| Previous changeset 1:8cfc17e27132 (2015-11-11) Next changeset 3:95a7ddf617e7 (2018-09-27) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40 |
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modified:
macros.xml samtools_stats.xml test-data/samtools_stats_out1.tab test-data/samtools_stats_out2.tab |
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added:
test-data/samtools_stats_out2__gcc.tab test-data/samtools_stats_out2__mpc.tab test-data/samtools_stats_out2__sn.tab |
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removed:
test-data/samtools_stats_out2/gcc.tab test-data/samtools_stats_out2/mpc.tab test-data/samtools_stats_out2/sn.tab tool_dependencies.xml |
| b |
| diff -r 8cfc17e27132 -r 24c5d43cb545 macros.xml --- a/macros.xml Wed Nov 11 12:55:15 2015 -0500 +++ b/macros.xml Tue May 09 11:19:01 2017 -0400 |
| [ |
| @@ -1,16 +1,17 @@ <macros> <xml name="requirements"> <requirements> - <requirement type="package" version="1.2">samtools</requirement> + <requirement type="package" version="1.3.1">samtools</requirement> <yield/> </requirements> </xml> + <token name="@TOOL_VERSION@">1.3.1</token> <xml name="citations"> <citations> <citation type="bibtex"> @misc{SAM_def, title={Definition of SAM/BAM format}, - url = {https://samtools.github.io/hts-specs/SAMv1.pdf},} + url = {https://samtools.github.io/hts-specs/},} </citation> <citation type="doi">10.1093/bioinformatics/btp352</citation> <citation type="doi">10.1093/bioinformatics/btr076</citation> @@ -41,7 +42,7 @@ </citations> </xml> <xml name="version_command"> - <version_command>samtools --version | head -n 1 | awk '{ print $2 }'</version_command> + <version_command><![CDATA[samtools 2>&1 | grep Version]]></version_command> </xml> <xml name="stdio"> <stdio> @@ -64,7 +65,5 @@ 5. Click **Save** The medatada will be re-detected and you will be able to see the list of reference sequences in the "**Select references (chromosomes and contigs) you would like to restrict bam to**" drop-down. - </token> - </macros> |
| b |
| diff -r 8cfc17e27132 -r 24c5d43cb545 samtools_stats.xml --- a/samtools_stats.xml Wed Nov 11 12:55:15 2015 -0500 +++ b/samtools_stats.xml Tue May 09 11:19:01 2017 -0400 |
| [ |
| b'@@ -1,144 +1,171 @@\n-<tool id="samtools_stats" name="Stats" version="2.0">\n+<tool id="samtools_stats" name="Stats" version="2.0.1">\n <description>generate statistics for BAM dataset</description>\n <macros>\n- <import>macros.xml</import>\n- </macros>\n- <expand macro="requirements"></expand>\n- <expand macro="stdio"></expand>\n- <expand macro="version_command"></expand>\n+ <import>macros.xml</import>\n+ </macros>\n+ <expand macro="requirements"/>\n+ <expand macro="stdio"/>\n+ <expand macro="version_command"/>\n <command><![CDATA[\n #if $use_reference.use_ref_selector == "yes":\n #if $use_reference.reference_source.reference_source_selector == "history":\n- ln -s "${use_reference.reference_source.ref_file}" && samtools faidx `basename "${use_reference.reference_source.ref_file}"` && samtools stats\n- #else:\n- samtools stats\n- #end if\n- #else:\n- samtools stats\n- #end if\n- "${input_file}"\n- --coverage ${coverage_min},${coverage_max},${coverage_step}\n- ${remove_dups}\n- #if str( $filter_by_flags.filter_flags ) == "filter":\n- #if $filter_by_flags.require_flags:\n- --required-flag ${sum([int(flag) for flag in str($filter_by_flags.require_flags).split(\',\')])}\n- #end if\n- #if $filter_by_flags.exclude_flags:\n- --filtering-flag ${sum([int(flag) for flag in str($filter_by_flags.exclude_flags).split(\',\')])}\n+ ln -s \'${use_reference.reference_source.ref_file}\' &&\n+ samtools faidx `basename \'${use_reference.reference_source.ref_file}\'` &&\n #end if\n #end if\n- --GC-depth ${gc_depth}\n- --insert-size ${insert_size}\n+\n+ samtools stats\n+ \'${input_file}\'\n+ --coverage ${coverage_min},${coverage_max},${coverage_step}\n+ ${remove_dups}\n \n- ## The code below is commented out because using -I/--id options causes the following exception\n- ## Samtools-htslib: init_group_id() header parsing not yet implemented\n+ #if str( $filter_by_flags.filter_flags ) == "filter":\n+ #if $filter_by_flags.require_flags:\n+ --required-flag ${sum([int(flag) for flag in str($filter_by_flags.require_flags).split(\',\')])}\n+ #end if\n+ #if $filter_by_flags.exclude_flags:\n+ --filtering-flag ${sum([int(flag) for flag in str($filter_by_flags.exclude_flags).split(\',\')])}\n+ #end if\n+ #end if\n \n- ##if str($read_group) != "":\n- ## -I "${read_group}"\n- ##end if\n+ --GC-depth ${gc_depth}\n+ --insert-size ${insert_size}\n \n- #if str($read_length) != "0":\n- --read-length "${read_length}"\n- #end if\n- --most-inserts ${most_inserts}\n- --trim-quality ${trim_quality}\n- #if $use_reference.use_ref_selector == "yes":\n- #if $use_reference.reference_source.reference_source_selector != "history":\n- --ref-seq "${use_reference.reference_source.ref_file.fields.path}"\n- #else:\n- --ref-seq "${use_reference.reference_source.ref_file}"\n+ ## The code below is commented out because using -I/--id options causes the following exception\n+ ## Samtools-htslib: init_group_id() header parsing not yet implemented\n+ ##if str($read_group) != "":\n+ ## -I "${read_group}"\n+ ##end if\n+\n+ #if str($read_length):\n+ --read-length ${read_length}\n #end if\n- #end if\n- > "${output}"\n+\n+ --most-inserts ${most_inserts}\n+ --trim-quality ${trim_quality}\n+\n+ #if $use_reference.use_ref_selector == "yes":\n+ #if $use_reference.reference_source.reference_source_selector != "history":\n+ --re'..b'+ <param name="use_ref_selector" argument="--ref-seq" type="select" label="Use reference sequence" help="Required for GC-depth and mismatches-per-cycle calculation">\n <option value="yes">Use reference</option>\n <option selected="True" value="no">Do not use reference</option>\n </param>\n@@ -228,8 +254,9 @@\n </param>\n <when value="cached">\n <param name="ref_file" type="select" label="Using genome">\n- <options from_data_table="fasta_indexes" />\n- <filter type="data_meta" ref="input_file" key="dbkey" column="1" />\n+ <options from_data_table="fasta_indexes">\n+ <filter type="data_meta" ref="input_file" key="dbkey" column="1" />\n+ </options>\n </param>\n </when>\n <when value="history">\n@@ -243,7 +270,7 @@\n </inputs>\n \n <outputs>\n- <data format="tabular" name="output" label="${tool.name} on ${on_string}">\n+ <data name="output" format="tabular" label="${tool.name} on ${on_string}">\n <discover_datasets pattern="(?P<designation>.