| Previous changeset 7:8da0eade1f59 (2014-12-19) Next changeset 9:db57b46b05bf (2015-05-13) |
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Commit message:
Uploaded updated cuffdiff. |
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modified:
cuffdiff_wrapper.xml tool_dependencies.xml |
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added:
cummeRbund.R test-data/cuffdiff_out.sqlite |
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removed:
test-data/cuffdiff_out1.txt test-data/cuffdiff_out10.txt test-data/cuffdiff_out11.txt test-data/cuffdiff_out2.txt test-data/cuffdiff_out3.txt test-data/cuffdiff_out4.txt test-data/cuffdiff_out5.txt test-data/cuffdiff_out6.txt test-data/cuffdiff_out7.txt test-data/cuffdiff_out8.txt test-data/cuffdiff_out9.txt |
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| diff -r 8da0eade1f59 -r 88fcac97c2a0 cuffdiff_wrapper.xml --- a/cuffdiff_wrapper.xml Fri Dec 19 11:57:43 2014 -0500 +++ b/cuffdiff_wrapper.xml Tue Dec 23 15:55:31 2014 -0500 |
| [ |
| @@ -1,12 +1,16 @@ -<tool id="cuffdiff" name="Cuffdiff" version="@VERSION@.0"> +<tool id="cuffdiff" name="Cuffdiff" version="@VERSION@.1"> <description>find significant changes in transcript expression, splicing, and promoter use</description> - <expand macro="requirements" /> + <requirements> + <requirement type="set_environment">CUFFDIFF_SCRIPT_PATH</requirement> + <requirement type="package" version="2.2.1">cufflinks</requirement> + <requirement type="package" version="2.8.2">cummeRbund</requirement> + </requirements> <expand macro="stdio" /> <macros> <import>cuff_macros.xml</import> </macros> <version_command>cuffdiff 2>&1 | head -n 1</version_command> - <command> + <command><![CDATA[ cuffdiff --no-update-check --FDR=$fdr @@ -64,6 +68,9 @@ $gtf_input @CONDITION_SAMPLES@ + && + R --vanilla --no-save -f \$CUFFDIFF_SCRIPT_PATH/cummeRbund.R && mv cummeRbund.sqlite "${output_cummerbund}" + ]]> </command> <inputs> <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."/> @@ -179,52 +186,7 @@ </conditional> </inputs> <outputs> - <!-- Optional read group datasets. --> - <data format="tabular" name="isoforms_read_group" label="${tool.name} on ${on_string}: isoforms read group tracking" from_work_dir="isoforms.read_group_tracking" > - <filter>(include_read_group_files == 'Yes')</filter> - </data> - <data format="tabular" name="genes_read_group" label="${tool.name} on ${on_string}: genes read group tracking" from_work_dir="genes.read_group_tracking" > - <filter>(include_read_group_files == 'Yes')</filter> - </data> - <data format="tabular" name="cds_read_group" label="${tool.name} on ${on_string}: CDs read group tracking" from_work_dir="cds.read_group_tracking" > - <filter>(include_read_group_files == 'Yes')</filter> - </data> - <data format="tabular" name="tss_groups_read_group" label="${tool.name} on ${on_string}: TSS groups read group tracking" from_work_dir="tss_groups.read_group_tracking" > - <filter>(include_read_group_files == 'Yes')</filter> - </data> - <data format="text" name="read_group_info" label="${tool.name} on ${on_string}: read group info" from_work_dir="read_groups.info" > - <filter>(include_read_group_files == 'Yes')</filter> - </data> - <data format="text" name="run_info" label="${tool.name} on ${on_string}: run info" from_work_dir="run.info" > - <filter>(include_read_group_files == 'Yes')</filter> - </data> - <!-- Standard datasets. --> - <data format="tabular" name="splicing_diff" label="${tool.name} on ${on_string}: splicing differential expression testing" from_work_dir="splicing.diff" /> - <data format="tabular" name="promoters_diff" label="${tool.name} on ${on_string}: promoters differential expression testing" from_work_dir="promoters.diff" /> - <data format="tabular" name="cds_diff" label="${tool.name} on ${on_string}: CDS overloading diffential expression testing" from_work_dir="cds.diff" /> - <data format="tabular" name="cds_exp_fpkm_tracking" label="${tool.name} on ${on_string}: CDS FPKM differential expression testing" from_work_dir="cds_exp.diff" /> - <data format="tabular" name="cds_fpkm_tracking" label="${tool.name} on ${on_string}: CDS FPKM tracking" from_work_dir="cds.fpkm_tracking" /> - <data format="tabular" name="cds_count_tracking" label="${tool.name} on ${on_string}: CDS count tracking" from_work_dir="cds.count_tracking" > - <filter>(include_count_files == 'Yes')</filter> - </data> - - <data format="tabular" name="tss_groups_exp" label="${tool.name} on ${on_string}: TSS groups differential expression testing" from_work_dir="tss_group_exp.diff" /> - <data format="tabular" name="tss_groups_fpkm_tracking" label="${tool.name} on ${on_string}: TSS groups FPKM tracking" from_work_dir="tss_groups.fpkm_tracking" /> - <data format="tabular" name="tss_groups_count_tracking" label="${tool.name} on ${on_string}: TSS count FPKM tracking" from_work_dir="tss_groups.count_tracking" > - <filter>(include_count_files == 'Yes')</filter> - </data> - - <data format="tabular" name="genes_exp" label="${tool.name} on ${on_string}: gene differential expression testing" from_work_dir="gene_exp.diff" /> - <data format="tabular" name="genes_fpkm_tracking" label="${tool.name} on ${on_string}: gene FPKM tracking" from_work_dir="genes.fpkm_tracking" /> - <data format="tabular" name="genes_count_tracking" label="${tool.name} on ${on_string}: gene count tracking" from_work_dir="genes.count_tracking" > - <filter>(include_count_files == 'Yes')</filter> - </data> - - <data format="tabular" name="isoforms_exp" label="${tool.name} on ${on_string}: transcript differential expression testing" from_work_dir="isoform_exp.diff" /> - <data format="tabular" name="isoforms_fpkm_tracking" label="${tool.name} on ${on_string}: transcript FPKM tracking" from_work_dir="isoforms.fpkm_tracking" /> - <data format="tabular" name="isoforms_count_tracking" label="${tool.name} on ${on_string}: transcript count tracking" from_work_dir="isoforms.count_tracking" > - <filter>(include_count_files == 'Yes')</filter> - </data> + <data format="sqlite" name="output_cummerbund" label="${tool.name} on ${on_string}: cummeRbund SQLite database" /> </outputs> <tests> @@ -254,17 +216,7 @@ <param name="do_normalization" value="No" /> <param name="multiread_correct" value="No"/> <param name="sAdditional" value="No"/> - <output name="splicing_diff" file="cuffdiff_out9.txt"/> - <output name="promoters_diff" file="cuffdiff_out10.txt"/> - <output name="cds_diff" file="cuffdiff_out11.txt"/> - <output name="cds_exp_fpkm_tracking" file="cuffdiff_out4.txt"/> - <output name="cds_fpkm_tracking" file="cuffdiff_out8.txt"/> - <output name="tss_groups_exp" file="cuffdiff_out3.txt" lines_diff="200"/> - <output name="tss_groups_fpkm_tracking" file="cuffdiff_out7.txt"/> - <output name="genes_exp" file="cuffdiff_out2.txt" lines_diff="200"/> - <output name="genes_fpkm_tracking" file="cuffdiff_out6.txt" lines_diff="200"/> - <output name="isoforms_exp" file="cuffdiff_out1.txt" lines_diff="200"/> - <output name="isoforms_fpkm_tracking" file="cuffdiff_out5.txt" lines_diff="200"/> + <output name="output_cummerbund" ftype="sqlite" file="cuffdiff_out.sqlite"/> </test> </tests> <help> |
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| diff -r 8da0eade1f59 -r 88fcac97c2a0 cummeRbund.R --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/cummeRbund.R Tue Dec 23 15:55:31 2014 -0500 |
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| @@ -0,0 +1,2 @@ +library("cummeRbund") +cuff <- readCufflinks(dir = ".", dbFile = 'cummeRbund.sqlite') \ No newline at end of file |
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| diff -r 8da0eade1f59 -r 88fcac97c2a0 test-data/cuffdiff_out.sqlite |
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| Binary file test-data/cuffdiff_out.sqlite has changed |
