_000079\tXkr4\tTSS85\tchr1:3375001-3375028\t-\t-\t0\t0\t0\tOK\t0\t0\t0\tOK\n+XLOC_000080\t-\t-\tXLOC_000080\tXkr4\tTSS86\tchr1:3377211-3377262\t-\t-\t0\t0\t0\tOK\t0\t0\t0\tOK\n+XLOC_000081\t-\t-\tXLOC_000081\tXkr4\tTSS87\tchr1:3379888-3379915\t-\t-\t0\t0\t0\tOK\t0\t0\t0\tOK\n+XLOC_000082\t-\t-\tXLOC_000082\tXkr4\tTSS88\tchr1:3386739-3386836\t-\t-\t0\t0\t0\tOK\t0\t0\t0\tOK\n+XLOC_000083\t-\t-\tXLOC_000083\tXkr4\tTSS89\tchr1:3391325-3391352\t-\t-\t0\t0\t0\tOK\t0\t0\t0\tOK\n+XLOC_000084\t-\t-\tXLOC_000084\tXkr4\tTSS90\tchr1:3435841-3435880\t-\t-\t0\t0\t0\tOK\t0\t0\t0\tOK\n+XLOC_000085\t-\t-\tXLOC_000085\tXkr4\tTSS91\tchr1:3447761-3447788\t-\t-\t0\t0\t0\tOK\t0\t0\t0\tOK\n+XLOC_000086\t-\t-\tXLOC_000086\tXkr4\tTSS92\tchr1:3450906-3450965\t-\t-\t0\t0\t0\tOK\t0\t0\t0\tOK\n+XLOC_000087\t-\t-\tXLOC_000087\tXkr4\tTSS93\tchr1:3451051-3451109\t-\t-\t0\t0\t0\tOK\t0\t0\t0\tOK\n' |
| b |
| diff -r 604fa75232a2 -r 8da0eade1f59 test-data/cuffdiff_out7.txt --- a/test-data/cuffdiff_out7.txt Thu Jan 16 13:13:52 2014 -0500 +++ b/test-data/cuffdiff_out7.txt Fri Dec 19 11:57:43 2014 -0500 |
| b |
| b'@@ -1,15 +1,15 @@\n tracking_id\tclass_code\tnearest_ref_id\tgene_id\tgene_short_name\ttss_id\tlocus\tlength\tcoverage\tq1_FPKM\tq1_conf_lo\tq1_conf_hi\tq1_status\tq2_FPKM\tq2_conf_lo\tq2_conf_hi\tq2_status\n-TSS1\t-\t-\tXLOC_000001\tXkr4\tTSS1\tchr1:3204754-3204833\t-\t-\t0\t0\t0\tOK\t5.42247e+06\t0\t1.83844e+07\tOK\n-TSS10\t-\t-\tXLOC_000008\t-\tTSS10\tchr1:3190858-3191434\t-\t-\t227564\t0\t483427\tOK\t240951\t0\t505030\tOK\n-TSS11\t-\t-\tXLOC_000009\t-\tTSS11\tchr1:3191512-3192077\t-\t-\t241366\t0\t509259\tOK\t482731\t109420\t856042\tOK\n-TSS13\t-\t-\tXLOC_000010\t-\tTSS13\tchr1:3192250-3192336\t-\t-\t1.91712e+06\t0\t7.66198e+06\tOK\t1.91712e+06\t0\t7.66198e+06\tOK\n-TSS14\t-\t-\tXLOC_000011\t-\tTSS14\tchr1:3192441-3192494\t-\t-\t0\t0\t0\tOK\t5.56023e+07\t0\t1.86077e+08\tOK\n-TSS15\t-\t-\tXLOC_000012\t-\tTSS15\tchr1:3192550-3192629\t-\t-\t0\t0\t0\tOK\t2.71123e+06\t0\t1.08357e+07\tOK\n+TSS1\t-\t-\tXLOC_000001\tXkr4\tTSS1\tchr1:3204754-3204833\t-\t-\t0\t0\t0\tOK\t9.45986e+06\t0\t3.33035e+07\tOK\n+TSS10\t-\t-\tXLOC_000008\t-\tTSS10\tchr1:3190858-3191434\t-\t-\t408511\t54526.1\t762496\tOK\t420354\t61509.1\t779200\tOK\n+TSS11\t-\t-\tXLOC_000009\t-\tTSS11\tchr1:3191512-3192077\t-\t-\t433286\t63552.3\t803020\tOK\t842157\t342520\t1.34179e+06\tOK\n+TSS13\t-\t-\tXLOC_000010\t-\tTSS13\tchr1:3192250-3192336\t-\t-\t3.44151e+06\t0\t1.31756e+07\tOK\t3.34455e+06\t0\t1.30786e+07\tOK\n+TSS14\t-\t-\tXLOC_000011\t-\tTSS14\tchr1:3192441-3192494\t-\t-\t0\t0\t0\tOK\t9.7002e+07\t0\t3.17699e+08\tOK\n+TSS15\t-\t-\tXLOC_000012\t-\tTSS15\tchr1:3192550-3192629\t-\t-\t0\t0\t0\tOK\t4.72993e+06\t0\t1.84961e+07\tOK\n