+)\\.tab" ext="tabular" visible="true" directory="split" />\n </data>\n </outputs>\n@@ -263,34 +290,17 @@\n <param name="split_output_selector" value="yes" />\n <param name="generate_tables" value="sn,mpc,gcc" />\n <output name="output" file="samtools_stats_out2.tab" lines_diff="4">\n- <discovered_dataset designation="Summary numbers" ftype="tabular" file="samtools_stats_out2/sn.tab" />\n- <discovered_dataset designation="ACGT content per cycle" ftype="tabular" file="samtools_stats_out2/gcc.tab" />\n- <discovered_dataset designation="Mismatches per cycle" ftype="tabular" file="samtools_stats_out2/mpc.tab" />\n+ <discovered_dataset designation="Summary numbers" ftype="tabular" file="samtools_stats_out2__sn.tab" />\n+ <discovered_dataset designation="ACGT content per cycle" ftype="tabular" file="samtools_stats_out2__gcc.tab" />\n+ <discovered_dataset designation="Mismatches per cycle" ftype="tabular" file="samtools_stats_out2__mpc.tab" />\n </output>\n </test>\n </tests>\n <help><![CDATA[\n **What it does**\n \n-This tool runs the ``samtools stats`` command. It has the following options::\n-\n- -c, --coverage <int>,<int>,<int> Coverage distribution min,max,step [1,1000,1]\n- -d, --remove-dups Exclude from statistics reads marked as duplicates\n- -f, --required-flag <str|int> Required flag, 0 for unset. See also `samtools flags` [0]\n- -F, --filtering-flag <str|int> Filtering flag, 0 for unset. See also `samtools flags` [0]\n- --GC-depth <float> the size of GC-depth bins (decreasing bin size increases memory requirement) [2e4]\n- -h, --help This help message\n- -i, --insert-size <int> Maximum insert size [8000]\n- -I, --id <string> Include only listed read group or sample name\n- -l, --read-length <int> Include in the statistics only reads with the given read length []\n- -m, --most-inserts <float> Report only the main part of inserts [0.99]\n- -q, --trim-quality <int> The BWA trimming parameter [0]\n- -r, --ref-seq <file> Reference sequence (required for GC-depth and mismatches-per-cycle calculation). Galaxy\n- will provide options for selecting a reference cached as this Galaxy instance or choosing\n- one from history.\n- \n-\n+This tool runs the ``samtools stats`` command.\n ]]></help>\n- <expand macro="citations"></expand>\n+ <expand macro="citations"/>\n </tool>\n \n' |
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| diff -r 8cfc17e27132 -r 24c5d43cb545 test-data/samtools_stats_out1.tab --- a/test-data/samtools_stats_out1.tab Wed Nov 11 12:55:15 2015 -0500 +++ b/test-data/samtools_stats_out1.tab Tue May 09 11:19:01 2017 -0400 |
| [ |
| b'@@ -1,5 +1,6 @@\n-# This file was produced by samtools stats (1.2+htslib-1.2.1) and can be plotted using plot-bamstats\n-# The command line was: stats --coverage 1,1000,1 --GC-depth 20000.0 --insert-size 8000 --most-inserts 0.99 --trim-quality 0 --ref-seq /Users/anton/galaxy-git/database/files/000/dataset_9.dat /Users/anton/galaxy-git/database/files/000/dataset_10.dat\n+# This file was produced by samtools stats (1.3.1+htslib-1.3.1) and can be plotted using plot-bamstats\n+# This file contains statistics for all reads.\n+# The command line was: stats --coverage 1,1000,1 --GC-depth 20000.0 --insert-size 8000 --most-inserts 0.99 --trim-quality 0 --ref-seq /tmp/tmpO1aTrb/files/000/dataset_2.dat /tmp/tmpO1aTrb/files/000/dataset_1.dat\n # CHK, Checksum\t[2]Read Names\t[3]Sequences\t[4]Qualities\n # CHK, CRC32 of reads which passed filtering followed by addition (32bit overflow)\n CHK\t1bd20fd8\t58ad2167\t29883386\n@@ -836,258 +837,258 @@\n GCL\t52.01\t1\n GCL\t52.51\t0\n GCL\t53.02\t1\n-# ACGT content per cycle. Use `grep ^GCC | cut -f 2-` to extract this part. The columns are: cycle, and A,C,G,T counts [%]\n-GCC\t1\t21.50\t29.50\t33.50\t15.50\n-GCC\t2\t30.00\t16.00\t11.00\t43.00\n-GCC\t3\t33.00\t25.00\t9.00\t33.00\n-GCC\t4\t17.00\t29.00\t13.00\t41.00\n-GCC\t5\t37.00\t22.00\t12.00\t29.00\n-GCC\t6\t36.00\t26.00\t17.00\t21.00\n-GCC\t7\t29.50\t13.50\t31.50\t25.50\n-GCC\t8\t50.50\t14.50\t19.50\t15.50\n-GCC\t9\t17.00\t33.00\t18.00\t32.00\n-GCC\t10\t37.00\t14.00\t21.00\t28.00\n-GCC\t11\t20.50\t14.50\t29.50\t35.50\n-GCC\t12\t30.00\t24.00\t22.00\t24.00\n-GCC\t13\t27.00\t15.00\t21.00\t37.00\n-GCC\t14\t24.00\t22.00\t26.00\t28.00\n-GCC\t15\t25.50\t20.50\t24.50\t29.50\n-GCC\t16\t31.00\t15.00\t20.00\t34.00\n-GCC\t17\t28.00\t25.00\t14.00\t33.00\n-GCC\t18\t30.50\t28.50\t19.50\t21.50\n-GCC\t19\t29.00\t26.00\t21.00\t24.00\n-GCC\t20\t22.50\t23.50\t17.50\t36.50\n-GCC\t21\t35.50\t17.50\t19.50\t27.50\n-GCC\t22\t37.50\t28.50\t15.50\t18.50\n-GCC\t23\t31.00\t19.00\t13.00\t37.00\n-GCC\t24\t37.00\t12.00\t22.00\t29.00\n-GCC\t25\t35.50\t22.50\t17.50\t24.50\n-GCC\t26\t33.50\t18.50\t15.50\t32.50\n-GCC\t27\t34.50\t14.50\t25.50\t25.50\n-GCC\t28\t31.00\t14.00\t24.00\t31.00\n-GCC\t29\t30.00\t27.00\t24.00\t19.00\n-GCC\t30\t31.00\t20.00\t14.00\t35.00\n-GCC\t31\t33.50\t29.50\t13.50\t23.50\n-GCC\t32\t42.50\t20.50\t19.50\t17.50\n-GCC\t33\t25.50\t23.50\t14.50\t36.50