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| diff -r 8da0eade1f59 -r 88fcac97c2a0 test-data/cuffdiff_out1.txt --- a/test-data/cuffdiff_out1.txt Fri Dec 19 11:57:43 2014 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| b'@@ -1,91 +0,0 @@\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\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\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\t6.86386e+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\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\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\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\t3.12869\t1.23747\t0.38685\t0.435206\tno\n-TCONS_00000028\tXLOC_000042\tXkr4\tchr1:3243018-3243079\tq1\tq2\tOK\t0\t3.03053e+07\tinf\t-nan\t0.01975\t0.101571\tno\n-TCONS_00000029\tXLOC_000044\tXkr4\tchr1:3243347-3243401\tq1\tq2\tOK\t0\t5.79991e+07\tinf\t-nan\t0.01975\t0.101571\tno\n-TCONS_00000030\tXLOC_000046\tXkr4\tchr1:3256974-3257011\tq1\tq2\tOK\t0\t2.35423e+09\tinf\t-nan\t0.01975\t0.101571\tno\n-TCONS_00000031\tXLOC_000048\tXkr4\tchr1:3277190-3277218\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n-TCONS_00000033\tXLOC_000052\tXkr4\tchr1:3280686-3280741\tq1\tq2\tOK\t0\t2.61334e+07\tinf\t-nan\t0.12465\t0.186975\tno\n-TCONS_00000034\tXLOC_000057\tXkr4\tchr1:3290488-3290553\tq1\tq2\tOK\t0\t1.11503e+07\tinf\t-nan\t0.12465\t0.186975\tno\n-TCONS_00000037\tXLOC_000060\tXkr4\tchr1:3299443-3299664\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n-TCONS_00000038\tXLOC_000062\tXkr4\tchr1:3300051-3300078\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n-TCONS_00000039\tXLOC_000065\tXkr4\tchr1:3318999-3319051\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n-TCONS_00000040\tXLOC_000068\tXkr4\tchr1:3355887-3356119\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n-TCONS_00000041\tXLOC_000071\tXkr4\tchr1:3363214-3363278\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n-TCONS_00000042\tXLOC_000073\tXkr4\tchr1:3363753-3363849\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n-TCONS_00000043\tXLOC_000075\tXkr4\tchr1:3367135-3367162\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n-TCONS_00000044\tXLOC_000077\tXkr4\tchr1:3367333-3367382\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n-TCONS_00000045\tXLOC_000080\tXkr4\tchr1:3377211-3377262\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n-TCONS_00000046\tXLOC_000083\tXkr4\tchr1:3391325-3391352\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n-TCONS_00000047\tXLOC_000084\tXkr4\tchr1:3435841-3435880\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n-TCONS_00000048\tXLOC_000085\tXkr4\tchr1:3447761-3447788\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n-TCONS_00000049\tXLOC_000086\tXkr4\tchr1:3450906-3450965\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n-TCONS_00000050\tXLOC_000087\tXkr4\tchr1:3451051-3451109\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n-TCONS_00000051\tX'..b'354\t0.0412311\t0.0469899\t0.96715\t0.96715\tno\n-TCONS_00000056\tXLOC_000009\t-\tchr1:3191512-3192077\tq1\tq2\tOK\t433286\t842157\t0.958769\t1.27887\t0.20385\t0.2718\tno\n-TCONS_00000057\tXLOC_000010\t-\tchr1:3192250-3192336\tq1\tq2\tOK\t3.44151e+06\t3.34455e+06\t-0.0412311\t-0.014084\t0.67715\t0.716982\tno\n-TCONS_00000058\tXLOC_000013\t-\tchr1:3192649-3192676\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n-TCONS_00000059\tXLOC_000018\t-\tchr1:3194706-3194733\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n-TCONS_00000060\tXLOC_000024\t-\tchr1:3197425-3197452\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n-TCONS_00000062\tXLOC_000027\t-\tchr1:3200430-3200457\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n-TCONS_00000063\tXLOC_000028\t-\tchr1:3201007-3201039\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n-TCONS_00000065\tXLOC_000030\t-\tchr1:3201596-3201666\tq1\tq2\tOK\t1.6359e+07\t0\t-inf\t-nan\t0.0148\t0.101571\tno\n-TCONS_00000066\tXLOC_000032\t-\tchr1:3201725-3201809\tq1\tq2\tOK\t1.5136e+07\t0\t-inf\t-nan\t0.06005\t0.186975\tno\n-TCONS_00000067\tXLOC_000033\tXkr4\tchr1:3211521-3211561\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n-TCONS_00000068\tXLOC_000036\tXkr4\tchr1:3212717-3212801\tq1\tq2\tOK\t3.784e+06\t0\t-inf\t-nan\t0.12165\t0.186975\tno\n-TCONS_00000069\tXLOC_000037\tXkr4\tchr1:3213095-3213242\tq1\tq2\tOK\t863189\t0\t-inf\t-nan\t0.1957\t0.270969\tno\n-TCONS_00000070\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\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\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\t1.55919e+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\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-TCONS_00000099\tXLOC_000081\tXkr4\tchr1:3379888-3379915\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n-TCONS_00000100\tXLOC_000082\tXkr4\tchr1:3386739-3386836\tq1\tq2\tNOTEST\t0\t0\t0\t0\t1\t1\tno\n' |
| b |
| diff -r 8da0eade1f59 -r 88fcac97c2a0 test-data/cuffdiff_out10.txt --- a/test-data/cuffdiff_out10.txt Fri Dec 19 11:57:43 2014 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,88 +0,0 @@ -test_id gene_id gene locus sample_1 sample_2 status value_1 value_2 sqrt(JS) test_stat p_value q_value significant -XLOC_000001 XLOC_000001 Xkr4 chr1:3204754-3204833 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000002 XLOC_000002 - chr1:3111449-3111490 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000003 XLOC_000003 - chr1:3111545-3111576 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000004 XLOC_000004 - chr1:3174765-3174792 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000005 XLOC_000005 - chr1:3187401-3187428 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000006 XLOC_000006 - chr1:3188521-3188548 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000007 XLOC_000007 - chr1:3189810-3190789 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000008 XLOC_000008 - chr1:3190858-3191434 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000009 XLOC_000009 - chr1:3191512-3192077 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000010 XLOC_000010 - chr1:3192250-3192336 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000011 XLOC_000011 - chr1:3192441-3192494 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000012 XLOC_000012 - chr1:3192550-3192629 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000013 XLOC_000013 - chr1:3192649-3192676 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000014 XLOC_000014 - chr1:3192731-3192811 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000015 XLOC_000015 - chr1:3192940-3193042 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000016 XLOC_000016 - chr1:3194185-3194226 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000017 XLOC_000017 - chr1:3194302-3194329 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000018 XLOC_000018 - chr1:3194706-3194733 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000019 XLOC_000019 - chr1:3195083-3195110 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000020 XLOC_000020 - chr1:3195450-3195477 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000021 XLOC_000021 - chr1:3197089-3197116 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000022 XLOC_000022 - chr1:3197246-3197273 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000023 XLOC_000023 - chr1:3197346-3197373 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000024 XLOC_000024 - chr1:3197425-3197452 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000025 XLOC_000025 - chr1:3200022-3200191 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000026 XLOC_000026 - chr1:3200325-3200352 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000027 XLOC_000027 - chr1:3200430-3200457 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000028 XLOC_000028 - chr1:3201007-3201039 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000029 XLOC_000029 - chr1:3201077-3201481 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000030 XLOC_000030 - chr1:3201596-3201666 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000031 XLOC_000031 - chr1:3201672-3201699 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000032 XLOC_000032 - chr1:3201725-3201809 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000033 XLOC_000033 Xkr4 chr1:3211521-3211561 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000034 XLOC_000034 Xkr4 chr1:3212213-3212292 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000035 XLOC_000035 Xkr4 chr1:3212367-3212439 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000036 XLOC_000036 Xkr4 chr1:3212717-3212801 