TSS16\t-\t-\tXLOC_000013\t-\tTSS16\tchr1:3192649-3192676\t-\t-\t0\t0\t0\tOK\t0\t0\t0\tOK\n TSS17\t-\t-\tXLOC_000014\t-\tTSS17\tchr1:3192731-3192811\t-\t-\t0\t0\t0\tOK\t0\t0\t0\tOK\n-TSS18\t-\t-\tXLOC_000015\t-\tTSS18\tchr1:3192940-3193042\t-\t-\t0\t0\t0\tOK\t3.93442e+06\t0\t1.25021e+07\tOK\n-TSS19\t-\t-\tXLOC_000016\t-\tTSS19\tchr1:3194185-3194226\t-\t-\t0\t0\t0\tOK\t1.39654e+08\t0\t5.58144e+08\tOK\n-TSS2\t-\t-\tXLOC_000002\t-\tTSS2\tchr1:3111449-3111490\t-\t-\t0\t0\t0\tOK\t1.39654e+08\t0\t5.58144e+08\tOK\n+TSS18\t-\t-\tXLOC_000015\t-\tTSS18\tchr1:3192940-3193042\t-\t-\t0\t0\t0\tOK\t6.86386e+06\t0\t2.14243e+07\tOK\n+TSS19\t-\t-\tXLOC_000016\t-\tTSS19\tchr1:3194185-3194226\t-\t-\t0\t0\t0\tOK\t2.43637e+08\t0\t9.52723e+08\tOK\n+TSS2\t-\t-\tXLOC_000002\t-\tTSS2\tchr1:3111449-3111490\t-\t-\t0\t0\t0\tOK\t2.43637e+08\t0\t9.52723e+08\tOK\n TSS20\t-\t-\tXLOC_000017\t-\tTSS20\tchr1:3194302-3194329\t-\t-\t0\t0\t0\tOK\t0\t0\t0\tOK\n TSS21\t-\t-\tXLOC_000018\t-\tTSS21\tchr1:3194706-3194733\t-\t-\t0\t0\t0\tOK\t0\t0\t0\tOK\n TSS22\t-\t-\tXLOC_000019\t-\tTSS22\tchr1:3195083-3195110\t-\t-\t0\t0\t0\tOK\t0\t0\t0\tOK\n@@ -18,62 +18,62 @@\n TSS25\t-\t-\tXLOC_000022\t-\tTSS25\tchr1:3197246-3197273\t-\t-\t0\t0\t0\tOK\t0\t0\t0\tOK\n TSS26\t-\t-\tXLOC_000023\t-\tTSS26\tchr1:3197346-3197373\t-\t-\t0\t0\t0\tOK\t0\t0\t0\tOK\n TSS27\t-\t-\tXLOC_000024\t-\tTSS27\tchr1:3197425-3197452\t-\t-\t0\t0\t0\tOK\t0\t0\t0\tOK\n-TSS28\t-\t-\tXLOC_000025\t-\tTSS28\tchr1:3200022-3200191\t-\t-\t460348\t0\t1.54058e+06\tOK\t460348\t0\t1.54058e+06\tOK\n+TSS28\t-\t-\tXLOC_000025\t-\tTSS28\tchr1:3200022-3200191\t-\t-\t826392\t0\t2.65361e+06\tOK\t803108\t0\t2.63033e+06\tOK\n TSS29\t-\t-\tXLOC_000026\t-\tTSS29\tchr1:3200325-3200352\t-\t-\t0\t0\t0\tOK\t0\t0\t0\tOK\n TSS3\t-\t-\tXLOC_000003\t-\tTSS3\tchr1:3111545-3111576\t-\t-\t0\t0\t0\tOK\t0\t0\t0\tOK\n TSS30\t-\t-\tXLOC_000027\t-\tTSS30\tchr1:3200430-3200457\t-\t-\t0\t0\t0\tOK\t0\t0\t0\tOK\n TSS31\t-\t-\tXLOC_000028\t-\tTSS31\tchr1:3201007-3201039\t-\t-\t0\t0\t0\tOK\t0\t0\t0\tOK\n-TSS32\t-\t-\tXLOC_000029\t-\tTSS32\tchr1:3201077-3201481\t-\t-\t37206.6\t0\t124514\tOK\t186033\t0\t476912\tOK\n-TSS33\t-\t-\tXLOC_000030\t-\tTSS33\tchr1:3201596-3201666\t-\t-\t9.11292e+06\t0\t3.08965e+07\tOK\t0\t0\t0\tOK\n+TSS32\t-\t-\tXLOC_000029\t-\tTSS32\tchr1:3201077-3201481\t-\t-\t66791.3\t0\t214473\tOK\t324548\t0\t802006\tOK\n+TSS33\t-\t-\tXLOC_000030\t-\tTSS33\tchr1:3201596-3201666\t-\t-\t1.6359e+07\t0\t5.96409e+07\tOK\t0\t0\t0\tOK\n TSS34\t-\t-\tXLOC_000031\t-\tTSS34\tchr1:3201672-3201699\t-\t-\t0\t0\t0\tOK\t0\t0\t0\tOK\n-TSS35\t-\t-\tXLOC_000032\t-\tTSS35\tchr1:3201725-3201809\t-\t-\t8.43162e+06\t0\t2.67925e+07\tOK\t0\t0\t0\tOK\n+TSS35\t-\t-\tXLOC_000032\t-\tTSS35\tchr1:3201725-3201809\t-\t-\t1.5136e+07\t0\t4.63396e+07\tOK\t0\t0\t0\tOK\n