\n-GCC\t34\t39.50\t16.50\t20.50\t23.50\n-GCC\t35\t32.50\t23.50\t21.50\t22.50\n-GCC\t36\t42.00\t25.00\t16.00\t17.00\n-GCC\t37\t38.00\t17.00\t19.00\t26.00\n-GCC\t38\t24.00\t26.00\t25.00\t25.00\n-GCC\t39\t22.50\t41.50\t18.50\t17.50\n-GCC\t40\t32.00\t16.00\t21.00\t31.00\n-GCC\t41\t33.00\t28.00\t19.00\t20.00\n-GCC\t42\t30.50\t25.50\t19.50\t24.50\n-GCC\t43\t35.00\t29.00\t15.00\t21.00\n-GCC\t44\t20.00\t27.00\t22.00\t31.00\n-GCC\t45\t40.50\t21.50\t21.50\t16.50\n-GCC\t46\t26.50\t20.50\t22.50\t30.50\n-GCC\t47\t38.50\t29.50\t16.50\t15.50\n-GCC\t48\t27.50\t24.50\t17.50\t30.50\n-GCC\t49\t28.50\t32.50\t10.50\t28.50\n-GCC\t50\t46.50\t20.50\t9.50\t23.50\n-GCC\t51\t34.50\t28.50\t13.50\t23.50\n-GCC\t52\t41.50\t23.50\t20.50\t14.50\n-GCC\t53\t20.00\t28.00\t26.00\t26.00\n-GCC\t54\t31.50\t18.50\t24.50\t25.50\n-GCC\t55\t30.50\t22.50\t16.50\t30.50\n-GCC\t56\t33.50\t22.50\t13.50\t30.50\n-GCC\t57\t23.00\t24.00\t23.00\t30.00\n-GCC\t58\t25.00\t37.00\t19.00\t19.00\n-GCC\t59\t34.00\t23.00\t24.00\t19.00\n-GCC\t60\t29.00\t28.00\t17.00\t26.00\n-GCC\t61\t25.50\t23.50\t24.50\t26.50\n-GCC\t62\t31.50\t22.50\t16.50\t29.50\n-GCC\t63\t27.50\t28.50\t25.50\t18.50\n-GCC\t64\t33.50\t21.50\t25.50\t19.50\n-GCC\t65\t35.50\t19.50\t18.50\t26.50\n-GCC\t66\t34.00\t25.00\t15.00\t26.00\n-GCC\t67\t37.00\t23.00\t19.00\t21.00\n-GCC\t68\t36.50\t29.50\t13.50\t20.50\n-GCC\t69\t38.50\t19.50\t20.50\t21.50\n-GCC\t70\t38.50\t16.50\t18.50\t26.50\n-GCC\t71\t25.50\t38.50\t21.50\t14.50\n-GCC\t72\t29.00\t29.00\t25.00\t17.00\n-GCC\t73\t32.50\t20.50\t21.50\t25.50\n-GCC\t74\t28.50\t32.50\t12.50\t26.50\n-GCC\t75\t41.50\t12.50\t18.50\t27.50\n-GCC\t76\t24.50\t29.50\t23.50\t22.50\n-GCC\t77\t36.00\t21.00\t18.00\t25.00\n-GCC\t78\t27.00\t34.00\t22.00\t17.00\n-GCC\t79\t21.50\t26.50\t25.50\t26.50\n-GCC\t80\t34.00\t19.00\t28.00\t19.00\n-GCC\t81\t17.00\t26.00\t26.00\t31.00\n-GCC\t82\t31.00\t30.00\t23.00\t16.00\n-GCC\t83\t31.50\t26.50\t12.50\t29.50\n-GCC\t84\t19.00\t41.00\t21.00\t19.00\n-GCC\t85\t37.50\t24.50\t16.50\t21.50\n-GCC\t86\t15.00\t48.00\t15.00\t22.00\n-GCC\t87\t41.00\t16.00\t18.00\t25.00\n-GCC\t88\t23.50\t27.50\t27.50\t21.50\n-GCC\t89\t26.50\t27.50\t26.50\t19.50\n-GCC\t90\t18.50\t23.50\t24.50\t33.50\n-GCC\t91\t27.00\t32.00\t22.00\t19.00\n-'..b'.50\t32.50\t0.00\t0.00\n+GCC\t166\t17.50\t37.50\t28.50\t16.50\t0.00\t0.00\n+GCC\t167\t16.50\t21.50\t31.50\t30.50\t0.00\t0.00\n+GCC\t168\t14.00\t25.00\t30.00\t31.00\t0.00\t0.00\n+GCC\t169\t18.50\t20.50\t23.50\t37.50\t0.00\t0.00\n+GCC\t170\t19.00\t23.00\t28.00\t30.00\t0.00\t0.00\n+GCC\t171\t20.00\t28.00\t33.00\t19.00\t0.00\t0.00\n+GCC\t172\t19.00\t20.00\t32.00\t29.00\t0.00\t0.00\n+GCC\t173\t24.50\t16.50\t33.50\t25.50\t0.00\t0.00\n+GCC\t174\t17.50\t23.50\t33.50\t25.50\t0.00\t0.00\n+GCC\t175\t33.50\t17.50\t35.50\t13.50\t0.00\t0.00\n+GCC\t176\t16.50\t32.50\t28.50\t22.50\t0.00\t0.00\n+GCC\t177\t19.00\t22.00\t27.00\t32.00\t0.00\t0.00\n+GCC\t178\t16.00\t26.00\t30.00\t28.00\t0.00\t0.00\n+GCC\t179\t18.00\t18.00\t22.00\t42.00\t0.00\t0.00\n+GCC\t180\t21.00\t22.00\t34.00\t23.00\t0.00\t0.00\n+GCC\t181\t20.50\t19.50\t35.50\t24.50\t0.00\t0.00\n+GCC\t182\t32.50\t18.50\t22.50\t26.50\t0.00\t0.00\n+GCC\t183\t24.50\t13.50\t28.50\t33.50\t0.00\t0.00\n+GCC\t184\t15.00\t29.00\t30.00\t26.00\t0.00\t0.00\n+GCC\t185\t15.00\t32.00\t33.00\t20.00\t0.00\t0.00\n+GCC\t186\t22.50\t23.50\t34.50\t19.50\t0.00\t0.00\n+GCC\t187\t19.00\t14.00\t40.00\t27.00\t0.00\t0.00\n+GCC\t188\t27.50\t21.50\t27.50\t23.50\t0.00\t0.00\n+GCC\t189\t17.00\t22.00\t34.00\t27.00\t0.00\t0.00\n+GCC\t190\t23.00\t30.00\t23.00\t24.00\t0.00\t0.00\n+GCC\t191\t25.00\t22.00\t28.00\t25.00\t0.00\t0.00\n+GCC\t192\t34.50\t24.50\t13.50\t27.50\t0.00\t0.00\n+GCC\t193\t18.50\t25.50\t25.50\t30.50\t0.00\t0.00\n+GCC\t194\t18.50\t33.50\t24.50\t23.50\t0.00\t0.00\n+GCC\t195\t16.00\t26.00\t23.00\t35.00\t0.00\t0.00\n+GCC\t196\t21.50\t25.50\t24.50\t28.50\t0.00\t0.00\n+GCC\t197\t20.00\t21.00\t23.00\t36.00\t0.00\t0.00\n+GCC\t198\t17.00\t21.00\t37.00\t25.00\t0.00\t0.00\n+GCC\t199\t20.50\t18.50\t25.50\t35.50\t0.00\t0.00\n+GCC\t200\t21.00\t29.00\t21.00\t29.00\t0.00\t0.00\n+GCC\t201\t27.00\t21.00\t23.00\t29.00\t0.00\t0.00\n+GCC\t202\t21.50\t24.50\t19.50\t34.50\t0.00\t0.00\n+GCC\t203\t21.50\t24.50\t26.50\t27.50\t0.00\t0.00\n+GCC\t204\t27.00\t29.00\t24.00\t20.00\t0.00\t0.00\n+GCC\t205\t19.50\t21.50\t22.50\t36.50\t0.00\t0.00\n+GCC\t206\t26.50\t24.50\t21.50\t27.50\t0.00\t0.00\n+GCC\t207\t22.50\t21.50\t19.50\t36.50\t0.00\t0.00\n+GCC\t208\t14.00\t35.00\t29.00\t22.00\t0.00\t0.00\n+GCC\t209\t16.00\t23.00\t12.00\t49.00\t0.00\t0.00\n+GCC\t210\t18.50\t19.50\t40.50\t21.50\t0.00\t0.00\n+GCC\t211\t26.00\t20.00\t22.00\t32.00\t0.00\t0.00\n+GCC\t212\t21.00\t31.00\t18.00\t30.00\t0.00\t0.00\n+GCC\t213\t24.00\t15.00\t31.00\t30.00\t0.00\t0.00\n+GCC\t214\t17.50\t24.50\t25.50\t32.50\t0.00\t0.00\n+GCC\t215\t26.00\t24.00\t23.00\t27.00\t0.00\t0.00\n+GCC\t216\t21.50\t17.50\t25.50\t35.50\t0.00\t0.00\n+GCC\t217\t26.00\t29.00\t17.00\t28.00\t0.00\t0.00\n+GCC\t218\t20.00\t27.00\t21.00\t32.00\t0.00\t0.00\n+GCC\t219\t17.00\t21.00\t21.00\t41.00\t0.00\t0.00\n+GCC\t220\t25.50\t23.50\t23.50\t27.50\t0.00\t0.00\n+GCC\t221\t21.50\t23.50\t20.50\t34.50\t0.00\t0.00\n+GCC\t222\t21.50\t21.50\t18.50\t38.50\t0.00\t0.00\n+GCC\t223\t20.00\t27.00\t28.00\t25.00\t0.00\t0.00\n+GCC\t224\t22.50\t22.50\t24.50\t30.50\t0.00\t0.00\n+GCC\t225\t14.50\t35.50\t30.50\t19.50\t0.00\t0.00\n+GCC\t226\t20.00\t23.00\t26.00\t31.00\t0.00\t0.00\n+GCC\t227\t20.50\t24.50\t23.50\t31.50\t0.00\t0.00\n+GCC\t228\t33.00\t19.00\t26.00\t22.00\t0.00\t0.00\n+GCC\t229\t22.50\t24.50\t18.50\t34.50\t0.00\t0.00\n+GCC\t230\t21.00\t32.00\t16.00\t31.00\t0.00\t0.00\n+GCC\t231\t23.00\t28.00\t30.00\t19.00\t0.00\t0.00\n+GCC\t232\t23.50\t21.50\t12.50\t42.50\t0.00\t0.00\n+GCC\t233\t21.00\t27.00\t25.00\t27.00\t0.00\t0.00\n+GCC\t234\t