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000037 XLOC_000037 Xkr4 chr1:3213095-3213242 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000038 XLOC_000038 Xkr4 chr1:3240606-3240633 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000039 XLOC_000039 Xkr4 chr1:3242479-3242512 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000040 XLOC_000040 Xkr4 chr1:3242633-3242923 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000041 XLOC_000041 Xkr4 chr1:3242924-3243005 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000042 XLOC_000042 Xkr4 chr1:3243018-3243079 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000043 XLOC_000043 Xkr4 chr1:3243108-3243154 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000044 XLOC_000044 Xkr4 chr1:3243347-3243401 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000045 XLOC_000045 Xkr4 chr1:3254079-3254106 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000046 XLOC_000046 Xkr4 chr1:3256974-3257011 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000047 XLOC_000047 Xkr4 chr1:3277155-3277182 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000048 XLOC_000048 Xkr4 chr1:3277190-3277218 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000049 XLOC_000049 Xkr4 chr1:3277913-3278390 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000050 XLOC_000050 Xkr4 chr1:3280117-3280144 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000051 XLOC_000051 Xkr4 chr1:3280498-3280525 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000052 XLOC_000052 Xkr4 chr1:3280686-3280741 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000053 XLOC_000053 Xkr4 chr1:3282504-3282531 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000054 XLOC_000054 Xkr4 chr1:3282650-3282677 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000055 XLOC_000055 Xkr4 chr1:3282760-3282832 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000056 XLOC_000056 Xkr4 chr1:3284966-3284993 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000057 XLOC_000057 Xkr4 chr1:3290488-3290553 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000058 XLOC_000058 Xkr4 chr1:3290798-3290859 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000059 XLOC_000059 Xkr4 chr1:3290919-3291273 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000060 XLOC_000060 Xkr4 chr1:3299443-3299664 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000061 XLOC_000061 Xkr4 chr1:3299691-3299733 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000062 XLOC_000062 Xkr4 chr1:3300051-3300078 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000063 XLOC_000063 Xkr4 chr1:3307748-3307775 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000064 XLOC_000064 Xkr4 chr1:3318620-3318647 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000065 XLOC_000065 Xkr4 chr1:3318999-3319051 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000066 XLOC_000066 Xkr4 chr1:3330527-3330554 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000067 XLOC_000067 Xkr4 chr1:3351240-3351311 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000068 XLOC_000068 Xkr4 chr1:3355887-3356119 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000069 XLOC_000069 Xkr4 chr1:3356180-3356225 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000070 XLOC_000070 Xkr4 chr1:3363076-3363176 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000071 XLOC_000071 Xkr4 chr1:3363214-3363278 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000072 XLOC_000072 Xkr4 chr1:3363387-3363446 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000073 XLOC_000073 Xkr4 chr1:3363753-3363849 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000074 XLOC_000074 Xkr4 chr1:3364871-3364919 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000075 XLOC_000075 Xkr4 chr1:3367135-3367162 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000076 XLOC_000076 Xkr4 chr1:3367210-3367237 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000077 XLOC_000077 Xkr4 chr1:3367333-3367382 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000078 XLOC_000078 Xkr4 chr1:3369580-3369607 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000079 XLOC_000079 Xkr4 chr1:3375001-3375028 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000080 XLOC_000080 Xkr4 chr1:3377211-3377262 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000081 XLOC_000081 Xkr4 chr1:3379888-3379915 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000082 XLOC_000082 Xkr4 chr1:3386739-3386836 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000083 XLOC_000083 Xkr4 chr1:3391325-3391352 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000084 XLOC_000084 Xkr4 chr1:3435841-3435880 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000085 XLOC_000085 Xkr4 chr1:3447761-3447788 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000086 XLOC_000086 Xkr4 chr1:3450906-3450965 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000087 XLOC_000087 Xkr4 chr1:3451051-3451109 q1 q2 NOTEST 0 0 0 0 1 1 no |
| b |
| diff -r 8da0eade1f59 -r 88fcac97c2a0 test-data/cuffdiff_out11.txt --- a/test-data/cuffdiff_out11.txt Fri Dec 19 11:57:43 2014 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,1 +0,0 @@ -test_id gene_id gene locus sample_1 sample_2 status value_1 value_2 sqrt(JS) test_stat p_value q_value significant |
| b |
| diff -r 8da0eade1f59 -r 88fcac97c2a0 test-data/cuffdiff_out2.txt --- a/test-data/cuffdiff_out2.txt Fri Dec 19 11:57:43 2014 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,88 +0,0 @@ -test_id gene_id gene locus sample_1 sample_2 status value_1 value_2 log2(fold_change) test_stat p_value q_value significant -XLOC_000001 XLOC_000001 Xkr4 chr1:3204754-3204833 q1 q2 OK 0 9.45986e+06 inf -nan 0.01975 0.09875 no -XLOC_000002 XLOC_000002 - chr1:3111449-3111490 q1 q2 OK 0 2.43637e+08 inf -nan 0.12465 0.181781 no -XLOC_000003 XLOC_000003 - chr1:3111545-3111576 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000004 XLOC_000004 - chr1:3174765-3174792 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000005 XLOC_000005 - chr1:3187401-3187428 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000006 XLOC_000006 - chr1:3188521-3188548 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000007 XLOC_000007 - chr1:3189810-3190789 q1 q2 OK 358326 522345 0.543731 1.1445 0.1952 0.27328 no -XLOC_000008 XLOC_000008 - chr1:3190858-3191434 q1 q2 OK 408511 420354 0.0412311 0.0469899 0.96715 0.96715 no -XLOC_000009 XLOC_000009 - chr1:3191512-3192077 q1 q2 OK 433286 842157 0.958769 1.27887 0.20385 0.274413 no -XLOC_000010 XLOC_000010 - chr1:3192250-3192336 q1 q2 OK 3.44151e+06 3.34455e+06 -0.0412311 -0.014084 0.67715 0.718189 no -XLOC_000011 XLOC_000011 - chr1:3192441-3192494 q1 q2 OK 0 9.7002e+07 inf -nan 0.07975 0.181781 no -XLOC_000012 XLOC_000012 - chr1:3192550-3192629 q1 q2 OK 0 4.72993e+06 inf -nan 0.12465 0.181781 no -XLOC_000013 XLOC_000013 - chr1:3192649-3192676 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000014 XLOC_000014 - chr1:3192731-3192811 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000015 XLOC_000015 - chr1:3192940-3193042 q1 q2 OK 0 6.86386e+06 inf -nan 0.0612 0.181781 no -XLOC_000016 XLOC_000016 - chr1:3194185-3194226 q1 q2 OK 0 2.43637e+08 inf -nan 0.12465 0.181781 no -XLOC_000017 XLOC_000017 - chr1:3194302-3194329 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000018 XLOC_000018 - chr1:3194706-3194733 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000019 XLOC_000019 - chr1:3195083-3195110 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000020 XLOC_000020 - chr1:3195450-3195477 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000021 XLOC_000021 - chr1:3197089-3197116 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000022 XLOC_000022 - chr1:3197246-3197273 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000023 XLOC_000023 - chr1:3197346-3197373 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000024 XLOC_000024 - chr1:3197425-3197452 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000025 XLOC_000025 - chr1:3200022-3200191 q1 q2 OK 826392 803108 -0.0412311 -0.0180163 0.8625 0.887868 no -XLOC_000026 XLOC_000026 - chr1:3200325-3200352 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000027 