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Changeset 0:0d71d9467847 (2015-04-22)

Next changeset 1:8cfc17e27132 (2015-11-11)

Commit message:
Uploaded

added:
macros.xml
samtools_stats.xml
samtools_stats_tool_test_output.html
test-data/phiX.bam
test-data/samtools_stats_input.bam
test-data/samtools_stats_out1.tab
test-data/samtools_stats_out2.tab
test-data/samtools_stats_out2/gcc.tab
test-data/samtools_stats_out2/mpc.tab
test-data/samtools_stats_out2/sn.tab
test-data/samtools_stats_ref.fa
tool-data/fasta_indexes.loc.sample
tool_data_table_conf.xml.sample
tool_dependencies.xml

diff -r 000000000000 -r 0d71d9467847 macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml Wed Apr 22 10:29:35 2015 -0400

@@ -0,0 +1,70 @@
+<macros>
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="1.2">samtools</requirement>
+            <yield/>
+        </requirements>
+    </xml>
+    <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},}
+            </citation>
+            <citation type="doi">10.1093/bioinformatics/btp352</citation>
+            <citation type="doi">10.1093/bioinformatics/btr076</citation>
+            <citation type="doi">10.1093/bioinformatics/btr509</citation>
+            <citation type="bibtex">
+                @misc{Danecek_et_al,
+                Author={Danecek, P., Schiffels, S., Durbin, R.},
+                title={Multiallelic calling model in bcftools (-m)},
+                url = {http://samtools.github.io/bcftools/call-m.pdf},}
+            </citation>
+            <citation type="bibtex">
+                @misc{Durbin_VCQC,
+                Author={Durbin, R.},
+                title={Segregation based metric for variant call QC},
+                url = {http://samtools.github.io/bcftools/rd-SegBias.pdf},}
+            </citation>
+            <citation type="bibtex">
+                @misc{Li_SamMath,
+                Author={Li, H.},
+                title={Mathematical Notes on SAMtools Algorithms},
+                url = {http://www.broadinstitute.org/gatk/media/docs/Samtools.pdf},}
+            </citation>
+            <citation type="bibtex">
+                @misc{SamTools_github,
+                title={SAMTools GitHub page},
+                url = {https://github.com/samtools/samtools},}
+            </citation>
+        </citations>
+    </xml>
+    <xml name="version_command">
+        <version_command>samtools --version | head -n 1 | awk '{ print $2 }'</version_command>
+    </xml>
+    <xml name="stdio">
+        <stdio>
+            <exit_code range="1:" level="fatal" description="Error" />
+        </stdio>
+    </xml>
+    <token name="@no-chrom-options@">
+-----
+
+.. class:: warningmark
+
+**No options available? How to re-detect metadata**
+
+If you see a "No options available" within the "**Select references (chromosomes and contigs) you would like to restrict bam to**" drop down, you need to re-detect metadata for the dataset you are trying to process. To do this follow these steps:
+
+1. Click on the **pencil** icon adjacent to the dataset in the history
+2. A new menu will appear in the center pane of the interface
+3. Click **Datatype** tab
+4. Set **New Type** to **BAM**
+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>

diff -r 000000000000 -r 0d71d9467847 samtools_stats.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/samtools_stats.xml Wed Apr 22 10:29:35 2015 -0400