16.50\t27.50\t22.50\t33.50\t0.00\t0.00\n+GCC\t235\t20.00\t15.00\t28.00\t37.00\t0.00\t0.00\n+GCC\t236\t28.00\t23.00\t21.00\t28.00\t0.00\t0.00\n+GCC\t237\t20.50\t19.50\t22.50\t37.50\t0.00\t0.00\n+GCC\t238\t21.50\t29.50\t24.50\t24.50\t0.00\t0.00\n+GCC\t239\t20.00\t8.00\t17.00\t55.00\t0.00\t0.00\n+GCC\t240\t28.00\t24.00\t16.00\t32.00\t0.00\t0.00\n+GCC\t241\t22.50\t22.50\t16.50\t38.50\t0.00\t0.00\n+GCC\t242\t29.00\t25.00\t13.00\t33.00\t0.00\t0.00\n+GCC\t243\t22.50\t15.50\t23.50\t38.50\t0.00\t0.00\n+GCC\t244\t20.50\t23.50\t16.50\t39.50\t0.00\t0.00\n+GCC\t245\t28.00\t23.00\t19.00\t30.00\t0.00\t0.00\n+GCC\t246\t21.00\t29.00\t25.00\t25.00\t0.00\t0.00\n+GCC\t247\t32.00\t14.00\t13.00\t41.00\t0.00\t0.00\n+GCC\t248\t18.00\t18.00\t25.00\t39.00\t0.00\t0.00\n+GCC\t249\t25.00\t23.00\t21.00\t31.00\t0.00\t0.00\n+GCC\t250\t27.50\t22.50\t17.50\t32.50\t0.00\t0.00\n+GCC\t251\t13.50\t20.50\t36.50\t29.50\t0.00\t0.00\n # Insert sizes. Use `grep ^IS | cut -f 2-` to extract this part. The columns are: insert size, pairs total, inward oriented pairs, outward oriented pairs, other pairs\n # Read lengths. Use `grep ^RL | cut -f 2-` to extract this part. The columns are: read length, count\n RL\t251\t200\n' |
| b |
| diff -r 8cfc17e27132 -r 24c5d43cb545 test-data/samtools_stats_out2.tab --- a/test-data/samtools_stats_out2.tab Wed Nov 11 12:55:15 2015 -0500 +++ b/test-data/samtools_stats_out2.tab Tue May 09 11:19:01 2017 -0400 |
| [ |
| b'@@ -1,5 +1,6 @@\n-# This file was produced by samtools stats (1.2+htslib-1.2.1) and can be plotted using plot-bamstats\n-# The command line was: stats --coverage 1,1000,1 --GC-depth 20000.0 --insert-size 8000 --most-inserts 0.99 --trim-quality 0 --ref-seq /Users/anton/galaxy-git/database/files/000/dataset_9.dat /Users/anton/galaxy-git/database/files/000/dataset_10.dat\n+# This file was produced by samtools stats (1.3.1+htslib-1.3.1) and can be plotted using plot-bamstats\n+# This file contains statistics for all reads.\n+# The command line was: stats --coverage 1,1000,1 --GC-depth 20000.0 --insert-size 8000 --most-inserts 0.99 --trim-quality 0 --ref-seq /tmp/tmpO1aTrb/files/000/dataset_5.dat /tmp/tmpO1aTrb/files/000/dataset_4.dat\n # CHK, Checksum\t[2]Read Names\t[3]Sequences\t[4]Qualities\n # CHK, CRC32 of reads which passed filtering followed by addition (32bit overflow)\n CHK\t1bd20fd8\t58ad2167\t29883386\n@@ -836,258 +837,258 @@\n GCL\t52.01\t1\n GCL\t52.51\t0\n GCL\t53.02\t1\n-# ACGT content per cycle. Use `grep ^GCC | cut -f 2-` to extract this part. The columns are: cycle, and A,C,G,T counts [%]\n-GCC\t1\t21.50\t29.50\t33.50\t15.50\n-GCC\t2\t30.00\t16.00\t11.00\t43.00\n-GCC\t3\t33.00\t25.00\t9.00\t33.00\n-GCC\t4\t17.00\t29.00\t13.00\t41.00\n-GCC\t5\t37.00\t22.00\t12.00\t29.00\n-GCC\t6\t36.00\t26.00\t17.00\t21.00\n-GCC\t7\t29.50\t13.50\t31.50\t25.50\n-GCC\t8\t50.50\t14.50\t19.50\t15.50\n-GCC\t9\t17.00\t33.00\t18.00\t32.00\n-GCC\t10\t37.00\t14.00\t21.00\t28.00\n-GCC\t11\t20.50\t14.50\t29.50\t35.50\n-GCC\t12\t30.00\t24.00\t22.00\t24.00\n-GCC\t13\t27.00\t15.00\t21.00\t37.00\n-GCC\t14\t24.00\t22.00\t26.00\t28.00\n-GCC\t15\t25.50\t20.50\t24.50\t29.50\n-GCC\t16\t31.00\t15.00\t20.00\t34.00\n-GCC\t17\t28.00\t25.00\t14.00\t33.00\n-GCC\t18\t30.50\t28.50\t19.50\t21.50\n-GCC\t19\t29.00\t26.00\t21.00\t24.00\n-GCC\t20\t22.50\t23.50\t17.50\t36.50\n-GCC\t21\t35.50\t17.50\t19.50\t27.50\n-GCC\t22\t37.50\t28.50\t15.50\t18.50\n-GCC\t23\t31.00\t19.00\t13.00\t37.00\n-GCC\t24\t37.00\t12.00\t22.00\t29.00\n-GCC\t25\t35.50\t22.50\t17.50\t24.50\n-GCC\t26\t33.50\t18.50\t15.50\t32.50\n-GCC\t27\t34.50\t14.50\t25.50\t25.50\n-GCC\t28\t31.00\t14.00\t24.00\t31.00\n-GCC\t29\t30.00\t27.00\t24.00\t19.00\n-GCC\t30\t31.00\t20.00\t14.00\t35.00\n-GCC\t31\t33.50\t29.50\t13.50\t23.50\n-GCC\t32\t42.50\t20.50\t19.50\t17.50\n-GCC\t33\t25.50\t23.50\t14.50\t36.50\n-GCC\t34\t39.50\t16.50\t20.50\t23.50\n-GCC\t35\t32.50\t23.50\t21.50\t22.50\n-GCC\t36\t42.00\t25.00\t16.00\t17.00\n-GCC\t37\t38.00\t17.00\t19.00\t26.00\n-GCC\t38\t24.00\t26.00\t25.00\t25.00\n-GCC\t39\t22.50\t41.50\t18.50\t17.50\n-GCC\t40\t32.00\t16.00\t21.00\t31.00\n-GCC\t41\t33.00\t28.00\t19.00\t20.00\n-GCC\t42\t30.50\t25.50\t19.50\t24.50\n-GCC\t43\t35.00\t29.00\t15.00\t21.00\n-GCC\t44\t20.00\t27.00\t22.00\t31.00\n-GCC\t45\t40.50\t21.50\t21.50\t16.50\n-GCC\t46\t26.50\t20.50\t22.50\t30.50\n-GCC\t47\t38.50\t29.50\t16.50\t15.50\n-GCC\t48\t27.50\t24.50\t17.50\t30.50\n-GCC\t49\t28.50\t32.50\t10.50\t28.50\n-GCC\t50\t46.50\t20.50\t9.50\t23.50\n-GCC\t51\t34.50\t28.50\t13.50\t23.50\n-GCC\t52\t41.50\t23.50\t20.50\t14.50\n-GCC\t53\t20.00\t28.00\t26.00\t26.00\n-GCC\t54\t31.50\t18.50\t24.50\t25.50\n-GCC\t55\t30.50\t22.50\t16.50\t30.50\n-GCC\t56\t33.50\t22.50\t13.50\t30.50\n-GCC\t57\t23.00\t24.00\t23.00\t30.00\n-GCC\t58\t25.00\t37.00\t19.00\t19.00\n-GCC\t59\t34.00\t23.00\t24.00\t19.00\n-GCC\t60\t29.00\t28.00\t17.00\t26.00\n-GCC\t61\t25.50\t23.50\t24.50\t26.50\n-GCC\t62\t31.50\t22.50\t16.50\t29.50\n-GCC\t63\t27.50\t28.50\t25.50\t18.50\n-GCC\t64\t33.50\t21.50\t25.50\t19.50\n-GCC\t65\t35.50\t19.50\t18.50\t26.50\n-GCC\t66\t34.00\t25.00\t15.00\t26.00\n-GCC\t67\t37.00\t23.00\t19.00\t21.00\n-GCC\t68\t36.50\t29.50\t13.50\t20.50\n-GCC\t69\t38.50\t19.50\t20.50\t21.50\n-GCC\t70\t38.50\t16.50\t18.50\t26.50\n-GCC\t71\t25.50\t38.50\t21.50\t14.50\n-GCC\t72\t29.00\t29.00\t25.00\t17.00\n-GCC\t73\t32.50\t20.50\t21.50\t25.50\n-GCC\t74\t28.50\t32.50\t12.50\t26.50\n-GCC\t75\t41.50\t12.50\t18.50\t27.50\n-GCC\t76\t24.50\t29.50\t23.50\t22.50\n-GCC\t77\t36.00\t21.00\t18.00\t25.00\n-GCC\t78\t27.00\t34.00\t22.00\t17.00\n-GCC\t79\t21.50\t26.50\t25.50\t26.50\n-GCC\t80\t34.00\t19.00\t28.00\t19.00\n-GCC\t81\t17.00\t26.00\t26.00\t31.00\n-GCC\t82\t31.00\t30.00\t23.00\t16.00\n-GCC\t83\t31.50\t26.50\t12.50\t29.50\n-GCC\t84\t19.00\t41.00