XLOC_000027 - chr1:3200430-3200457 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000028 XLOC_000028 - chr1:3201007-3201039 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000029 XLOC_000029 - chr1:3201077-3201481 q1 q2 OK 66791.3 324548 2.2807 1.1905 0.3026 0.383188 no -XLOC_000030 XLOC_000030 - chr1:3201596-3201666 q1 q2 OK 1.6359e+07 0 -inf -nan 0.0148 0.09875 no -XLOC_000031 XLOC_000031 - chr1:3201672-3201699 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000032 XLOC_000032 - chr1:3201725-3201809 q1 q2 OK 1.5136e+07 0 -inf -nan 0.06005 0.181781 no -XLOC_000033 XLOC_000033 Xkr4 chr1:3211521-3211561 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000034 XLOC_000034 Xkr4 chr1:3212213-3212292 q1 q2 OK 0 9.45986e+06 inf -nan 0.01975 0.09875 no -XLOC_000035 XLOC_000035 Xkr4 chr1:3212367-3212439 q1 q2 OK 0 2.80837e+07 inf -nan 0.0612 0.181781 no -XLOC_000036 XLOC_000036 Xkr4 chr1:3212717-3212801 q1 q2 OK 3.784e+06 0 -inf -nan 0.12165 0.181781 no -XLOC_000037 XLOC_000037 Xkr4 chr1:3213095-3213242 q1 q2 OK 5.10781e+06 2.08209e+06 -1.29467 -0.482193 0.5916 0.647062 no -XLOC_000038 XLOC_000038 Xkr4 chr1:3240606-3240633 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000039 XLOC_000039 Xkr4 chr1:3242479-3242512 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000040 XLOC_000040 Xkr4 chr1:3242633-3242923 q1 q2 OK 48522.7 424400 3.12869 1.23747 0.38685 0.450823 no -XLOC_000041 XLOC_000041 Xkr4 chr1:3242924-3243005 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000042 XLOC_000042 Xkr4 chr1:3243018-3243079 q1 q2 OK 0 3.03053e+07 inf -nan 0.01975 0.09875 no -XLOC_000043 XLOC_000043 Xkr4 chr1:3243108-3243154 q1 q2 OK 8.616e+07 0 -inf -nan 0.12165 0.181781 no -XLOC_000044 XLOC_000044 Xkr4 chr1:3243347-3243401 q1 q2 OK 0 5.79991e+07 inf -nan 0.01975 0.09875 no -XLOC_000045 XLOC_000045 Xkr4 chr1:3254079-3254106 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000046 XLOC_000046 Xkr4 chr1:3256974-3257011 q1 q2 OK 0 2.35423e+09 inf -nan 0.01975 0.09875 no -XLOC_000047 XLOC_000047 Xkr4 chr1:3277155-3277182 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000048 XLOC_000048 Xkr4 chr1:3277190-3277218 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000049 XLOC_000049 Xkr4 chr1:3277913-3278390 q1 q2 OK 228872 47662.2 -2.26362 -1.16262 0.30655 0.383188 no -XLOC_000050 XLOC_000050 Xkr4 chr1:3280117-3280144 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000051 XLOC_000051 Xkr4 chr1:3280498-3280525 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000052 XLOC_000052 Xkr4 chr1:3280686-3280741 q1 q2 OK 0 2.61334e+07 inf -nan 0.12465 0.181781 no -XLOC_000053 XLOC_000053 Xkr4 chr1:3282504-3282531 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000054 XLOC_000054 Xkr4 chr1:3282650-3282677 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000055 XLOC_000055 Xkr4 chr1:3282760-3282832 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000056 XLOC_000056 Xkr4 chr1:3284966-3284993 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000057 XLOC_000057 Xkr4 chr1:3290488-3290553 q1 q2 OK 0 1.11503e+07 inf -nan 0.12465 0.181781 no -XLOC_000058 XLOC_000058 Xkr4 chr1:3290798-3290859 q1 q2 OK 1.55919e+07 0 -inf -nan 0.12165 0.181781 no -XLOC_000059 XLOC_000059 Xkr4 chr1:3290919-3291273 q1 q2 OK 294879 85971.3 -1.7782 -0.902752 0.36915 0.445526 no -XLOC_000060 XLOC_000060 Xkr4 chr1:3299443-3299664 q1 q2 OK 807732 156995 -2.36316 -0.89463 0.3993 0.450823 no -XLOC_000061 XLOC_000061 Xkr4 chr1:3299691-3299733 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000062 XLOC_000062 Xkr4 chr1:3300051-3300078 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000063 XLOC_000063 Xkr4 chr1:3307748-3307775 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000064 XLOC_000064 Xkr4 chr1:3318620-3318647 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000065 XLOC_000065 Xkr4 chr1:3318999-3319051 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000066 XLOC_000066 Xkr4 chr1:3330527-3330554 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000067 XLOC_000067 Xkr4 chr1:3351240-3351311 q1 q2 OK 7.68169e+06 0 -inf -nan 0.12165 0.181781 no -XLOC_000068 XLOC_000068 Xkr4 chr1:3355887-3356119 q1 q2 OK 504790 0 -inf -nan 0.04565 0.181781 no -XLOC_000069 XLOC_000069 Xkr4 chr1:3356180-3356225 q1 q2 OK 1.02717e+08 0 -inf -nan 0.12165 0.181781 no -XLOC_000070 XLOC_000070 Xkr4 chr1:3363076-3363176 q1 q2 OK 3.81001e+06 0 -inf -nan 0.0148 0.09875 no -XLOC_000071 XLOC_000071 Xkr4 chr1:3363214-3363278 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000072 XLOC_000072 Xkr4 chr1:3363387-3363446 q1 q2 OK 5.53654e+07 0 -inf -nan 0.0773 0.181781 no -XLOC_000073 XLOC_000073 Xkr4 chr1:3363753-3363849 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000074 XLOC_000074 Xkr4 chr1:3364871-3364919 q1 q2 OK 6.28966e+07 0 -inf -nan 0.12165 0.181781 no -XLOC_000075 XLOC_000075 Xkr4 chr1:3367135-3367162 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000076 XLOC_000076 Xkr4 chr1:3367210-3367237 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000077 XLOC_000077 Xkr4 chr1:3367333-3367382 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000078 XLOC_000078 Xkr4 chr1:3369580-3369607 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000079 XLOC_000079 Xkr4 chr1:3375001-3375028 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000080 XLOC_000080 Xkr4 chr1:3377211-3377262 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000081 XLOC_000081 Xkr4 chr1:3379888-3379915 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000082 XLOC_000082 Xkr4 chr1:3386739-3386836 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000083 XLOC_000083 Xkr4 chr1:3391325-3391352 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000084 XLOC_000084 Xkr4 chr1:3435841-3435880 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000085 XLOC_000085 Xkr4 chr1:3447761-3447788 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000086 XLOC_000086 Xkr4 chr1:3450906-3450965 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000087 XLOC_000087 Xkr4 chr1:3451051-3451109 q1 q2 NOTEST 0 0 0 0 1 1 no |
| b |
| diff -r 8da0eade1f59 -r 88fcac97c2a0 test-data/cuffdiff_out3.txt --- a/test-data/cuffdiff_out3.txt Fri Dec 19 11:57:43 2014 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,89 +0,0 @@ -test_id gene_id gene locus sample_1 sample_2 status value_1 value_2 log2(fold_change) test_stat p_value q_value significant -TSS1 XLOC_000001 Xkr4 chr1:3204754-3204833 q1 q2 OK 0 9.45986e+06 inf -nan 0.01975 0.09875 no -TSS10 XLOC_000008 - chr1:3190858-3191434 q1 q2 OK 408511 420354 0.0412311 0.0469899 0.96715 0.96715 no -TSS11 XLOC_000009 - chr1:3191512-3192077 q1 q2 OK 433286 842157 0.958769 1.27887 0.20385 0.274413 no -TSS13 XLOC_000010 - chr1:3192250-3192336 q1 q2 OK 3.44151e+06 3.34455e+06 -0.0412311 -0.014084 0.67715 0.718189 no -TSS14 XLOC_000011 - chr1:3192441-3192494 q1 q2 OK 0 9.7002e+07 inf -nan 0.07975 0.181781 no -TSS15 XLOC_000012 - chr1:3192550-3192629 q1 q2 OK 0 4.72993e+06 inf -nan 0.12465 0.181781 no -TSS16 XLOC_000013 - chr1:3192649-3192676 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS17 XLOC_000014 - chr1:3192731-3192811 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS18 XLOC_000015 - chr1:3192940-3193042 q1 q2 OK 0 6.86386e+06 inf -nan 0.0612 0.181781 no -TSS19 XLOC_000016 - chr1:3194185-3194226 q1 q2 OK 0 2.43637e+08 inf -nan 0.12465 0.181781 no -TSS2 XLOC_000002 - chr1:3111449-3111490 q1 q2 OK 0 2.43637e+08 inf -nan 0.12465 0.181781 no -TSS20 XLOC_000017 - chr1:3194302-3194329 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS21 XLOC_000018 - chr1:3194706-3194733 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS22 XLOC_000019 - chr1:3195083-3195110 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS23 XLOC_000020 - chr1:3195450-3195477 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS24 XLOC_000021 - chr1:3197089-3197116 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS25 XLOC_000022 - chr1:3197246-3197273 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS26 XLOC_000023 - chr1:3197346-3197373 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS27 XLOC_000024 - chr1:3197425-3197452 