TSS36\t-\t-\tXLOC_000033\tXkr4\tTSS36\tchr1:3211521-3211561\t-\t-\t0\t0\t0\tOK\t0\t0\t0\tOK\n-TSS37\t-\t-\tXLOC_000034\tXkr4\tTSS37\tchr1:3212213-3212292\t-\t-\t0\t0\t0\tOK\t5.42247e+06\t0\t1.83844e+07\tOK\n-TSS38\t-\t-\tXLOC_000035\tXkr4\tTSS38\tchr1:3212367-3212439\t-\t-\t0\t0\t0\tOK\t1.60978e+07\t0\t5.11527e+07\tOK\n-TSS39\t-\t-\tXLOC_000036\tX'..b'\tOK\n-TSS52\t-\t-\tXLOC_000049\tXkr4\tTSS52\tchr1:3277913-3278390\t-\t-\t127495\t0\t331348\tOK\t27320.3\t0\t91429.2\tOK\n+TSS52\t-\t-\tXLOC_000049\tXkr4\tTSS52\tchr1:3277913-3278390\t-\t-\t228872\t0\t561229\tOK\t47662.2\t0\t156103\tOK\n TSS54\t-\t-\tXLOC_000050\tXkr4\tTSS54\tchr1:3280117-3280144\t-\t-\t0\t0\t0\tOK\t0\t0\t0\tOK\n TSS55\t-\t-\tXLOC_000051\tXkr4\tTSS55\tchr1:3280498-3280525\t-\t-\t0\t0\t0\tOK\t0\t0\t0\tOK\n-TSS56\t-\t-\tXLOC_000052\tXkr4\tTSS56\tchr1:3280686-3280741\t-\t-\t0\t0\t0\tOK\t1.49798e+07\t0\t5.98686e+07\tOK\n+TSS56\t-\t-\tXLOC_000052\tXkr4\tTSS56\tchr1:3280686-3280741\t-\t-\t0\t0\t0\tOK\t2.61334e+07\t0\t1.02193e+08\tOK\n TSS57\t-\t-\tXLOC_000053\tXkr4\tTSS57\tchr1:3282504-3282531\t-\t-\t0\t0\t0\tOK\t0\t0\t0\tOK\n TSS58\t-\t-\tXLOC_000054\tXkr4\tTSS58\tchr1:3282650-3282677\t-\t-\t0\t0\t0\tOK\t0\t0\t0\tOK\n TSS59\t-\t-\tXLOC_000055\tXkr4\tTSS59\tchr1:3282760-3282832\t-\t-\t0\t0\t0\tOK\t0\t0\t0\tOK\n TSS6\t-\t-\tXLOC_000006\t-\tTSS6\tchr1:3188521-3188548\t-\t-\t0\t0\t0\tOK\t0\t0\t0\tOK\n TSS60\t-\t-\tXLOC_000056\tXkr4\tTSS60\tchr1:3284966-3284993\t-\t-\t0\t0\t0\tOK\t0\t0\t0\tOK\n-TSS61\t-\t-\tXLOC_000057\tXkr4\tTSS61\tchr1:3290488-3290553\t-\t-\t0\t0\t0\tOK\t6.39146e+06\t0\t2.55442e+07\tOK\n-TSS62\t-\t-\tXLOC_000058\tXkr4\tTSS62\tchr1:3290798-3290859\t-\t-\t8.68561e+06\t0\t3.4713e+07\tOK\t0\t0\t0\tOK\n-TSS63\t-\t-\tXLOC_000059\tXkr4\tTSS63\tchr1:3290919-3291273\t-\t-\t164265\t0\t453103\tOK\t49279.4\t0\t164917\tOK\n-TSS65\t-\t-\tXLOC_000060\tXkr4\tTSS65\tchr1:3299443-3299664\t-\t-\t449954\t0\t1.56567e+06\tOK\t89990.7\t0\t449954\tOK\n+TSS61\t-\t-\tXLOC_000057\tXkr4\tTSS61\tchr1:3290488-3290553\t-\t-\t0\t0\t0\tOK\t1.11503e+07\t0\t4.36026e+07\tOK\n+TSS62\t-\t-\tXLOC_000058\tXkr4\tTSS62\tchr1:3290798-3290859\t-\t-\t1.55919e+07\t0\t5.96926e+07\tOK\t0\t0\t0\tOK\n+TSS63\t-\t-\tXLOC_000059\tXkr4\tTSS63\tchr1:3290919-3291273\t-\t-\t294879\t0\t740137\tOK\t85971.3\t0\t281572\tOK\n+TSS65\t-\t-\tXLOC_000060\tXkr4\tTSS65\tchr1:3299443-3299664\t-\t-\t807732\t0\t2.39056e+06\tOK\t156995\t0\t613917\tOK\n TSS66\t-\t-\tXLOC_000060\tXkr4\tTSS66\tchr1:3299443-3299664\t-\t-\t0\t0\t0\tOK\t0\t0\t0\tOK\n TSS67\t-\t-\tXLOC_000061\tXkr4\tTSS67\tchr1:3299691-3299733\t-\t-\t0\t0\t0\tOK\t0\t0\t0\tOK\n TSS68\t-\t-\tXLOC_000062\tXkr4\tTSS68\tchr1:3300051-3300078\t-\t-\t0\t0\t0\tOK\t0\t0\t0\tOK\n