\t21.00\t19.00\n-GCC\t85\t37.50\t24.50\t16.50\t21.50\n-GCC\t86\t15.00\t48.00\t15.00\t22.00\n-GCC\t87\t41.00\t16.00\t18.00\t25.00\n-GCC\t88\t23.50\t27.50\t27.50\t21.50\n-GCC\t89\t26.50\t27.50\t26.50\t19.50\n-GCC\t90\t18.50\t23.50\t24.50\t33.50\n-GCC\t91\t27.00\t32.00\t22.00\t19.00\n-'..b'.50\t32.50\t0.00\t0.00\n+GCC\t166\t17.50\t37.50\t28.50\t16.50\t0.00\t0.00\n+GCC\t167\t16.50\t21.50\t31.50\t30.50\t0.00\t0.00\n+GCC\t168\t14.00\t25.00\t30.00\t31.00\t0.00\t0.00\n+GCC\t169\t18.50\t20.50\t23.50\t37.50\t0.00\t0.00\n+GCC\t170\t19.00\t23.00\t28.00\t30.00\t0.00\t0.00\n+GCC\t171\t20.00\t28.00\t33.00\t19.00\t0.00\t0.00\n+GCC\t172\t19.00\t20.00\t32.00\t29.00\t0.00\t0.00\n+GCC\t173\t24.50\t16.50\t33.50\t25.50\t0.00\t0.00\n+GCC\t174\t17.50\t23.50\t33.50\t25.50\t0.00\t0.00\n+GCC\t175\t33.50\t17.50\t35.50\t13.50\t0.00\t0.00\n+GCC\t176\t16.50\t32.50\t28.50\t22.50\t0.00\t0.00\n+GCC\t177\t19.00\t22.00\t27.00\t32.00\t0.00\t0.00\n+GCC\t178\t16.00\t26.00\t30.00\t28.00\t0.00\t0.00\n+GCC\t179\t18.00\t18.00\t22.00\t42.00\t0.00\t0.00\n+GCC\t180\t21.00\t22.00\t34.00\t23.00\t0.00\t0.00\n+GCC\t181\t20.50\t19.50\t35.50\t24.50\t0.00\t0.00\n+GCC\t182\t32.50\t18.50\t22.50\t26.50\t0.00\t0.00\n+GCC\t183\t24.50\t13.50\t28.50\t33.50\t0.00\t0.00\n+GCC\t184\t15.00\t29.00\t30.00\t26.00\t0.00\t0.00\n+GCC\t185\t15.00\t32.00\t33.00\t20.00\t0.00\t0.00\n+GCC\t186\t22.50\t23.50\t34.50\t19.50\t0.00\t0.00\n+GCC\t187\t19.00\t14.00\t40.00\t27.00\t0.00\t0.00\n+GCC\t188\t27.50\t21.50\t27.50\t23.50\t0.00\t0.00\n+GCC\t189\t17.00\t22.00\t34.00\t27.00\t0.00\t0.00\n+GCC\t190\t23.00\t30.00\t23.00\t24.00\t0.00\t0.00\n+GCC\t191\t25.00\t22.00\t28.00\t25.00\t0.00\t0.00\n+GCC\t192\t34.50\t24.50\t13.50\t27.50\t0.00\t0.00\n+GCC\t193\t18.50\t25.50\t25.50\t30.50\t0.00\t0.00\n+GCC\t194\t18.50\t33.50\t24.50\t23.50\t0.00\t0.00\n+GCC\t195\t16.00\t26.00\t23.00\t35.00\t0.00\t0.00\n+GCC\t196\t21.50\t25.50\t24.50\t28.50\t0.00\t0.00\n+GCC\t197\t20.00\t21.00\t23.00\t36.00\t0.00\t0.00\n+GCC\t198\t17.00\t21.00\t37.00\t25.00\t0.00\t0.00\n+GCC\t199\t20.50\t18.50\t25.50\t35.50\t0.00\t0.00\n+GCC\t200\t21.00\t29.00\t21.00\t29.00\t0.00\t0.00\n+GCC\t201\t27.00\t21.00\t23.00\t29.00\t0.00\t0.00\n+GCC\t202\t21.50\t24.50\t19.50\t34.50\t0.00\t0.00\n+GCC\t203\t21.50\t24.50\t26.50\t27.50\t0.00\t0.00\n+GCC\t204\t27.00\t29.00\t24.00\t20.00\t0.00\t0.00\n+GCC\t205\t19.50\t21.50\t22.50\t36.50\t0.00\t0.00\n+GCC\t206\t26.50\t24.50\t21.50\t27.50\t0.00\t0.00\n+GCC\t207\t22.50\t21.50\t19.50\t36.50\t0.00\t0.00\n+GCC\t208\t14.00\t35.00\t29.00\t22.00\t0.00\t0.00\n+GCC\t209\t16.00\t23.00\t12.00\t49.00\t0.00\t0.00\n+GCC\t210\t18.50\t19.50\t40.50\t21.50\t0.00\t0.00\n+GCC\t211\t26.00\t20.00\t22.00\t32.00\t0.00\t0.00\n+GCC\t212\t21.00\t31.00\t18.00\t30.00\t0.00\t0.00\n+GCC\t213\t24.00\t15.00\t31.00\t30.00\t0.00\t0.00\n+GCC\t214\t17.50\t24.50\t25.50\t32.50\t0.00\t0.00\n+GCC\t215\t26.00\t24.00\t23.00\t27.00\t0.00\t0.00\n+GCC\t216\t21.50\t17.50\t25.50\t35.50\t0.00\t0.00\n+GCC\t217\t26.00\t29.00\t17.00\t28.00\t0.00\t0.00\n+GCC\t218\t20.00\t27.00\t21.00\t32.00\t0.00\t0.00\n+GCC\t219\t17.00\t21.00\t21.00\t41.00\t0.00\t0.00\n+GCC\t220\t25.50\t23.50\t23.50\t27.50\t0.00\t0.00\n+GCC\t221\t21.50\t23.50\t20.50\t34.50\t0.00\t0.00\n+GCC\t222\t21.50\t21.50\t18.50\t38.50\t0.00\t0.00\n+GCC\t223\t20.00\t27.00\t28.00\t25.00\t0.00\t0.00\n+GCC\t224\t22.50\t22.50\t24.50\t30.50\t0.00\t0.00\n+GCC\t225\t14.50\t35.50\t30.50\t19.50\t0.00\t0.00\n+GCC\t226\t20.00\t23.00\t26.00\t31.00\t0.00\t0.00\n+GCC\t227\t20.50\t24.50\t23.50\t31.50\t0.00\t0.00\n+GCC\t228\t33.00\t19.00\t26.00\t22.00\t0.00\t0.00\n+GCC\t229\t22.50\t24.50\t18.50\t34.50\t0.00\t0.00\n+GCC\t230\t21.00\t32.00\t16.00\t31.00\t0.00\t0.00\n+GCC\t231\t23.00\t28.00\t30.00\t19.00\t0.00\t0.00\n+GCC\t232\t23.50\t21.50\t12.50\t42.50\t0.00\t0.00\n+GCC\t233\t21.00\t27.00\t25.00\t27.00\t0.00\t0.00\n+GCC\t234\t16.50\t27.50\t22.50\t33.50\t0.00\t0.00\n+GCC\t235\t20.00\t15.00\t28.00\t37.00\t0.00\t0.00\n+GCC\t236\t28.00\t23.00\t21.00\t28.00\t0.00\t0.00\n+GCC\t237\t20.50\t19.50\t22.50\t37.50\t0.00\t0.00\n+GCC\t238\t21.50\t29.50\t24.50\t24.50\t0.00\t0.00\n+GCC\t239\t20.00\t8.00\t17.00\t55.00\t0.00\t0.00\n+GCC\t240\t28.00\t24.00\t16.00\t32.00\t0.00\t0.00\n+GCC\t241\t22.50\t22.50\t16.50\t38.50\t0.00\t0.00\n+GCC\t242\t29.00\t25.00\t13.00\t33.00\t0.00\t0.00\n+GCC\t243\t22.50\t15.50\t23.50\t38.50\t0.00\t0.00\n+GCC\t244\t20.50\t23.50\t16.50\t39.50\t0.00\t0.00\n+GCC\t245\t28.00\t23.00\t19.00\t30.00\t0.00\t0.00\n+GCC\t246\t21.00\t29.00\t25.00\t25.00\t0.00\t0.00\n+GCC\t247\t32.00\t14.00\t13.00\t41.00\t0.00\t0.00\n+GCC\t248\t18.00\t18.00\t25.00\t39.00\t0.00\t0.00\n+GCC\t249\t25.00\t23.00\t21.00\t31.00\t0.00\t0.00\n+GCC\t250\t27.50\t22.50\t17.50\t32.50\t0.00\t0.00\n+GCC\t251\t13.50\t20.50\t36.50\t29.50\t0.00\t0.00\n # Insert sizes. Use `grep ^IS | cut -f 2-` to extract this part. The columns are: insert size, pairs total, inward oriented pairs, outward oriented pairs, other pairs\n # Read lengths. Use `grep ^RL | cut -f 2-` to extract this part. The columns are: read length, count\n RL\t251\t200\n' |
| b |