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS28 XLOC_000025 - chr1:3200022-3200191 q1 q2 OK 826392 803108 -0.0412311 -0.0180163 0.8625 0.887868 no -TSS29 XLOC_000026 - chr1:3200325-3200352 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS3 XLOC_000003 - chr1:3111545-3111576 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS30 XLOC_000027 - chr1:3200430-3200457 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS31 XLOC_000028 - chr1:3201007-3201039 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS32 XLOC_000029 - chr1:3201077-3201481 q1 q2 OK 66791.3 324548 2.2807 1.1905 0.3026 0.383188 no -TSS33 XLOC_000030 - chr1:3201596-3201666 q1 q2 OK 1.6359e+07 0 -inf -nan 0.0148 0.09875 no -TSS34 XLOC_000031 - chr1:3201672-3201699 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS35 XLOC_000032 - chr1:3201725-3201809 q1 q2 OK 1.5136e+07 0 -inf -nan 0.06005 0.181781 no -TSS36 XLOC_000033 Xkr4 chr1:3211521-3211561 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS37 XLOC_000034 Xkr4 chr1:3212213-3212292 q1 q2 OK 0 9.45986e+06 inf -nan 0.01975 0.09875 no -TSS38 XLOC_000035 Xkr4 chr1:3212367-3212439 q1 q2 OK 0 2.80837e+07 inf -nan 0.0612 0.181781 no -TSS39 XLOC_000036 Xkr4 chr1:3212717-3212801 q1 q2 OK 3.784e+06 0 -inf -nan 0.12165 0.181781 no -TSS4 XLOC_000004 - chr1:3174765-3174792 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS40 XLOC_000037 Xkr4 chr1:3213095-3213242 q1 q2 OK 5.10781e+06 2.08209e+06 -1.29467 -0.482193 0.5916 0.647062 no -TSS41 XLOC_000038 Xkr4 chr1:3240606-3240633 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS42 XLOC_000039 Xkr4 chr1:3242479-3242512 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS43 XLOC_000040 Xkr4 chr1:3242633-3242923 q1 q2 OK 48522.7 424400 3.12869 1.23747 0.38685 0.451325 no -TSS44 XLOC_000041 Xkr4 chr1:3242924-3243005 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS45 XLOC_000042 Xkr4 chr1:3243018-3243079 q1 q2 OK 0 3.03053e+07 inf -nan 0.01975 0.09875 no -TSS46 XLOC_000043 Xkr4 chr1:3243108-3243154 q1 q2 OK 8.616e+07 0 -inf -nan 0.12165 0.181781 no -TSS47 XLOC_000044 Xkr4 chr1:3243347-3243401 q1 q2 OK 0 5.79991e+07 inf -nan 0.01975 0.09875 no -TSS48 XLOC_000045 Xkr4 chr1:3254079-3254106 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS49 XLOC_000046 Xkr4 chr1:3256974-3257011 q1 q2 OK 0 2.35423e+09 inf -nan 0.01975 0.09875 no -TSS5 XLOC_000005 - chr1:3187401-3187428 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS50 XLOC_000047 Xkr4 chr1:3277155-3277182 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS51 XLOC_000048 Xkr4 chr1:3277190-3277218 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS52 XLOC_000049 Xkr4 chr1:3277913-3278390 q1 q2 OK 228872 47662.2 -2.26362 -1.16262 0.30655 0.383188 no -TSS54 XLOC_000050 Xkr4 chr1:3280117-3280144 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS55 XLOC_000051 Xkr4 chr1:3280498-3280525 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS56 XLOC_000052 Xkr4 chr1:3280686-3280741 q1 q2 OK 0 2.61334e+07 inf -nan 0.12465 0.181781 no -TSS57 XLOC_000053 Xkr4 chr1:3282504-3282531 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS58 XLOC_000054 Xkr4 chr1:3282650-3282677 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS59 XLOC_000055 Xkr4 chr1:3282760-3282832 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS6 XLOC_000006 - chr1:3188521-3188548 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS60 XLOC_000056 Xkr4 chr1:3284966-3284993 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS61 XLOC_000057 Xkr4 chr1:3290488-3290553 q1 q2 OK 0 1.11503e+07 inf -nan 0.12465 0.181781 no -TSS62 XLOC_000058 Xkr4 chr1:3290798-3290859 q1 q2 OK 1.55919e+07 0 -inf -nan 0.12165 0.181781 no -TSS63 XLOC_000059 Xkr4 chr1:3290919-3291273 q1 q2 OK 294879 85971.3 -1.7782 -0.902752 0.36915 0.445526 no -TSS65 XLOC_000060 Xkr4 chr1:3299443-3299664 q1 q2 OK 807732 156995 -2.36316 -0.933704 0.4205 0.474758 no -TSS66 XLOC_000060 Xkr4 chr1:3299443-3299664 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS67 XLOC_000061 Xkr4 chr1:3299691-3299733 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS68 XLOC_000062 Xkr4 chr1:3300051-3300078 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS69 XLOC_000063 Xkr4 chr1:3307748-3307775 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS7 XLOC_000007 - chr1:3189810-3190789 q1 q2 OK 358326 522345 0.543731 1.1445 0.1952 0.27328 no -TSS70 XLOC_000064 Xkr4 chr1:3318620-3318647 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS71 XLOC_000065 Xkr4 chr1:3318999-3319051 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS72 XLOC_000066 Xkr4 chr1:3330527-3330554 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS73 XLOC_000067 Xkr4 chr1:3351240-3351311 q1 q2 OK 7.68169e+06 0 -inf -nan 0.12165 0.181781 no -TSS74 XLOC_000068 Xkr4 chr1:3355887-3356119 q1 q2 OK 504790 0 -inf -nan 0.04565 0.181781 no -TSS75 XLOC_000069 Xkr4 chr1:3356180-3356225 q1 q2 OK 1.02717e+08 0 -inf -nan 0.12165 0.181781 no -TSS76 XLOC_000070 Xkr4 chr1:3363076-3363176 q1 q2 OK 3.81001e+06 0 -inf -nan 0.0148 0.09875 no -TSS77 XLOC_000071 Xkr4 chr1:3363214-3363278 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS78 XLOC_000072 Xkr4 chr1:3363387-3363446 q1 q2 OK 5.53654e+07 0 -inf -nan 0.0773 0.181781 no -TSS79 XLOC_000073 Xkr4 chr1:3363753-3363849 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS80 XLOC_000074 Xkr4 chr1:3364871-3364919 q1 q2 OK 6.28966e+07 0 -inf -nan 0.12165 0.181781 no -TSS81 XLOC_000075 Xkr4 chr1:3367135-3367162 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS82 XLOC_000076 Xkr4 chr1:3367210-3367237 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS83 XLOC_000077 Xkr4 chr1:3367333-3367382 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS84 XLOC_000078 Xkr4 chr1:3369580-3369607 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS85 XLOC_000079 Xkr4 chr1:3375001-3375028 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS86 XLOC_000080 Xkr4 chr1:3377211-3377262 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS87 XLOC_000081 Xkr4 chr1:3379888-3379915 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS88 XLOC_000082 Xkr4 chr1:3386739-3386836 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS89 XLOC_000083 Xkr4 chr1:3391325-3391352 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS90 XLOC_000084 Xkr4 chr1:3435841-3435880 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS91 XLOC_000085 Xkr4 chr1:3447761-3447788 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS92 XLOC_000086 Xkr4 chr1:3450906-3450965 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS93 XLOC_000087 Xkr4 chr1:3451051-3451109 q1 q2 NOTEST 0 0 0 0 1 1 no |
| b |
| diff -r 8da0eade1f59 -r 88fcac97c2a0 test-data/cuffdiff_out4.txt --- a/test-data/cuffdiff_out4.txt Fri Dec 19 11:57:43 2014 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,1 +0,0 @@ -test_id gene_id gene locus sample_1 sample_2 status value_1 value_2 log2(fold_change) test_stat p_value q_value significant |
| b |
| diff -r 8da0eade1f59 -r 88fcac97c2a0 test-data/cuffdiff_out5.txt --- a/test-data/cuffdiff_out5.txt Fri Dec 19 11:57:43 2014 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,91 +0,0 @@\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\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-\tTSS14\tchr1:3192441-3192494\t53\t-\t0\t0\t0\tOK\t9.7002e+07\t0\t3.17699e+08\tOK\n-TCONS_00000010\t-\t-\tXLOC_000012\t-\tTSS15\tchr1:3192550-3192629\t79\t-\t0\t0\t0\tOK\t4.72993e+06\t0\t1.84961e+07\tOK\n-TCONS_00000011\t-\t-\tXLOC_000014\t-\tTSS17\tchr1:3192731-3192811\t80\t-\t0\t0\t0\tOK\t0\t0\t0\tOK\n-TCONS_00000012\t-\t-\tXLOC_000015\t-\tTSS18\tchr1:3192940-3193042\t102\t-\t0\t0\t0\tOK\t6.86386e+06\t0\t2.14243e+07\tOK\n-TCONS_00000013\t-\t-\tXLOC_000016\t-\tTSS19\tchr1:3194185-3194226\t41\t-\t0\t0\t0\tOK\t2.43637e+08\t0\t9.52723e+08\tOK\n-TCONS_00000014\t-\t-\tXLOC_000017\t-\tTSS20\tchr1:3194302-3194329\t27\t-\t0\t0\t0\tOK\t0\t0\t0\tOK\n-TCONS_00000015\t-\t-\tXLOC_000019\t-\tTSS22\tchr1:3195083-3195110\t27\t-\t0\t0\t0\tOK\t0\t0\t0\tOK\n-TCONS_00000016\t-\t-\tXLOC_000020\t-\tTSS23\tchr1:3195450-3195477\t27\t-\t0\t0\t0\tOK\t0\t0\t0\tOK\n-TCONS_00000017\t-\t-\tXLOC_000021\t-\tTSS24\tchr1:3197089-3197116\t27\t-\t0\t0\t0\tOK\t0\t0\t0\tOK\n-TCONS_00000018\t-\t-\tXLOC_000022\t-\tTSS25\tchr1:3197246-3197273\t27\t-\t0\t0\t0\tOK\t0\t0\t0\tOK\n-TCONS_00000019\t-\t-\tXLOC_000023\t-\tTSS26\tchr1:3197346-3197373\t27\t-\t0\t0\t0\tOK\t0\t0\t0\tOK\n-TCONS_00000020\t-\t-\tXLOC_000025\t-\tTSS28\tchr1:3200022-3200191\t169\t-\t826392\t0\t2.65361e+06\tOK\t803108\t0\t2.63033e+06\tOK\n-TCONS_00000021\t-\t-\tXLOC_000026\t-\tTSS29\tchr1:3200325-3200352\t27\t-\t0\t0\t0\tOK\t0\t0\t0\tOK\n-TCONS_00000022\t-\t-\tXLOC_000029\t-\tTSS32\tchr1:3201077-3201481\t404\t-\t66791.3\t0\t214473\tOK\t324548\t0\t802006\tOK\n-TCONS_00000023\t-\t-\tXLOC_000031\t-\tTSS34\tchr1:3201672-3201699\t27\t-\t0\t0\t0\tOK\t0\t0\t0\tOK\n-TCONS_00000024\ti\tXkr4\tXLOC_000034\tXkr4\tTSS37\tchr1:3212213-3212292\t79\t-\t0\t0\t0\tOK\t9.45986e+06\t0\t3.33035e+07\tOK\n-TCONS_00000025\ti\tXkr4\tXLOC_000035\tXkr4\tTSS38\tchr1:3212367-3212439\t72\t-\t0\t0\t0\tOK\t2.80837e+07\t0\t8.76584e+07\tOK\n-TCONS_00000026\ti\tXkr4\tXLOC_000037\tXkr4\tTSS40\tchr1:3213095-3213242\t97\t-\t4.24463e+06\t0\t1.55814e+07\tOK\t2.08209e+06\t0\t8.14187e+06\tOK\n-TCONS_00000027\ti\tXkr4\tXLOC_000040\tXkr4\tTSS43\tchr1:3242633-3242923\t290\t-\t48522.7\t0\t185766\tOK\t424400\t0\t1.30289e+06\tOK\n-TCONS_00000028\ti\tXkr4\tXLOC_000042\tXkr4\tTSS45\tchr1:3243018-3243079\t61\t-\t0\t0\t0\tOK\t3.03053e+07\t0\t1.0669e+08\tOK\n-TCONS_00000029\ti\tXkr4\tXLOC_000044\tXkr4\tTSS47\tchr1:3243347-3243401\t54\t-\t0\t0\t0\tOK\t5.79991e+07\t0\t2.04186e+08\tOK\n-TCONS_00000030\ti\tXkr4\tXLOC_000046\tXkr4\tTSS49\tchr1:3256974-3257011\t37\t-\t0\t0\t0\tOK\t2.35423e+09\t0\t8.28806e+09\tOK\n-TCONS_00000031\ti\tXkr4\tXLOC_000048\tXkr4\tTSS51\tchr1:3277190-3277218\t28\t-\t0\t0\t0\tOK\t0\t0\t0\tOK\n-TCONS_00000033\ti\tXkr4\tXLOC_000052\tXkr4\tTSS56\tchr1:3280686-3280741\t55\t-\t0\t0\t0\tOK\t2.61334e+07\t0\t1.02193e+08\tOK\n-TCONS_00000034\ti\tXkr4\tXLOC_000057\tXkr4\tTSS61\tchr1:3290488-3290553\t65\t-\t0\t0\t0\tOK\t1.11503e+07\t0\t4.36026e+07\tOK\n-TCONS_00000037\ti\tXkr4\tXLOC_000060\tXkr4\tTSS66\tchr1:3299443-3299664\t55\t-\t0\t0\t163195\tOK\t0\t0\t163195\tOK\n-TCONS_00000038\ti\tXkr4\tXLOC_000062\tXkr4\tTSS68\tchr1:3300051-3300078\t27\t-\t0\t0\t0\tOK\t0\t0\t0\tOK\n-TCONS_00000039\ti\tXkr4\tXLOC_000065\tXkr4\tTSS71\tchr1:3318999-3319051\t52\t-\t0\t0\t0\tOK\t0\t0\t0\tOK\n-TCONS_00000040\ti\tXkr4\tXLOC_000068\tXkr4\tTSS74\tchr1:3355887-3356119\t27\t-\t0\t0\t332434\tOK\t0\t0\t0\tOK\n-TCONS_00000041\ti\tXkr4\tXLOC_000071\tXkr4\tTSS77\tchr1:3363214-3363278\t64\t-\t0\t0\t0\tOK\t0\t0\t0\tOK\n-TCONS_00000042\ti\tXkr4\tXLOC_000073\tXkr4\tTSS79\tchr1:3363753-3363849\t96\t-\t0\t0\t0\tOK\t0\t0\t0\tOK\n-TCONS_00000043\ti\tXkr4\tXLOC_000075\tXkr4\tTSS81\tchr1:3367135-3367162\t27\t-\t0\t0\t0\tOK\t0\t0\t0\tOK\n-TCONS_00000044\ti\tXkr4\tXLOC_000077\tXkr4\tTSS83\tchr1:3367333-3367382\t49\t-\t0\t0\t0\tOK\t0\t0\t0\tOK\n-TCONS_00000045\ti\tXkr4\tXLOC_000080\tXkr4\tTSS86\tchr1:3377211-3377262\t51\t-\t0\t0\t0\tOK\t0\t0\t0\tOK\n-TCONS_00000046\ti\tXkr4\tXLOC_000083\tXkr4\tTSS89\tchr1:3391325-3391352\t27\t-\t0\t0\t0\tOK\t0\t0\t0\tOK\n-TCONS_00000047\ti\tXkr4\tXLOC_000084\tXkr4\tTSS90\tchr1:3435841-3435880\t39\t-\t0\t0\t0\tOK\t0\t0\t0\tOK\n-TCONS_0000'..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 8da0eade1f59 -r 88fcac97c2a0 test-data/cuffdiff_out6.txt --- a/test-data/cuffdiff_out6.txt Fri Dec 19 11:57:43 2014 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,88 +0,0 @@\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\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-\t358326\t135086\t581565\tOK\t522345\t410780\t633911\tOK\n-XLOC_000008\t-\t-\tXLOC_000008\t-\tTSS10\tchr1:3190858-3191434\t-\t-\t408511\t54526.1\t762496\tOK\t420354\t61509.1\t779200\tOK\n-XLOC_000009\t-\t-\tXLOC_000009\t-\tTSS11\tchr1:3191512-3192077\t-\t-\t433286\t63552.3\t803020\tOK\t842157\t342520\t1.34179e+06\tOK\n-XLOC_000010\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-XLOC_000011\t-\t-\tXLOC_000011\t-\tTSS14\tchr1:3192441-3192494\t-\t-\t0\t0\t0\tOK\t9.7002e+07\t0\t3.17699e+08\tOK\n-XLOC_000012\t-\t-\tXLOC_000012\t-\tTSS15\tchr1:3192550-3192629\t-\t-\t0\t0\t0\tOK\t4.72993e+06\t0\t1.84961e+07\tOK\n-XLOC_000013\t-\t-\tXLOC_000013\t-\tTSS16\tchr1:3192649-3192676\t-\t-\t0\t0\t0\tOK\t0\t0\t0\tOK\n-XLOC_000014\t-\t-\tXLOC_000014\t-\tTSS17\tchr1:3192731-3192811\t-\t-\t0\t0\t0\tOK\t0\t0\t0\tOK\n-XLOC_000015\t-\t-\tXLOC_000015\t-\tTSS18\tchr1:3192940-3193042\t-\t-\t0\t0\t0\tOK\t6.86386e+06\t0\t2.14243e+07\tOK\n-XLOC_000016\t-\t-\tXLOC_000016\t-\tTSS19\tchr1:3194185-3194226\t-\t-\t0\t0\t0\tOK\t2.43637e+08\t0\t9.52723e+08\tOK\n-XLOC_000017\t-\t-\tXLOC_000017\t-\tTSS20\tchr1:3194302-3194329\t-\t-\t0\t0\t0\tOK\t0\t0\t0\tOK\n-XLOC_000018\t-\t-\tXLOC_000018\t-\tTSS21\tchr1:3194706-3194733\t-\t-\t0\t0\t0\tOK\t0\t0\t0\tOK\n-XLOC_000019\t-\t-\tXLOC_000019\t-\tTSS22\tchr1:3195083-3195110\t-\t-\t0\t0\t0\tOK\t0\t0\t0\tOK\n-XLOC_000020\t-\t-\tXLOC_000020\t-\tTSS23\tchr1:3195450-3195477\t-\t-\t0\t0\t0\tOK\t0\t0\t0\tOK\n-XLOC_000021\t-\t-\tXLOC_000021\t-\tTSS24\tchr1:3197089-3197116\t-\t-\t0\t0\t0\tOK\t0\t0\t0\tOK\n-XLOC_000022\t-\t-\tXLOC_000022\t-\tTSS25\tchr1:3197246-3197273\t-\t-\t0\t0\t0\tOK\t0\t0\t0\tOK\n-XLOC_000023\t-\t-\tXLOC_000023\t-\tTSS26\tchr1:3197346-3197373\t-\t-\t0\t0\t0\tOK\t0\t0\t0\tOK\n-XLOC_000024\t-\t-\tXLOC_000024\t-\tTSS27\tchr1:3197425-3197452\t-\t-\t0\t0\t0\tOK\t0\t0\t0\tOK\n-XLOC_000025\t-\t-\tXLOC_000025\t-\tTSS28\tchr1:3200022-3200191\t-\t-\t826392\t0\t2.65361e+06\tOK\t803108\t0\t2.63033e+06\tOK\n-XLOC_000026\t-\t-\tXLOC_000026\t-\tTSS29\tchr1:3200325-3200352\t-\t-\t0\t0\t0\tOK\t0\t0\t0\tOK\n-XLOC_000027\t-\t-\tXLOC_000027\t-\tTSS30\tchr1:3200430-3200457\t-\t-\t0\t0\t0\tOK\t0\t0\t0\tOK\n-XLOC_000028\t-\t-\tXLOC_000028\t-\tTSS31\tchr1:3201007-3201039\t-\t-\t0\t0\t0\tOK\t0\t0\t0\tOK\n-XLOC_000029\t-\t-\tXLOC_000029\t-\tTSS32\tchr1:3201077-3201481\t-\t-\t66791.3\t0\t214473\tOK\t324548\t0\t802006\tOK\n-XLOC_000030\t-\t-\tXLOC_000030\t-\tTSS33\tchr1:3201596-3201666\t-\t-\t1.6359e+07\t0\t5.96409e+07\tOK\t0\t0\t0\tOK\n-XLOC_000031\t-\t-\tXLOC_000031\t-\tTSS34\tchr1:3201672-3201699\t-\t-\t0\t0\t0\tOK\t0\t0\t0\tOK\n-XLOC_000032\t-\t-\tXLOC_000032\t-\tTSS35\tchr1:3201725-3201809\t-\t-\t1.5136e+07\t0\t4.63396e+07\tOK\t0\t0\t0\tOK\n-XLOC_000033\t-\t-\tXLOC_000033\tXkr4\tTSS36\tchr1:3211521-3211561\t-\t-\t0\t0\t0\tOK\t0\t0\t0\tOK\n-XLOC_000034\t-\t-\tXLOC_000034\tXkr4\tTSS37\tchr1:3212213-3212292\t-\t-\t0\t0\t0\tOK\t9.45986e+06\t0\t3.33035e+07\tOK\n-XLOC_000035\t-\t-\tXLOC_000035\tXkr4\tTSS38\tchr1:3212367-3212439\t-\t-\t0\t0\t0\tOK\t2.80837e+07\t0\t8.76584e+07\tOK\n-XLOC_000036\t-\t-\tXLOC_000036\tXkr4\tTSS39\tchr1:3212717-3212801\t-\t-\t3.784e+06\t0\t1.44868e+07\tOK\t0\t0\t0\tOK\n-XLOC_000037\t-\t-\tXLOC_000037\tXkr4\tTSS40\tchr1:3213095-3213242\t-\t-\t5.10781e+06\t0\t1.69588e+07\tOK\t2.08209e+06\t0\t8.1421e+06\tOK\n-XLOC_000038\t-\t-\tXLOC_000038\tXkr4\tTSS41\tchr1:3240606-3240633\t-\t-\t0\t0\t0\tOK\t0\t0\t0\tOK\n-XLOC_000039\t-\t-\tXLOC_000039\tXkr4\tTSS42\tchr1:3242479-3242512\t-\t-\t0\t0\t0\tOK\t0\t0\t0\tOK\n-XLOC_000040\t-\t-\tXLOC_000040\tXkr4\tTSS43\tchr1:3242633-3242923\t-\t-\t48522.7\t0\t185766\tOK\t424400\t0\t1.30289e+06\tOK\n-XLOC_000041\t-\t-\tXLOC_000041\tXkr4\tTSS44\tchr1:3242924-3243005\t-\t-\t0\t0\t0\tOK\t0\t0\t0\tOK\n-XLOC_000042\t-\t-\tXLOC_000042\tXkr4\tTSS4'..