TSS69\t-\t-\tXLOC_000063\tXkr4\tTSS69\tchr1:3307748-3307775\t-\t-\t0\t0\t0\tOK\t0\t0\t0\tOK\n-TSS7\t-\t-\tXLOC_000007\t-\tTSS7\tchr1:3189810-3190789\t-\t-\t199608\t33901.5\t365315\tOK\t299412\t183619\t415206\tOK\n+TSS7\t-\t-\tXLOC_000007\t-\tTSS7\tchr1:3189810-3190789\t-\t-\t358326\t135086\t581565\tOK\t522345\t410780\t633911\tOK\n TSS70\t-\t-\tXLOC_000064\tXkr4\tTSS70\tchr1:3318620-3318647\t-\t-\t0\t0\t0\tOK\t0\t0\t0\tOK\n TSS71\t-\t-\tXLOC_000065\tXkr4\tTSS71\tchr1:3318999-3319051\t-\t-\t0\t0\t0\tOK\t0\t0\t0\tOK\n TSS72\t-\t-\tXLOC_000066\tXkr4\tTSS72\tchr1:3330527-3330554\t-\t-\t0\t0\t0\tOK\t0\t0\t0\tOK\n-TSS73\t-\t-\tXLOC_000067\tXkr4\tTSS73\tchr1:3351240-3351311\t-\t-\t4.27915e+06\t0\t1.71021e+07\tOK\t0\t0\t0\tOK\n-TSS74\t-\t-\tXLOC_000068\tXkr4\tTSS74\tchr1:3355887-3356119\t-\t-\t281197\t0\t1.06014e+06\tOK\t0\t0\t0\tOK\n-TSS75\t-\t-\tXLOC_000069\tXkr4\tTSS75\tchr1:3356180-3356225\t-\t-\t5.72196e+07\t0\t2.28684e+08\tOK\t0\t0\t0\tOK\n-TSS76\t-\t-\tXLOC_000070\tXkr4\tTSS76\tchr1:3363076-3363176\t-\t-\t2.1224e+06\t0\t7.19579e+06\tOK\t0\t0\t0\tOK\n+TSS73\t-\t-\tXLOC_000067\tXkr4\tTSS73\tchr1:3351240-3351311\t-\t-\t7.68169e+06\t0\t2.94088e+07\tOK\t0\t0\t0\tOK\n+TSS74\t-\t-\tXLOC_000068\tXkr4\tTSS74\tchr1:3355887-3356119\t-\t-\t504790\t0\t1.59712e+06\tOK\t0\t0\t0\tOK\n+TSS75\t-\t-\tXLOC_000069\tXkr4\tTSS75\tchr1:3356180-3356225\t-\t-\t1.02717e+08\t0\t3.93246e+08\tOK\t0\t0\t0\tOK\n+TSS76\t-\t-\tXLOC_000070\tXkr4\tTSS76\tchr1:3363076-3363176\t-\t-\t3.81001e+06\t0\t1.38903e+07\tOK\t0\t0\t0\tOK\n TSS77\t-\t-\tXLOC_000071\tXkr4\tTSS77\tchr1:3363214-3363278\t-\t-\t0\t0\t0\tOK\t0\t0\t0\tOK\n-TSS78\t-\t-\tXLOC_000072\tXkr4\tTSS78\tchr1:3363387-3363446\t-\t-\t3.08417e+07\t0\t1.03214e+08\tOK\t0\t0\t0\tOK\n+TSS78\t-\t-\tXLOC_000072\tXkr4\tTSS78\tchr1:3363387-3363446\t-\t-\t5.53654e+07\t0\t1.77783e+08\tOK\t0\t0\t0\tOK\n TSS79\t-\t-\tXLOC_000073\tXkr4\tTSS79\tchr1:3363753-3363849\t-\t-\t0\t0\t0\tOK\t0\t0\t0\tOK\n-TSS80\t-\t-\tXLOC_000074\tXkr4\tTSS80\tchr1:3364871-3364919\t-\t-\t3.50371e+07\t0\t1.40029e+08\tOK\t0\t0\t0\tOK\n+TSS80\t-\t-\tXLOC_000074\tXkr4\tTSS80\tchr1:3364871-3364919\t-\t-\t6.28966e+07\t0\t2.40795e+08\tOK\t0\t0\t0\tOK\n TSS81\t-\t-\tXLOC_000075\tXkr4\tTSS81\tchr1:3367135-3367162\t-\t-\t0\t0\t0\tOK\t0\t0\t0\tOK\n TSS82\t-\t-\tXLOC_000076\tXkr4\tTSS82\tchr1:3367210-3367237\t-\t-\t0\t0\t0\tOK\t0\t0\t0\tOK\n TSS83\t-\t-\tXLOC_000077\tXkr4\tTSS83\tchr1:3367333-3367382\t-\t-\t0\t0\t0\tOK\t0\t0\t0\tOK\n' |
| b |
| diff -r 604fa75232a2 -r 8da0eade1f59 test-data/cuffdiff_out9.txt --- a/test-data/cuffdiff_out9.txt Thu Jan 16 13:13:52 2014 -0500 +++ b/test-data/cuffdiff_out9.txt Fri Dec 19 11:57:43 2014 -0500 |
| b |