| diff -r 8cfc17e27132 -r 24c5d43cb545 test-data/samtools_stats_out2/gcc.tab --- a/test-data/samtools_stats_out2/gcc.tab Wed Nov 11 12:55:15 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,252 +0,0 @@ -# ACGT content per cycle. The columns are: cycle, and A,C,G,T counts (percent) -1 21.50 29.50 33.50 15.50 -2 30.00 16.00 11.00 43.00 -3 33.00 25.00 9.00 33.00 -4 17.00 29.00 13.00 41.00 -5 37.00 22.00 12.00 29.00 -6 36.00 26.00 17.00 21.00 -7 29.50 13.50 31.50 25.50 -8 50.50 14.50 19.50 15.50 -9 17.00 33.00 18.00 32.00 -10 37.00 14.00 21.00 28.00 -11 20.50 14.50 29.50 35.50 -12 30.00 24.00 22.00 24.00 -13 27.00 15.00 21.00 37.00 -14 24.00 22.00 26.00 28.00 -15 25.50 20.50 24.50 29.50 -16 31.00 15.00 20.00 34.00 -17 28.00 25.00 14.00 33.00 -18 30.50 28.50 19.50 21.50 -19 29.00 26.00 21.00 24.00 -20 22.50 23.50 17.50 36.50 -21 35.50 17.50 19.50 27.50 -22 37.50 28.50 15.50 18.50 -23 31.00 19.00 13.00 37.00 -24 37.00 12.00 22.00 29.00 -25 35.50 22.50 17.50 24.50 -26 33.50 18.50 15.50 32.50 -27 34.50 14.50 25.50 25.50 -28 31.00 14.00 24.00 31.00 -29 30.00 27.00 24.00 19.00 -30 31.00 20.00 14.00 35.00 -31 33.50 29.50 13.50 23.50 -32 42.50 20.50 19.50 17.50 -33 25.50 23.50 14.50 36.50 -34 39.50 16.50 20.50 23.50 -35 32.50 23.50 21.50 22.50 -36 42.00 25.00 16.00 17.00 -37 38.00 17.00 19.00 26.00 -38 24.00 26.00 25.00 25.00 -39 22.50 41.50 18.50 17.50 -40 32.00 16.00 21.00 31.00 -41 33.00 28.00 19.00 20.00 -42 30.50 25.50 19.50 24.50 -43 35.00 29.00 15.00 21.00 -44 20.00 27.00 22.00 31.00 -45 40.50 21.50 21.50 16.50 -46 26.50 20.50 22.50 30.50 -47 38.50 29.50 16.50 15.50 -48 27.50 24.50 17.50 30.50 -49 28.50 32.50 10.50 28.50 -50 46.50 20.50 9.50 23.50 -51 34.50 28.50 13.50 23.50 -52 41.50 23.50 20.50 14.50 -53 20.00 28.00 26.00 26.00 -54 31.50 18.50 24.50 25.50 -55 30.50 22.50 16.50 30.50 -56 33.50 22.50 13.50 30.50 -57 23.00 24.00 23.00 30.00 -58 25.00 37.00 19.00 19.00 -59 34.00 23.00 24.00 19.00 -60 29.00 28.00 17.00 26.00 -61 25.50 23.50 24.50 26.50 -62 31.50 22.50 16.50 29.50 -63 27.50 28.50 25.50 18.50 -64 33.50 21.50 25.50 19.50 -65 35.50 19.50 18.50 26.50 -66 34.00 25.00 15.00 26.00 -67 37.00 23.00 19.00 21.00 -68 36.50 29.50 13.50 20.50 -69 38.50 19.50 20.50 21.50 -70 38.50 16.50 18.50 26.50 -71 25.50 38.50 21.50 14.50 -72 29.00 29.00 25.00 17.00 -73 32.50 20.50 21.50 25.50 -74 28.50 32.50 12.50 26.50 -75 41.50 12.50 18.50 27.50 -76 24.50 29.50 23.50 22.50 -77 36.00 21.00 18.00 25.00 -78 27.00 34.00 22.00 17.00 -79 21.50 26.50 25.50 26.50 -80 34.00 19.00 28.00 19.00 -81 17.00 26.00 26.00 31.00 -82 31.00 30.00 23.00 16.00 -83 31.50 26.50 12.50 29.50 -84 19.00 41.00 21.00 19.00 -85 37.50 24.50 16.50 21.50 -86 15.00 48.00 15.00 22.00 -87 41.00 16.00 18.00 25.00 -88 23.50 27.50 27.50 21.50 -89 26.50 27.50 26.50 19.50 -90 18.50 23.50 24.50 33.50 -91 27.00 32.00 22.00 19.00 -92 23.50 17.50 27.50 31.50 -93 25.50 37.50 15.50 21.50 -94 27.00 17.00 24.00 32.00 -95 26.50 37.50 14.50 21.50 -96 29.50 25.50 16.50 28.50 -97 29.00 31.00 21.00 19.00 -98 18.00 33.00 22.00 27.00 -99 24.50 33.50 24.50 17.50 -100 24.50 16.50 24.50 34.50 -101 25.00 40.00 19.00 16.00 -102 17.50 17.50 32.50 32.50 -103 31.00 26.00 16.00 27.00 -104 26.50 29.50 20.50 23.50 -105 34.00 33.00 21.00 12.00 -106 23.00 31.00 26.00 20.00 -107 17.50 35.50 23.50 23.50 -108 24.50 30.50 23.50 21.50 -109 17.00 31.00 22.00 30.00 -110 16.00 35.00 24.00 25.00 -111 24.00 32.00 23.00 21.00 -112 37.00 28.00 16.00 19.00 -113 19.50 22.50 32.50 25.50 -114 17.00 31.00 35.00 17.00 -115 29.50 24.50 23.50 22.50 -116 22.00 30.00 34.00 14.00 -117 27.00 23.00 19.00 31.00 -118 25.50 14.50 34.50 25.50 -119 22.50 34.50 20.50 22.50 -120 17.50 24.50 26.50 31.50 -121 27.50 33.50 22.50 16.50 -122 17.00 23.00 25.00 35.00 -123 23.50 46.50 11.50 18.50 -124 9.00 32.00 34.00 25.00 -125 24.00 27.00 19.00 30.00 -126 26.00 17.00 28.00 29.00 -127 26.50 16.50 21.50 35.50 -128 18.00 34.00 31.00 17.00 -129 25.50 25.50 27.50 21.50 -130 25.00 20.00 22.00 33.00 -131 17.50 39.50 24.50 18.50 -132 21.00 28.00 23.00 28.00 -133 13.50 31.50 35.50 19.50 -134 24.50 19.50 30.50 25.50 -135 16.50 23.50 30.50 29.50 -136 28.00 32.00 15.00 25.00 -137 22.50 21.50 30.50 25.50 -138 14.50 34.50 24.50 26.50 -139 20.50 29.50 24.50 25.50 -140 17.00 23.00 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38.50 -244 20.50 23.50 16.50 39.50 -245 28.00 23.00 19.00 30.00 -246 21.00 29.00 25.00 25.00 -247 32.00 14.00 13.00 41.00 -248 18.00 18.00 25.00 39.00 -249 25.00 23.00 21.00 31.00 -250 27.50 22.50 17.50 32.50 -251 13.50 20.50 36.50 29.50 |
| b |
| diff -r 8cfc17e27132 -r 24c5d43cb545 test-data/samtools_stats_out2/mpc.tab --- a/test-data/samtools_stats_out2/mpc.tab Wed Nov 11 12:55:15 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b"@@ -1,253 +0,0 @@\n-# Columns correspond to qualities, rows to cycles. First column is the cycle number, second is the number of N's and the rest is the number of 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|
| b |
| diff -r 8cfc17e27132 -r 24c5d43cb545 test-data/samtools_stats_out2/sn.tab --- a/test-data/samtools_stats_out2/sn.tab Wed Nov 11 12:55:15 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,33 +0,0 @@ -# Summary Numbers - -raw total sequences: 200 -filtered sequences: 0 -sequences: 200 -is sorted: 1 -1st fragments: 100 -last fragments: 100 -reads mapped: 25 -reads mapped and paired: 0 # paired-end technology bit set + both mates mapped -reads unmapped: 175 -reads properly paired: 0 # proper-pair bit set -reads paired: 200 # paired-end technology bit set -reads duplicated: 0 # PCR or optical duplicate bit set -reads MQ0: 6 # mapped and MQ=0 -reads QC failed: 0 -non-primary alignments: 0 -total length: 50200 # ignores clipping -bases mapped: 6275 # ignores clipping -bases mapped (cigar): 6275 # more accurate -bases trimmed: 0 -bases duplicated: 0 -mismatches: 591 # from NM fields -error rate: 9.418327e-02 # mismatches / bases mapped (cigar) -average length: 251 -maximum length: 251 -average quality: 34.7 -insert size average: 0.0 -insert size standard deviation: 0.0 -inward oriented pairs: 0 -outward oriented pairs: 0 -pairs with other orientation: 0 -pairs on different chromosomes: 0 |
| b |
| diff -r 8cfc17e27132 -r 24c5d43cb545 test-data/samtools_stats_out2__gcc.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/samtools_stats_out2__gcc.tab Tue May 09 11:19:01 2017 -0400 |
| b |