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 8da0eade1f59 -r 88fcac97c2a0 test-data/cuffdiff_out7.txt --- a/test-data/cuffdiff_out7.txt Fri Dec 19 11:57:43 2014 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,89 +0,0 @@ -tracking_id class_code nearest_ref_id gene_id gene_short_name tss_id locus length coverage q1_FPKM q1_conf_lo q1_conf_hi q1_status q2_FPKM q2_conf_lo q2_conf_hi q2_status -TSS1 - - XLOC_000001 Xkr4 TSS1 chr1:3204754-3204833 - - 0 0 0 OK 9.45986e+06 0 3.33035e+07 OK -TSS10 - - XLOC_000008 - TSS10 chr1:3190858-3191434 - - 408511 54526.1 762496 OK 420354 61509.1 779200 OK -TSS11 - - XLOC_000009 - TSS11 chr1:3191512-3192077 - - 433286 63552.3 803020 OK 842157 342520 1.34179e+06 OK -TSS13 - - XLOC_000010 - TSS13 chr1:3192250-3192336 - - 3.44151e+06 0 1.31756e+07 OK 3.34455e+06 0 1.30786e+07 OK -TSS14 - - XLOC_000011 - TSS14 chr1:3192441-3192494 - - 0 0 0 OK 9.7002e+07 0 3.17699e+08 OK -TSS15 - - XLOC_000012 - TSS15 chr1:3192550-3192629 - - 0 0 0 OK 4.72993e+06 0 1.84961e+07 OK -TSS16 - - XLOC_000013 - TSS16 chr1:3192649-3192676 - - 0 0 0 OK 0 0 0 OK -TSS17 - - XLOC_000014 - TSS17 chr1:3192731-3192811 - - 0 0 0 OK 0 0 0 OK -TSS18 - - XLOC_000015 - TSS18 chr1:3192940-3193042 - - 0 0 0 OK 6.86386e+06 0 2.14243e+07 OK -TSS19 - - XLOC_000016 - TSS19 chr1:3194185-3194226 - - 0 0 0 OK 2.43637e+08 0 9.52723e+08 OK -TSS2 - - XLOC_000002 - TSS2 chr1:3111449-3111490 - - 0 0 0 OK 2.43637e+08 0 9.52723e+08 OK -TSS20 - - XLOC_000017 - TSS20 chr1:3194302-3194329 - - 0 0 0 OK 0 0 0 OK -TSS21 - - XLOC_000018 - TSS21 chr1:3194706-3194733 - - 0 0 0 OK 0 0 0 OK -TSS22 - - XLOC_000019 - TSS22 chr1:3195083-3195110 - - 0 0 0 OK 0 0 0 OK -TSS23 - - XLOC_000020 - TSS23 chr1:3195450-3195477 - - 0 0 0 OK 0 0 0 OK -TSS24 - - XLOC_000021 - TSS24 chr1:3197089-3197116 - - 0 0 0 OK 0 0 0 OK -TSS25 - - XLOC_000022 - TSS25 chr1:3197246-3197273 - - 0 0 0 OK 0 0 0 OK -TSS26 - - XLOC_000023 - TSS26 chr1:3197346-3197373 - - 0 0 0 OK 0 0 0 OK -TSS27 - - XLOC_000024 - TSS27 chr1:3197425-3197452 - - 0 0 0 OK 0 0 0 OK -TSS28 - - XLOC_000025 - TSS28 chr1:3200022-3200191 - - 826392 0 2.65361e+06 OK 803108 0 2.63033e+06 OK -TSS29 - - XLOC_000026 - TSS29 chr1:3200325-3200352 - - 0 0 0 OK 0 0 0 OK -TSS3 - - XLOC_000003 - TSS3 chr1:3111545-3111576 - - 0 0 0 OK 0 0 0 OK -TSS30 - - XLOC_000027 - TSS30 chr1:3200430-3200457 - - 0 0 0 OK 0 0 0 OK -TSS31 - - XLOC_000028 - TSS31 chr1:3201007-3201039 - - 0 0 0 OK 0 0 0 OK -TSS32 - - XLOC_000029 - TSS32 chr1:3201077-3201481 - - 66791.3 0 214473 OK 324548 0 802006 OK -TSS33 - - XLOC_000030 - TSS33 chr1:3201596-3201666 - - 1.6359e+07 0 5.96409e+07 OK 0 0 0 OK -TSS34 - - XLOC_000031 - TSS34 chr1:3201672-3201699 - - 0 0 0 OK 0 0 0 OK -TSS35 - - XLOC_000032 - TSS35 chr1:3201725-3201809 - - 1.5136e+07 0 4.63396e+07 OK 0 0 0 OK -TSS36 - - XLOC_000033 Xkr4 TSS36 chr1:3211521-3211561 - - 0 0 0 OK 0 0 0 OK -TSS37 - - XLOC_000034 Xkr4 TSS37 chr1:3212213-3212292 - - 0 0 0 OK 9.45986e+06 0 3.33035e+07 OK -TSS38 - - XLOC_000035 Xkr4 TSS38 chr1:3212367-3212439 - - 0 0 0 OK 2.80837e+07 0 8.76584e+07 OK -TSS39 - - XLOC_000036 Xkr4 TSS39 chr1:3212717-3212801 - - 3.784e+06 0 1.44868e+07 OK 0 0 0 OK -TSS4 - - XLOC_000004 - TSS4 chr1:3174765-3174792 - - 0 0 0 OK 0 0 0 OK -TSS40 - - XLOC_000037 Xkr4 TSS40 chr1:3213095-3213242 - - 5.10781e+06 0 1.69588e+07 OK 2.08209e+06 0 8.1421e+06 OK -TSS41 - - XLOC_000038 Xkr4 TSS41 chr1:3240606-3240633 - - 0 0 0 OK 0 0 0 OK -TSS42 - - XLOC_000039 Xkr4 TSS42 chr1:3242479-3242512 - - 0 0 0 OK 0 0 0 OK -TSS43 - - XLOC_000040 Xkr4 TSS43 chr1:3242633-3242923 - - 48522.7 0 185766 OK 424400 0 1.30289e+06 OK -TSS44 - - XLOC_000041 Xkr4 TSS44 chr1:3242924-3243005 - - 0 0 0 OK 0 0 0 OK -TSS45 - - XLOC_000042 Xkr4 TSS45 chr1:3243018-3243079 - - 0 0 0 OK 3.03053e+07 0 1.0669e+08 OK -TSS46 - - XLOC_000043 Xkr4 TSS46 chr1:3243108-3243154 - - 8.616e+07 0 3.29857e+08 OK 0 0 0 OK -TSS47 - - XLOC_000044 Xkr4 TSS47 chr1:3243347-3243401 - - 0 0 0 OK 5.79991e+07 0 2.04186e+08 OK -TSS48 - - XLOC_000045 Xkr4 TSS48 chr1:3254079-3254106 - - 0 0 0 OK 0 0 0 OK -TSS49 - - XLOC_000046 Xkr4 TSS49 chr1:3256974-3257011 - - 0 0 0 OK 2.35423e+09 0 8.28806e+09 OK -TSS5 - - XLOC_000005 - TSS5 chr1:3187401-3187428 - - 0 0 0 OK 0 0 0 OK -TSS50 - - XLOC_000047 Xkr4 TSS50 chr1:3277155-3277182 - - 0 0 0 OK 0 0 0 OK -TSS51 - - XLOC_000048 Xkr4 TSS51 chr1:3277190-3277218 - - 0 0 0 OK 0 0 0 OK -TSS52 - - XLOC_000049 Xkr4 TSS52 chr1:3277913-3278390 - - 228872 0 561229 OK 47662.2 0 156103 OK -TSS54 - - XLOC_000050 Xkr4 TSS54 chr1:3280117-3280144 - - 0 0 0 OK 0 0 0 OK -TSS55 - - XLOC_000051 Xkr4 TSS55 chr1:3280498-3280525 - - 0 0 0 OK 0 0 0 OK -TSS56 - - XLOC_000052 Xkr4 TSS56 chr1:3280686-3280741 - - 0 0 0 OK 2.61334e+07 0 1.02193e+08 OK -TSS57 - - XLOC_000053 Xkr4 TSS57 chr1:3282504-3282531 - - 0 0 0 OK 0 0 0 OK -TSS58 - - XLOC_000054 Xkr4 TSS58 chr1:3282650-3282677 - - 0 0 0 OK 0 0 0 OK -TSS59 - - XLOC_000055 Xkr4 TSS59 chr1:3282760-3282832 - - 0 0 0 OK 0 0 0 OK -TSS6 - - XLOC_000006 - TSS6 chr1:3188521-3188548 - - 0 0 0 OK 0 0 0 OK -TSS60 - - XLOC_000056 Xkr4 TSS60 chr1:3284966-3284993 - - 0 0 0 OK 0 0 0 OK -TSS61 - - XLOC_000057 Xkr4 TSS61 chr1:3290488-3290553 - - 0 0 0 OK 1.11503e+07 0 4.36026e+07 OK -TSS62 - - XLOC_000058 Xkr4 TSS62 chr1:3290798-3290859 - - 1.55919e+07 0 5.96926e+07 OK 0 0 0 OK -TSS63 - - XLOC_000059 Xkr4 TSS63 chr1:3290919-3291273 - - 294879 0 740137 OK 85971.3 0 281572 OK -TSS65 - - XLOC_000060 Xkr4 TSS65 chr1:3299443-3299664 - - 807732 0 2.39056e+06 OK 156995 0 613917 OK -TSS66 - - XLOC_000060 Xkr4 TSS66 chr1:3299443-3299664 - - 0 0 0 OK 0 0 0 OK -TSS67 - - XLOC_000061 Xkr4 TSS67 chr1:3299691-3299733 - - 0 0 0 OK 0 0 0 OK -TSS68 - - XLOC_000062 Xkr4 TSS68 chr1:3300051-3300078 - - 0 0 0 OK 0 0 0 OK -TSS69 - - XLOC_000063 Xkr4 TSS69 chr1:3307748-3307775 - - 0 0 0 OK 0 0 0 OK -TSS7 - - XLOC_000007 - TSS7 chr1:3189810-3190789 - - 358326 135086 581565 OK 522345 410780 633911 OK -TSS70 - - XLOC_000064 Xkr4 TSS70 chr1:3318620-3318647 - - 0 0 0 OK 0 0 0 OK -TSS71 - - XLOC_000065 Xkr4 TSS71 chr1:3318999-3319051 - - 0 0 0 OK 0 0 0 OK -TSS72 - - XLOC_000066 Xkr4 TSS72 chr1:3330527-3330554 - - 0 0 0 OK 0 0 0 OK -TSS73 - - XLOC_000067 Xkr4 TSS73 chr1:3351240-3351311 - - 7.68169e+06 0 2.94088e+07 OK 0 0 0 OK -TSS74 - - XLOC_000068 Xkr4 TSS74 chr1:3355887-3356119 - - 504790 0 1.59712e+06 OK 0 0 0 OK -TSS75 - - XLOC_000069 Xkr4 TSS75 chr1:3356180-3356225 - - 1.02717e+08 0 3.93246e+08 OK 0 0 0 OK -TSS76 - - XLOC_000070 Xkr4 TSS76 chr1:3363076-3363176 - - 3.81001e+06 0 1.38903e+07 OK 0 0 0 OK -TSS77 - - XLOC_000071 Xkr4 TSS77 chr1:3363214-3363278 - - 0 0 0 OK 0 0 0 OK -TSS78 - - XLOC_000072 Xkr4 TSS78 chr1:3363387-3363446 - - 5.53654e+07 0 1.77783e+08 OK 0 0 0 OK -TSS79 - - XLOC_000073 Xkr4 TSS79 chr1:3363753-3363849 - - 0 0 0 OK 0 0 0 OK -TSS80 - - XLOC_000074 Xkr4 TSS80 chr1:3364871-3364919 - - 6.28966e+07 0 2.40795e+08 OK 0 0 0 OK -TSS81 - - XLOC_000075 Xkr4 TSS81 chr1:3367135-3367162 - - 0 0 0 OK 0 0 0 OK -TSS82 - - XLOC_000076 Xkr4 TSS82 chr1:3367210-3367237 - - 0 0 0 OK 0 0 0 OK -TSS83 - - XLOC_000077 Xkr4 TSS83 chr1:3367333-3367382 - - 0 0 0 OK 0 0 0 OK -TSS84 - - XLOC_000078 Xkr4 TSS84 chr1:3369580-3369607 - - 0 0 0 OK 0 0 0 OK -TSS85 - - XLOC_000079 Xkr4 TSS85 chr1:3375001-3375028 - - 0 0 0 OK 0 0 0 OK -TSS86 - - XLOC_000080 Xkr4 TSS86 chr1:3377211-3377262 - - 0 0 0 OK 0 0 0 OK -TSS87 - - XLOC_000081 Xkr4 TSS87 chr1:3379888-3379915 - - 0 0 0 OK 0 0 0 OK -TSS88 - - XLOC_000082 Xkr4 TSS88 chr1:3386739-3386836 - - 0 0 0 OK 0 0 0 OK -TSS89 - - XLOC_000083 Xkr4 TSS89 chr1:3391325-3391352 - - 0 0 0 OK 0 0 0 OK -TSS90 - - XLOC_000084 Xkr4 TSS90 chr1:3435841-3435880 - - 0 0 0 OK 0 0 0 OK -TSS91 - - XLOC_000085 Xkr4 TSS91 chr1:3447761-3447788 - - 0 0 0 OK 0 0 0 OK -TSS92 - - XLOC_000086 Xkr4 TSS92 chr1:3450906-3450965 - - 0 0 0 OK 0 0 0 OK -TSS93 - - XLOC_000087 Xkr4 TSS93 chr1:3451051-3451109 - - 0 0 0 OK 0 0 0 OK |
| b |
| diff -r 8da0eade1f59 -r 88fcac97c2a0 test-data/cuffdiff_out8.txt --- a/test-data/cuffdiff_out8.txt Fri Dec 19 11:57:43 2014 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,1 +0,0 @@ -tracking_id class_code nearest_ref_id gene_id gene_short_name tss_id locus length coverage |
| b |