[

b'@@ -0,0 +1,296 @@\n+<tool id="samtools_stats" name="Stats" version="2.0">\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+ <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+ #end if\n+ #end if\n+ --GC-depth ${gc_depth}\n+ --insert-size ${insert_size}\n+\n+ ## The code below is commented out because using -I/--id options causes the following exception\n+ ## Samtools-htslib: init_group_id() header parsing not yet implemented\n+\n+ ##if str($read_group) != "":\n+ ## -I "${read_group}"\n+ ##end if\n+\n+ #if str($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 "${use_reference.reference_source.ref_file}"\n+ #end if\n+ #end if\n+ > "${output}"\n+ #if $split_output.split_output_selector == "yes":\n+ #set outputs_to_split = str($split_output.generate_tables).split(\',\')\n+ && mkdir split && echo ${split_output.generate_tables} &&\n+\n+ #if \'sn\' in $outputs_to_split:\n+ echo "# Summary Numbers\\n" > "split/Summary numbers.tab" &&\n+ grep -q ^SN "${output}" ; if [ $? = 0 ] ; then grep ^SN "${output}" | cut -f 2- >> "split/Summary numbers.tab" ; fi &&\n+ #end if\n+\n+ #if \'ffq\' in $outputs_to_split:\n+ echo "# Columns correspond to qualities and rows to cycles. First column is the cycle number\\n" > "split/First Fragment Qualities.tab" &&\n+ grep -q ^FFQ "${output}" ; if [ $? = 0 ] ; then grep ^FFQ "${output}" | cut -f 2- >> "split/First Fragment Qualities.tab" ; fi &&\n+ #end if\n+\n+ #if \'lfq\' in $outputs_to_split:\n+ echo "# Columns correspond to qualities and rows to cycles. First column is the cycle number" > "split/Last Fragment Qualities.tab" &&\n+ grep -q ^LFQ "${output}" ; if [ $? = 0 ] ; then grep ^LFQ "${output}" | cut -f 2- >> "split/Last Fragment Qualities.tab" ; fi &&\n+ #end if\n+\n+ #if \'mpc\' in $outputs_to_split:\n+ echo "# Columns correspond to qualities, rows to cycles. First column is the cycle number, second is the number of N\'s and the rest is the number of mismatches" > "split/Mismatches per cycle.tab" &&\n+ grep -q ^MPC "${output}" ; if [ $? = 0 ] ; then grep ^MPC "${output}" | cut -f 2- >> "split/Mismatches per cycle.tab" ; fi &&\n+ #end if\n+\n+ #if \'gcf\' in $outputs_to_split:\n+ echo "# GC'..b'nce for GC depth">\n+ <option value="cached">Locally cached</option>\n+ <option value="history">History</option>\n+ </param>\n+ <when value="cached">\n+ <param name="ref_file" type="select" label="Using genome">\n+ <options from_data_table="fasta_indexes" />\n+ <filter type="data_meta" ref="input_file" key="dbkey" column="1" />\n+ </param>\n+ </when>\n+ <when value="history">\n+ <param name="ref_file" type="data" format="fasta" label="Using file" />\n+ </when>\n+ </conditional>\n+ </when>\n+ <when value="no" />\n+ </conditional>\n+\n+ </inputs>\n+\n+ <outputs>\n+ <data format="tabular" name="output" label="${tool.name} on ${on_string}">\n+ <discover_datasets pattern="(?P<designation>.+)\\.tab" ext="tabular" visible="true" directory="split" />\n+ </data>\n+ </outputs>\n+ <tests>\n+ <test>\n+ <param name="input_file" value="samtools_stats_input.bam" ftype="bam" />\n+ <param name="use_ref_selector" value="yes" />\n+ <param name="reference_source_selector" value="history" />\n+ <param name="ref_file" value="samtools_stats_ref.fa" ftype="fasta" />\n+ <output name="output" file="samtools_stats_out1.tab" ftype="tabular" lines_diff="4" />\n+ </test>\n+ <test>\n+ <param name="input_file" value="samtools_stats_input.bam" ftype="bam" />\n+ <param name="use_ref_selector" value="yes" />\n+ <param name="reference_source_selector" value="history" />\n+ <param name="ref_file" value="samtools_stats_ref.fa" ftype="fasta" />\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+ </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+ ]]></help>\n+ <expand macro="citations"></expand>\n+</tool>\n+\n'

diff -r 000000000000 -r 0d71d9467847 samtools_stats_tool_test_output.html
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/samtools_stats_tool_test_output.html Wed Apr 22 10:29:35 2015 -0400