| b'@@ -5,85 +5,85 @@\n TSS13\tXLOC_000010\t-\tchr1:3192250-3192336\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n TSS14\tXLOC_000011\t-\tchr1:3192441-3192494\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n TSS15\tXLOC_000012\t-\tchr1:3192550-3192629\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n-TSS16\tXLOC_000013\t-\tchr1:3192649-3192676\tq1\tq2\tLOWDATA\t0\t0\t0\t0\t0\t1\tno\n-TSS17\tXLOC_000014\t-\tchr1:3192731-3192811\tq1\tq2\tLOWDATA\t0\t0\t0\t0\t0\t1\tno\n+TSS16\tXLOC_000013\t-\tchr1:3192649-3192676\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n+TSS17\tXLOC_000014\t-\tchr1:3192731-3192811\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n TSS18\tXLOC_000015\t-\tchr1:3192940-3193042\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n TSS19\tXLOC_000016\t-\tchr1:3194185-3194226\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n TSS2\tXLOC_000002\t-\tchr1:3111449-3111490\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n-TSS20\tXLOC_000017\t-\tchr1:3194302-3194329\tq1\tq2\tLOWDATA\t0\t0\t0\t0\t0\t1\tno\n-TSS21\tXLOC_000018\t-\tchr1:3194706-3194733\tq1\tq2\tLOWDATA\t0\t0\t0\t0\t0\t1\tno\n-TSS22\tXLOC_000019\t-\tchr1:3195083-3195110\tq1\tq2\tLOWDATA\t0\t0\t0\t0\t0\t1\tno\n-TSS23\tXLOC_000020\t-\tchr1:3195450-3195477\tq1\tq2\tLOWDATA\t0\t0\t0\t0\t0\t1\tno\n-TSS24\tXLOC_000021\t-\tchr1:3197089-3197116\tq1\tq2\tLOWDATA\t0\t0\t0\t0\t0\t1\tno\n-TSS25\tXLOC_000022\t-\tchr1:3197246-3197273\tq1\tq2\tLOWDATA\t0\t0\t0\t0\t0\t1\tno\n-TSS26\tXLOC_000023\t-\tchr1:3197346-3197373\tq1\tq2\tLOWDATA\t0\t0\t0\t0\t0\t1\tno\n-TSS27\tXLOC_000024\t-\tchr1:3197425-3197452\tq1\tq2\tLOWDATA\t0\t0\t0\t0\t0\t1\tno\n+TSS20\tXLOC_000017\t-\tchr1:3194302-3194329\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n+TSS21\tXLOC_000018\t-\tchr1:3194706-3194733\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n+TSS22\tXLOC_000019\t-\tchr1:3195083-3195110\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n+TSS23\tXLOC_000020\t-\tchr1:3195450-3195477\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n+TSS24\tXLOC_000021\t-\tchr1:3197089-3197116\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n+TSS25\tXLOC_000022\t-\tchr1:3197246-3197273\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n+TSS26\tXLOC_000023\t-\tchr1:3197346-3197373\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n+TSS27\tXLOC_000024\t-\tchr1:3197425-3197452\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n TSS28\tXLOC_000025\t-\tchr1:3200022-3200191\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n-TSS29\tXLOC_000026\t-\tchr1:3200325-3200352\tq1\tq2\tLOWDATA\t0\t0\t0\t0\t0\t1\tno\n-TSS3\tXLOC_000003\t-\tchr1:3111545-3111576\tq1\tq2\tLOWDATA\t0\t0\t0\t0\t0\t1\tno\n-TSS30\tXLOC_000027\t-\tchr1:3200430-3200457\tq1\tq2\tLOWDATA\t0\t0\t0\t0\t0\t1\tno\n-TSS31\tXLOC_000028\t-\tchr1:3201007-3201039\tq1\tq2\tLOWDATA\t0\t0\t0\t0\t0\t1\tno\n+TSS29\tXLOC_000026\t-\tchr1:3200325-3200352\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n+TSS3\tXLOC_000003\t-\tchr1:3111545-3111576\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n+TSS30\tXLOC_000027\t-\tchr1:3200430-3200457\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n+TSS31\tXLOC_000028\t-\tchr1:3201007-3201039\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n