| diff -r 8da0eade1f59 -r 88fcac97c2a0 test-data/cuffdiff_out9.txt --- a/test-data/cuffdiff_out9.txt Fri Dec 19 11:57:43 2014 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,89 +0,0 @@ -test_id gene_id gene locus sample_1 sample_2 status value_1 value_2 sqrt(JS) test_stat p_value q_value significant -TSS1 XLOC_000001 Xkr4 chr1:3204754-3204833 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS10 XLOC_000008 - chr1:3190858-3191434 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS11 XLOC_000009 - chr1:3191512-3192077 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS13 XLOC_000010 - chr1:3192250-3192336 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS14 XLOC_000011 - chr1:3192441-3192494 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS15 XLOC_000012 - chr1:3192550-3192629 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS16 XLOC_000013 - chr1:3192649-3192676 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS17 XLOC_000014 - chr1:3192731-3192811 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS18 XLOC_000015 - chr1:3192940-3193042 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS19 XLOC_000016 - chr1:3194185-3194226 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS2 XLOC_000002 - chr1:3111449-3111490 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS20 XLOC_000017 - chr1:3194302-3194329 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS21 XLOC_000018 - chr1:3194706-3194733 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS22 XLOC_000019 - chr1:3195083-3195110 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS23 XLOC_000020 - chr1:3195450-3195477 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS24 XLOC_000021 - chr1:3197089-3197116 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS25 XLOC_000022 - chr1:3197246-3197273 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS26 XLOC_000023 - chr1:3197346-3197373 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS27 XLOC_000024 - chr1:3197425-3197452 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS28 XLOC_000025 - chr1:3200022-3200191 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS29 XLOC_000026 - chr1:3200325-3200352 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS3 XLOC_000003 - chr1:3111545-3111576 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS30 XLOC_000027 - chr1:3200430-3200457 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS31 XLOC_000028 - chr1:3201007-3201039 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS32 XLOC_000029 - chr1:3201077-3201481 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS33 XLOC_000030 - chr1:3201596-3201666 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS34 XLOC_000031 - chr1:3201672-3201699 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS35 XLOC_000032 - chr1:3201725-3201809 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS36 XLOC_000033 Xkr4 chr1:3211521-3211561 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS37 XLOC_000034 Xkr4 chr1:3212213-3212292 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS38 XLOC_000035 Xkr4 chr1:3212367-3212439 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS39 XLOC_000036 Xkr4 chr1:3212717-3212801 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS4 XLOC_000004 - chr1:3174765-3174792 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS40 XLOC_000037 Xkr4 chr1:3213095-3213242 q1 q2 NOTEST 0 0 0.249947 0 0.5526 1 no -TSS41 XLOC_000038 Xkr4 chr1:3240606-3240633 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS42 XLOC_000039 Xkr4 chr1:3242479-3242512 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS43 XLOC_000040 Xkr4 chr1:3242633-3242923 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS44 XLOC_000041 Xkr4 chr1:3242924-3243005 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS45 XLOC_000042 Xkr4 chr1:3243018-3243079 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS46 XLOC_000043 Xkr4 chr1:3243108-3243154 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS47 XLOC_000044 Xkr4 chr1:3243347-3243401 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS48 XLOC_000045 Xkr4 chr1:3254079-3254106 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS49 XLOC_000046 Xkr4 chr1:3256974-3257011 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS5 XLOC_000005 - chr1:3187401-3187428 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS50 XLOC_000047 Xkr4 chr1:3277155-3277182 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS51 XLOC_000048 Xkr4 chr1:3277190-3277218 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS52 XLOC_000049 Xkr4 chr1:3277913-3278390 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS54 XLOC_000050 Xkr4 chr1:3280117-3280144 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS55 XLOC_000051 Xkr4 chr1:3280498-3280525 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS56 XLOC_000052 Xkr4 chr1:3280686-3280741 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS57 XLOC_000053 Xkr4 chr1:3282504-3282531 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS58 XLOC_000054 Xkr4 chr1:3282650-3282677 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS59 XLOC_000055 Xkr4 chr1:3282760-3282832 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS6 XLOC_000006 - chr1:3188521-3188548 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS60 XLOC_000056 Xkr4 chr1:3284966-3284993 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS61 XLOC_000057 Xkr4 chr1:3290488-3290553 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS62 XLOC_000058 Xkr4 chr1:3290798-3290859 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS63 XLOC_000059 Xkr4 chr1:3290919-3291273 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS65 XLOC_000060 Xkr4 chr1:3299443-3299664 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS66 XLOC_000060 Xkr4 chr1:3299443-3299664 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS67 XLOC_000061 Xkr4 chr1:3299691-3299733 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS68 XLOC_000062 Xkr4 chr1:3300051-3300078 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS69 XLOC_000063 Xkr4 chr1:3307748-3307775 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS7 XLOC_000007 - chr1:3189810-3190789 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS70 XLOC_000064 Xkr4 chr1:3318620-3318647 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS71 XLOC_000065 Xkr4 chr1:3318999-3319051 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS72 XLOC_000066 Xkr4 chr1:3330527-3330554 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS73 XLOC_000067 Xkr4 chr1:3351240-3351311 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS74 XLOC_000068 Xkr4 chr1:3355887-3356119 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS75 XLOC_000069 Xkr4 chr1:3356180-3356225 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS76 XLOC_000070 Xkr4 chr1:3363076-3363176 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS77 XLOC_000071 Xkr4 chr1:3363214-3363278 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS78 XLOC_000072 Xkr4 chr1:3363387-3363446 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS79 XLOC_000073 Xkr4 chr1:3363753-3363849 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS80 XLOC_000074 Xkr4 chr1:3364871-3364919 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS81 XLOC_000075 Xkr4 chr1:3367135-3367162 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS82 XLOC_000076 Xkr4 chr1:3367210-3367237 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS83 XLOC_000077 Xkr4 chr1:3367333-3367382 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS84 XLOC_000078 Xkr4 chr1:3369580-3369607 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS85 XLOC_000079 Xkr4 chr1:3375001-3375028 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS86 XLOC_000080 Xkr4 chr1:3377211-3377262 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS87 XLOC_000081 Xkr4 chr1:3379888-3379915 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS88 XLOC_000082 Xkr4 chr1:3386739-3386836 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS89 XLOC_000083 Xkr4 chr1:3391325-3391352 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS90 XLOC_000084 Xkr4 chr1:3435841-3435880 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS91 XLOC_000085 Xkr4 chr1:3447761-3447788 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS92 XLOC_000086 Xkr4 chr1:3450906-3450965 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS93 XLOC_000087 Xkr4 chr1:3451051-3451109 q1 q2 NOTEST 0 0 0 0 1 1 no |
| b |
| diff -r 8da0eade1f59 -r 88fcac97c2a0 tool_dependencies.xml --- a/tool_dependencies.xml Fri Dec 19 11:57:43 2014 -0500 +++ b/tool_dependencies.xml Tue Dec 23 15:55:31 2014 -0500 |
| b |
| @@ -1,6 +1,12 @@ <?xml version="1.0"?> <tool_dependency> + <set_environment version="1.0"> + <environment_variable action="set_to" name="CUFFDIFF_SCRIPT_PATH">$REPOSITORY_INSTALL_DIR</environment_variable> + </set_environment> <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> + <package name="cummeRbund" version="2.8.2"> + <repository changeset_revision="5aacc6d160ed" name="package_cummerbund_2_8_2" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> </tool_dependency> |