| b'@@ -0,0 +1,252 @@\n+# ACGT content per cycle. The columns are: cycle, and A,C,G,T counts (percent)\n+1\t21.94\t30.10\t34.18\t13.78\t2.04\t0.00\n+2\t30.00\t16.00\t11.00\t43.00\t0.00\t0.00\n+3\t33.00\t25.00\t9.00\t33.00\t0.00\t0.00\n+4\t17.00\t29.00\t13.00\t41.00\t0.00\t0.00\n+5\t37.00\t22.00\t12.00\t29.00\t0.00\t0.00\n+6\t36.00\t26.00\t17.00\t21.00\t0.00\t0.00\n+7\t29.50\t13.50\t31.50\t25.50\t0.00\t0.00\n+8\t50.50\t14.50\t19.50\t15.50\t0.00\t0.00\n+9\t17.00\t33.00\t18.00\t32.00\t0.00\t0.00\n+10\t37.00\t14.00\t21.00\t28.00\t0.00\t0.00\n+11\t20.50\t14.50\t29.50\t35.50\t0.00\t0.00\n+12\t30.00\t24.00\t22.00\t24.00\t0.00\t0.00\n+13\t27.00\t15.00\t21.00\t37.00\t0.00\t0.00\n+14\t24.24\t22.22\t26.26\t27.27\t1.01\t0.00\n+15\t25.50\t20.50\t24.50\t29.50\t0.00\t0.00\n+16\t31.00\t15.00\t20.00\t34.00\t0.00\t0.00\n+17\t28.00\t25.00\t14.00\t33.00\t0.00\t0.00\n+18\t30.50\t28.50\t19.50\t21.50\t0.00\t0.00\n+19\t29.00\t26.00\t21.00\t24.00\t0.00\t0.00\n+20\t22.50\t23.50\t17.50\t36.50\t0.00\t0.00\n+21\t35.50\t17.50\t19.50\t27.50\t0.00\t0.00\n+22\t37.50\t28.50\t15.50\t18.50\t0.00\t0.00\n+23\t31.31\t19.19\t13.13\t36.36\t1.01\t0.00\n+24\t37.00\t12.00\t22.00\t29.00\t0.00\t0.00\n+25\t35.50\t22.50\t17.50\t24.50\t0.00\t0.00\n+26\t33.50\t18.50\t15.50\t32.50\t0.00\t0.00\n+27\t34.50\t14.50\t25.50\t25.50\t0.00\t0.00\n+28\t31.00\t14.00\t24.00\t31.00\t0.00\t0.00\n+29\t30.00\t27.00\t24.00\t19.00\t0.00\t0.00\n+30\t31.00\t20.00\t14.00\t35.00\t0.00\t0.00\n+31\t33.50\t29.50\t13.50\t23.50\t0.00\t0.00\n+32\t42.50\t20.50\t19.50\t17.50\t0.00\t0.00\n+33\t25.50\t23.50\t14.50\t36.50\t0.00\t0.00\n+34\t39.50\t16.50\t20.50\t23.50\t0.00\t0.00\n+35\t32.50\t23.50\t21.50\t22.50\t0.00\t0.00\n+36\t42.00\t25.00\t16.00\t17.00\t0.00\t0.00\n+37\t38.00\t17.00\t19.00\t26.00\t0.00\t0.00\n+38\t24.00\t26.00\t25.00\t25.00\t0.00\t0.00\n+39\t22.50\t41.50\t18.50\t17.50\t0.00\t0.00\n+40\t32.00\t16.00\t21.00\t31.00\t0.00\t0.00\n+41\t33.00\t28.00\t19.00\t20.00\t0.00\t0.00\n+42\t30.50\t25.50\t19.50\t24.50\t0.00\t0.00\n+43\t35.00\t29.00\t15.00\t21.00\t0.00\t0.00\n+44\t20.00\t27.00\t22.00\t31.00\t0.00\t0.00\n+45\t40.50\t21.50\t21.50\t16.50\t0.00\t0.00\n+46\t26.50\t20.50\t22.50\t30.50\t0.00\t0.00\n+47\t38.50\t29.50\t16.50\t15.50\t0.00\t0.00\n+48\t27.50\t24.50\t17.50\t30.50\t0.00\t0.00\n+49\t28.50\t32.50\t10.50\t28.50\t0.00\t0.00\n+50\t46.50\t20.50\t9.50\t23.50\t0.00\t0.00\n+51\t34.50\t28.50\t13.50\t23.50\t0.00\t0.00\n+52\t41.50\t23.50\t20.50\t14.50\t0.00\t0.00\n+53\t20.00\t28.00\t26.00\t26.00\t0.00\t0.00\n+54\t31.50\t18.50\t24.50\t25.50\t0.00\t0.00\n+55\t30.50\t22.50\t16.50\t30.50\t0.00\t0.00\n+56\t33.50\t22.50\t13.50\t30.50\t0.00\t0.00\n+57\t23.00\t24.00\t23.00\t30.00\t0.00\t0.00\n+58\t25.00\t37.00\t19.00\t19.00\t0.00\t0.00\n+59\t34.00\t23.00\t24.00\t19.00\t0.00\t0.00\n+60\t29.00\t28.00\t17.00\t26.00\t0.00\t0.00\n+61\t25.50\t23.50\t24.50\t26.50\t0.00\t0.00\n+62\t31.50\t22.50\t16.50\t29.50\t0.00\t0.00\n+63\t27.50\t28.50\t25.50\t18.50\t0.00\t0.00\n+64\t33.50\t21.50\t25.50\t19.50\t0.00\t0.00\n+65\t35.50\t19.50\t18.50\t26.50\t0.00\t0.00\n+66\t34.00\t25.00\t15.00\t26.00\t0.00\t0.00\n+67\t37.00\t23.00\t19.00\t21.00\t0.00\t0.00\n+68\t36.50\t29.50\t13.50\t20.50\t0.00\t0.00\n+69\t38.50\t19.50\t20.50\t21.50\t0.00\t0.00\n+70\t38.50\t16.50\t18.50\t26.50\t0.00\t0.00\n+71\t25.50\t38.50\t21.50\t14.50\t0.00\t0.00\n+72\t29.00\t29.00\t25.00\t17.00\t0.00\t0.00\n+73\t32.50\t20.50\t21.50\t25.50\t0.00\t0.00\n+74\t28.50\t32.50\t12.50\t26.50\t0.00\t0.00\n+75\t41.50\t12.50\t18.50\t27.50\t0.00\t0.00\n+76\t24.50\t29.50\t23.50\t22.50\t0.00\t0.00\n+77\t36.00\t21.00\t18.00\t25.00\t0.00\t0.00\n+78\t27.00\t34.00\t22.00\t17.00\t0.00\t0.00\n+79\t21.50\t26.50\t25.50\t26.50\t0.00\t0.00\n+80\t34.00\t19.00\t28.00\t19.00\t0.00\t0.00\n+81\t17.00\t26.00\t26.00\t31.00\t0.00\t0.00\n+82\t31.00\t30.00\t23.00\t16.00\t0.00\t0.00\n+83\t31.50\t26.50\t12.50\t29.50\t0.00\t0.00\n+84\t19.00\t41.00\t21.00\t19.00\t0.00\t0.00\n+85\t37.50\t24.50\t16.50\t21.50\t0.00\t0.00\n+86\t15.00\t48.00\t15.00\t22.00\t0.00\t0.00\n+87\t41.00\t16.00\t18.00\t25.00\t0.00\t0.00\n+88\t23.50\t27.50\t27.50\t21.50\t0.00\t0.00\n+89\t26.50\t27.50\t26.50\t19.50\t0.00\t0.00\n+90\t18.50\t23.50\t24.50\t33.50\t0.00\t0.00\n+91\t27.00\t32.00\t22.00\t19.00\t0.00\t0.00\n+92\t23.50\t17.50\t27.50\t31.50\t0.00\t0.00\n+93\t25.50\t37.50\t15.50\t21.50\t0.00\t0.00\n+94\t27.00\t17.00\t24.00\t32.00\t0.00\t0.00\n+95\t26.77\t37.88\t14.65\t20.71\t1.01\t0.00\n+96\t29.50\t25.50\t16.50\t28.50\t0.00\t0.00\n+97\t29.00\t31.00\t21.00\t19.00\t0.00\t0.00\n+98\t18.18\t33.33\t22.22\t26.26\t1.01\t0.00\n+99\t24.50\t33.50\t24.50\t17.50\t0.00\t0.00\n+100\t24.50\t16.50\t24.50\t34.50\t0.00\t0.00\n+101\t25.00\t40.00\t19.00\t16.00\t0.00\t0.00\n+102\t17.50\t17.50\t32.50\t32.50\t0.00\t0.00\n+103\t31.00\t26.00\t16.00\t27.00\t0.00'..b'23.50\t26.50\t0.00\t0.00\n+150\t14.00\t29.00\t24.00\t33.00\t0.00\t0.00\n+151\t19.50\t30.50\t32.50\t17.50\t0.00\t0.00\n+152\t18.50\t17.50\t29.50\t34.50\t0.00\t0.00\n+153\t22.50\t22.50\t31.50\t23.50\t0.00\t0.00\n+154\t22.00\t21.00\t29.00\t28.00\t0.00\t0.00\n+155\t21.00\t26.00\t19.00\t34.00\t0.00\t0.00\n+156\t14.50\t23.50\t35.50\t26.50\t0.00\t0.00\n+157\t22.00\t31.00\t23.00\t24.00\t0.00\t0.00\n+158\t22.50\t29.50\t24.50\t23.50\t0.00\t0.00\n+159\t17.50\t12.50\t46.50\t23.50\t0.00\t0.00\n+160\t24.50\t26.50\t26.50\t22.50\t0.00\t0.00\n+161\t13.00\t23.00\t45.00\t19.00\t0.00\t0.00\n+162\t31.50\t16.50\t22.50\t29.50\t0.00\t0.00\n+163\t19.50\t21.50\t35.50\t23.50\t0.00\t0.00\n+164\t29.00\t18.00\t21.00\t32.00\t0.00\t0.00\n+165\t14.50\t17.50\t35.50\t32.50\t0.00\t0.00\n+166\t17.50\t37.50\t28.50\t16.50\t0.00\t0.00\n+167\t16.50\t21.50\t31.50\t30.50\t0.00\t0.00\n+168\t14.00\t25.00\t30.00\t31.00\t0.00\t0.00\n+169\t18.50\t20.50\t23.50\t37.50\t0.00\t0.00\n+170\t19.00\t23.00\t28.00\t30.00\t0.00\t0.00\n+171\t20.00\t28.00\t33.00\t19.00\t0.00\t0.00\n+172\t19.00\t20.00\t32.00\t29