TSS32\tXLOC_000029\t-\tchr1:3201077-3201481\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n TSS33\tXLOC_000030\t-\tchr1:3201596-3201666\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n-TSS34\tXLOC_000031\t-\tchr1:3201672-3201699\tq1\tq2\tLOWDATA\t0\t0\t0\t0\t0\t1\tno\n+TSS34\tXLOC_000031\t-\tchr1:3201672-3201699\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n TSS35\tXLOC_000032\t-\tchr1:3201725-3201809\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n-TSS36\tXLOC_000033\tXkr4\tchr1:3211521-3211561\tq1\tq2\tLOWDATA\t0\t0\t0\t0\t0\t1\tno\n+TSS36\tXLOC_000033\tXkr4\tchr1:3211521-3211561\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n TSS37\tXLOC_000034\tXkr4\tchr1:3212213-3212292\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n TSS38\tXLOC_000035\tXkr4\tchr1:3212367-3212439\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n TSS39\tXLOC_000036\tXkr4\tchr1:3212717-3212801\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n-TSS4\tXLOC_000004\t-\tchr1:3174765-3174792\tq1\tq2\tLOWDATA\t0\t0\t0\t0\t0\t1\tno\n-TSS40\tXLOC_000037\tXkr4\tchr1:3213095-3213242\tq1\tq2\tNOTEST\t0\t0\t0.249947\t0\t0.557805\t1\tno\n-TSS41\tXLOC_000038\tXkr4\tchr1:3240606-3240633\tq1\tq2\tLOWDATA\t0\t0\t0\t0\t0\t1\tno\n-TSS42\tXLOC_000039\tXkr4\tchr1:3242479-3242512\tq1\tq2\tLOWDATA\t0\t0\t0\t0\t0\t1\tno\n+TSS4\tXLOC_000004\t-\tchr1:3174765-3174792\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n+TSS40\tXLOC_000037\tXkr4\tchr1:3213095-3213242\tq1\tq2\tNOTEST\t0\t0\t0.249947\t0\t0.5526\t1\tno\n+TSS41\tXLOC_000038\tXkr4\tchr1:3240606-3240633\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n+TSS42\tXLOC_000039\tXkr4\tchr1:3242479-3242512\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n TSS43\tXLOC_000040\tXkr4\tchr1:3242633-3242923\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n-TSS44\tXLOC_000041\tXkr4\tchr1:3242924-3243005\tq1\tq2\tLOWDATA\t0\t0\t0\t0\t0\t1\tno\n+TSS44\tXLOC_000041\tXkr4\tchr1:3242924-3243005\tq1\tq2\t'..b'88-3290553\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n TSS62\tXLOC_000058\tXkr4\tchr1:3290798-3290859\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n TSS63\tXLOC_000059\tXkr4\tchr1:3290919-3291273\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n TSS65\tXLOC_000060\tXkr4\tchr1:3299443-3299664\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n-TSS66\tXLOC_000060\tXkr4\tchr1:3299443-3299664\tq1\tq2\tLOWDATA\t0\t0\t0\t0\t0\t1\tno\n-TSS67\tXLOC_000061\tXkr4\tchr1:3299691-3299733\tq1\tq2\tLOWDATA\t0\t0\t0\t0\t0\t1\tno\n-TSS68\tXLOC_000062\tXkr4\tchr1:3300051-3300078\tq1\tq2\tLOWDATA\t0\t0\t0\t0\t0\t1\tno\n-TSS69\tXLOC_000063\tXkr4\tchr1:3307748-3307775\tq1\tq2\tLOWDATA\t0\t0\t0\t0\t0\t1\tno\n+TSS66\tXLOC_000060\tXkr4\tchr1:3299443-3299664\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n+TSS67\tXLOC_000061\tXkr4\tchr1:3299691-3299733\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n+TSS68\tXLOC_000062\tXkr4\tchr1:3300051-3300078\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n+TSS69\tXLOC_000063\tXkr4\tchr1:3307748-3307775\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n TSS7\tXLOC_000007\t-\tchr1:3189810-3190789\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n-TSS70\tXLOC_000064\tXkr4\tchr1:3318620-3318647\tq1\tq2\tLOWDATA\t0\t0\t0\t0\t0\t1\tno\n-TSS71\tXLOC_000065\tXkr4\tchr1:3318999-3319051\tq1\tq2\tLOWDATA\t0\t0\t0\t0\t0\t1\tno\n-TSS72\tXLOC_000066\tXkr4\tchr1:3330527-3330554\tq1\tq2\tLOWDATA\t0\t0\t0\t0\t0\t1\tno\n+TSS70\tXLOC_000064\tXkr4\tchr1:3318620-3318647\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n+TSS71\tXLOC_000065\tXkr4\tchr1:3318999-3319051\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n+TSS72\tXLOC_000066\tXkr4\tchr1:3330527-3330554\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n TSS73\tXLOC_000067\tXkr4\tchr1:3351240-3351311\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n TSS74\tXLOC_000068\tXkr4\tchr1:3355887-3356119\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n TSS75\tXLOC_000069\tXkr4\tchr1:3356180-3356225\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n TSS76\tXLOC_000070\tXkr4\tchr1:3363076-3363176\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n-TSS77\tXLOC_000071\tXkr4\tchr1:3363214-3363278\tq1\tq2\tLOWDATA\t0\t0\t0\t0\t0\t1\tno\n+TSS77\tXLOC_000071\tXkr4\tchr1:3363214-3363278\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n TSS78\tXLOC_000072\tXkr4\tchr1:3363387-3363446\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n-TSS79\tXLOC_000073\tXkr4\tchr1:3363753-3363849\tq1\tq2\tLOWDATA\t0\t0\t0\t0\t0\t1\tno\n+TSS79\tXLOC_000073\tXkr4\tchr1:3363753-3363849\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n TSS80\tXLOC_000074\tXkr4\tchr1:3364871-3364919\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n-TSS81\tXLOC_000075\tXkr4\tchr1:3367135-3367162\tq1\tq2\tLOWDATA\t0\t0\t0\t0\t0\t1\tno\n-TSS82\tXLOC_000076\tXkr4\tchr1:3367210-3367237\tq1\tq2\tLOWDATA\t0\t0\t0\t0\t0\t1\tno\n-TSS83\tXLOC_000077\tXkr4\tchr1:3367333-3367382\tq1\tq2\tLOWDATA\t0\t0\t0\t0\t0\t1\tno\n-TSS84\tXLOC_000078\tXkr4\tchr1:3369580-3369607\tq1\tq2\tLOWDATA\t0\t0\t0\t0\t0\t1\tno\n-TSS