.00\t0.00\t0.00\n+173\t24.50\t16.50\t33.50\t25.50\t0.00\t0.00\n+174\t17.50\t23.50\t33.50\t25.50\t0.00\t0.00\n+175\t33.50\t17.50\t35.50\t13.50\t0.00\t0.00\n+176\t16.50\t32.50\t28.50\t22.50\t0.00\t0.00\n+177\t19.00\t22.00\t27.00\t32.00\t0.00\t0.00\n+178\t16.00\t26.00\t30.00\t28.00\t0.00\t0.00\n+179\t18.00\t18.00\t22.00\t42.00\t0.00\t0.00\n+180\t21.00\t22.00\t34.00\t23.00\t0.00\t0.00\n+181\t20.50\t19.50\t35.50\t24.50\t0.00\t0.00\n+182\t32.50\t18.50\t22.50\t26.50\t0.00\t0.00\n+183\t24.50\t13.50\t28.50\t33.50\t0.00\t0.00\n+184\t15.00\t29.00\t30.00\t26.00\t0.00\t0.00\n+185\t15.00\t32.00\t33.00\t20.00\t0.00\t0.00\n+186\t22.50\t23.50\t34.50\t19.50\t0.00\t0.00\n+187\t19.00\t14.00\t40.00\t27.00\t0.00\t0.00\n+188\t27.50\t21.50\t27.50\t23.50\t0.00\t0.00\n+189\t17.00\t22.00\t34.00\t27.00\t0.00\t0.00\n+190\t23.00\t30.00\t23.00\t24.00\t0.00\t0.00\n+191\t25.00\t22.00\t28.00\t25.00\t0.00\t0.00\n+192\t34.50\t24.50\t13.50\t27.50\t0.00\t0.00\n+193\t18.50\t25.50\t25.50\t30.50\t0.00\t0.00\n+194\t18.50\t33.50\t24.50\t23.50\t0.00\t0.00\n+195\t16.00\t26.00\t23.00\t35.00\t0.00\t0.00\n+196\t21.50\t25.50\t24.50\t28.50\t0.00\t0.00\n+197\t20.00\t21.00\t23.00\t36.00\t0.00\t0.00\n+198\t17.00\t21.00\t37.00\t25.00\t0.00\t0.00\n+199\t20.50\t18.50\t25.50\t35.50\t0.00\t0.00\n+200\t21.00\t29.00\t21.00\t29.00\t0.00\t0.00\n+201\t27.00\t21.00\t23.00\t29.00\t0.00\t0.00\n+202\t21.50\t24.50\t19.50\t34.50\t0.00\t0.00\n+203\t21.50\t24.50\t26.50\t27.50\t0.00\t0.00\n+204\t27.00\t29.00\t24.00\t20.00\t0.00\t0.00\n+205\t19.50\t21.50\t22.50\t36.50\t0.00\t0.00\n+206\t26.50\t24.50\t21.50\t27.50\t0.00\t0.00\n+207\t22.50\t21.50\t19.50\t36.50\t0.00\t0.00\n+208\t14.00\t35.00\t29.00\t22.00\t0.00\t0.00\n+209\t16.00\t23.00\t12.00\t49.00\t0.00\t0.00\n+210\t18.50\t19.50\t40.50\t21.50\t0.00\t0.00\n+211\t26.00\t20.00\t22.00\t32.00\t0.00\t0.00\n+212\t21.00\t31.00\t18.00\t30.00\t0.00\t0.00\n+213\t24.00\t15.00\t31.00\t30.00\t0.00\t0.00\n+214\t17.50\t24.50\t25.50\t32.50\t0.00\t0.00\n+215\t26.00\t24.00\t23.00\t27.00\t0.00\t0.00\n+216\t21.50\t17.50\t25.50\t35.50\t0.00\t0.00\n+217\t26.00\t29.00\t17.00\t28.00\t0.00\t0.00\n+218\t20.00\t27.00\t21.00\t32.00\t0.00\t0.00\n+219\t17.00\t21.00\t21.00\t41.00\t0.00\t0.00\n+220\t25.50\t23.50\t23.50\t27.50\t0.00\t0.00\n+221\t21.50\t23.50\t20.50\t34.50\t0.00\t0.00\n+222\t21.50\t21.50\t18.50\t38.50\t0.00\t0.00\n+223\t20.00\t27.00\t28.00\t25.00\t0.00\t0.00\n+224\t22.50\t22.50\t24.50\t30.50\t0.00\t0.00\n+225\t14.50\t35.50\t30.50\t19.50\t0.00\t0.00\n+226\t20.00\t23.00\t26.00\t31.00\t0.00\t0.00\n+227\t20.50\t24.50\t23.50\t31.50\t0.00\t0.00\n+228\t33.00\t19.00\t26.00\t22.00\t0.00\t0.00\n+229\t22.50\t24.50\t18.50\t34.50\t0.00\t0.00\n+230\t21.00\t32.00\t16.00\t31.00\t0.00\t0.00\n+231\t23.00\t28.00\t30.00\t19.00\t0.00\t0.00\n+232\t23.50\t21.50\t12.50\t42.50\t0.00\t0.00\n+233\t21.00\t27.00\t25.00\t27.00\t0.00\t0.00\n+234\t16.50\t27.50\t22.50\t33.50\t0.00\t0.00\n+235\t20.00\t15.00\t28.00\t37.00\t0.00\t0.00\n+236\t28.00\t23.00\t21.00\t28.00\t0.00\t0.00\n+237\t20.50\t19.50\t22.50\t37.50\t0.00\t0.00\n+238\t21.50\t29.50\t24.50\t24.50\t0.00\t0.00\n+239\t20.00\t8.00\t17.00\t55.00\t0.00\t0.00\n+240\t28.00\t24.00\t16.00\t32.00\t0.00\t0.00\n+241\t22.50\t22.50\t16.50\t38.50\t0.00\t0.00\n+242\t29.00\t25.00\t13.00\t33.00\t0.00\t0.00\n+243\t22.50\t15.50\t23.50\t38.50\t0.00\t0.00\n+244\t20.50\t23.50\t16.50\t39.50\t0.00\t0.00\n+245\t28.00\t23.00\t19.00\t30.00\t0.00\t0.00\n+246\t21.00\t29.00\t25.00\t25.00\t0.00\t0.00\n+247\t32.00\t14.00\t13.00\t41.00\t0.00\t0.00\n+248\t18.00\t18.00\t25.00\t39.00\t0.00\t0.00\n+249\t25.00\t23.00\t21.00\t31.00\t0.00\t0.00\n+250\t27.50\t22.50\t17.50\t32.50\t0.00\t0.00\n+251\t13.50\t20.50\t36.50\t29.50\t0.00\t0.00\n' |
| b |
| diff -r 8cfc17e27132 -r 24c5d43cb545 test-data/samtools_stats_out2__mpc.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/samtools_stats_out2__mpc.tab Tue May 09 11:19:01 2017 -0400 |
| b |
| b"@@ -0,0 +1,253 @@\n+# Columns correspond to qualities, rows to cycles. First column is the cycle number, second is the number of N's and the rest is the number of 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|
| b |
| diff -r 8cfc17e27132 -r 24c5d43cb545 test-data/samtools_stats_out2__sn.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/samtools_stats_out2__sn.tab Tue May 09 11:19:01 2017 -0400 |
| b |
| @@ -0,0 +1,33 @@ +# Summary Numbers + +raw total sequences: 200 +filtered sequences: 0 +sequences: 200 +is sorted: 1 +1st fragments: 100 +last fragments: 100 +reads mapped: 25 +reads mapped and paired: 0 # paired-end technology bit set + both mates mapped +reads unmapped: 175 +reads properly paired: 0 # proper-pair bit set +reads paired: 200 # paired-end technology bit set +reads duplicated: 0 # PCR or optical duplicate bit set +reads MQ0: 6 # mapped and MQ=0 +reads QC failed: 0 +non-primary alignments: 0 +total length: 50200 # ignores clipping +bases mapped: 6275 # ignores clipping +bases mapped (cigar): 6275 # more accurate +bases trimmed: 0 +bases duplicated: 0 +mismatches: 591 # from NM fields +error rate: 9.418327e-02 # mismatches / bases mapped (cigar) +average length: 251 +maximum length: 251 +average quality: 34.7 +insert size average: 0.0 +insert size standard deviation: 0.0 +inward oriented pairs: 0 +outward oriented pairs: 0 +pairs with other orientation: 0 +pairs on different chromosomes: 0 |
| b |
| diff -r 8cfc17e27132 -r 24c5d43cb545 tool_dependencies.xml --- a/tool_dependencies.xml Wed Nov 11 12:55:15 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,6 +0,0 @@ -<?xml version="1.0"?> -<tool_dependency> - <package name="samtools" version="1.2"> - <repository changeset_revision="f6ae3ba3f3c1" name="package_samtools_1_2" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> -</tool_dependency> |