85\tXLOC_000079\tXkr4\tchr1:3375001-3375028\tq1\tq2\tLOWDATA\t0\t0\t0\t0\t0\t1\tno\n-TSS86\tXLOC_000080\tXkr4\tchr1:3377211-3377262\tq1\tq2\tLOWDATA\t0\t0\t0\t0\t0\t1\tno\n-TSS87\tXLOC_000081\tXkr4\tchr1:3379888-3379915\tq1\tq2\tLOWDATA\t0\t0\t0\t0\t0\t1\tno\n-TSS88\tXLOC_000082\tXkr4\tchr1:3386739-3386836\tq1\tq2\tLOWDATA\t0\t0\t0\t0\t0\t1\tno\n-TSS89\tXLOC_000083\tXkr4\tchr1:3391325-3391352\tq1\tq2\tLOWDATA\t0\t0\t0\t0\t0\t1\tno\n-TSS90\tXLOC_000084\tXkr4\tchr1:3435841-3435880\tq1\tq2\tLOWDATA\t0\t0\t0\t0\t0\t1\tno\n-TSS91\tXLOC_000085\tXkr4\tchr1:3447761-3447788\tq1\tq2\tLOWDATA\t0\t0\t0\t0\t0\t1\tno\n-TSS92\tXLOC_000086\tXkr4\tchr1:3450906-3450965\tq1\tq2\tLOWDATA\t0\t0\t0\t0\t0\t1\tno\n-TSS93\tXLOC_000087\tXkr4\tchr1:3451051-3451109\tq1\tq2\tLOWDATA\t0\t0\t0\t0\t0\t1\tno\n+TSS81\tXLOC_000075\tXkr4\tchr1:3367135-3367162\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n+TSS82\tXLOC_000076\tXkr4\tchr1:3367210-3367237\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n+TSS83\tXLOC_000077\tXkr4\tchr1:3367333-3367382\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n+TSS84\tXLOC_000078\tXkr4\tchr1:3369580-3369607\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n+TSS85\tXLOC_000079\tXkr4\tchr1:3375001-3375028\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n+TSS86\tXLOC_000080\tXkr4\tchr1:3377211-3377262\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n+TSS87\tXLOC_000081\tXkr4\tchr1:3379888-3379915\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n+TSS88\tXLOC_000082\tXkr4\tchr1:3386739-3386836\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n+TSS89\tXLOC_000083\tXkr4\tchr1:3391325-3391352\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n+TSS90\tXLOC_000084\tXkr4\tchr1:3435841-3435880\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n+TSS91\tXLOC_000085\tXkr4\tchr1:3447761-3447788\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n+TSS92\tXLOC_000086\tXkr4\tchr1:3450906-3450965\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n+TSS93\tXLOC_000087\tXkr4\tchr1:3451051-3451109\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n' |
| b |
| diff -r 604fa75232a2 -r 8da0eade1f59 tool_dependencies.xml --- a/tool_dependencies.xml Thu Jan 16 13:13:52 2014 -0500 +++ b/tool_dependencies.xml Fri Dec 19 11:57:43 2014 -0500 |
| b |
| @@ -1,6 +1,6 @@ <?xml version="1.0"?> <tool_dependency> - <package name="cufflinks" version="2.1.1"> - <repository changeset_revision="394b13717223" name="package_cufflinks_2_1_1" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu" /> + <package name="cufflinks" version="2.2.1"> + <repository changeset_revision="899067a260d1" name="package_cufflinks_2_2_1" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> </tool_dependency> |