[

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sh -c \\"exit $return_code\\"\\ngalaxy.jobs.runners.local: DEBUG: (6) executing job script: /var/folders/2z/ntdb9g2n7tq6_bcq4dj9hj9r0000gn/T/tmp69oNhW/job_working_directory/000/6/galaxy_6.sh\\ngalaxy.jobs: DEBUG: (6) Persisting job destination (destination id: local:///)\\nrequests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\\nrequests.packages.urllib3.connectionpool: DEBUG: \\"GET /api/jobs/fa6d20d0fb68383f?key=73391df1185a0911acd55c3f7fae680e HTTP/1.1\\" 200 None\\ngalaxy.jobs.runners.local: DEBUG: execution finished: /var/folders/2z/ntdb9g2n7tq6_bcq4dj9hj9r0000gn/T/tmp69oNhW/job_working_directory/000/6/galaxy_6.sh\\nrequests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\\nrequests.packages.urllib3.connectionpool: DEBUG: \\"GET /api/jobs/fa6d20d0fb68383f?key=73391df1185a0911acd55c3f7fae680e HTTP/1.1\\" 200 None\\ngalaxy.jobs: DEBUG: job 6 ended (finish() executed in (6680.679 ms))\\nrequests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\\nrequests.packages.urllib3.connectionpool: DEBUG: \\"GET /api/jobs/fa6d20d0fb68383f?key=73391df1185a0911acd55c3f7fae680e HTTP/1.1\\" 200 None\\nrequests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\\nrequests.packages.urllib3.connectionpool: DEBUG: \\"GET /api/jobs/fa6d20d0fb68383f?full=true&key=73391df1185a0911acd55c3f7fae680e HTTP/1.1\\" 200 None\\nrequests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\\nrequests.packages.urllib3.connectionpool: DEBUG: \\"GET /api/jobs/fa6d20d0fb68383f?key=73391df1185a0911acd55c3f7fae680e HTTP/1.1\\" 200 None\\nrequests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\\nrequests.packages.urllib3.connectionpool: DEBUG: \\"GET /api/histories/5729865256bc2525/contents/fa6d20d0fb68383f/display?raw=true&key=73391df1185a0911acd55c3f7fae680e HTTP/1.1\\" 200 None\\nbase.twilltestcase: DEBUG: keepoutdir: /var/folders/2z/ntdb9g2n7tq6_bcq4dj9hj9r0000gn/T/tmp69oNhW/jobfiles, ofn: /var/folders/2z/ntdb9g2n7tq6_bcq4dj9hj9r0000gn/T/tmp69oNhW/jobfiles/samtools_stats_out2.tab\\nbase.twilltestcase: DEBUG: ## GALAXY_TEST_SAVE=/var/folders/2z/ntdb9g2n7tq6_bcq4dj9hj9r0000gn/T/tmp69oNhW/jobfiles. saved /var/folders/2z/ntdb9g2n7tq6_bcq4dj9hj9r0000gn/T/tmp69oNhW/jobfiles/samtools_stats_out2.tab\\nbase.twilltestcase: INFO: ## files diff on /Users/marten/devel/git/tools-devteam/tool_collections/samtools/samtools_stats/test-data/samtools_stats_out2.tab and /var/folders/2z/ntdb9g2n7tq6_bcq4dj9hj9r0000gn/T/tmp69oNhW/tmp/tmpYr1M8Csamtools_stats_out2.tab lines_diff=2, found diff = 4\\n--------------------- >> end captured logging << ---------------------\\n", "problem_type": "functional.test_toolbox.JobOutputsError"}, "id": "functional.test_toolbox.TestForTool_samtools_stats.test_tool_000001", "has_data": true}], "version": "0.1", "summary": {"num_skips": 0, "num_errors": 0, "num_failures": 2, "num_tests": 2}};\n+ renderTestResults(test_data);\n+ }\n+ </script>\n+ </body>\n+</html>\n'

diff -r 000000000000 -r 0d71d9467847 test-data/phiX.bam

Binary file test-data/phiX.bam has changed

diff -r 000000000000 -r 0d71d9467847 test-data/samtools_stats_input.bam

Binary file test-data/samtools_stats_input.bam has changed

diff -r 000000000000 -r 0d71d9467847 test-data/samtools_stats_out1.tab
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/samtools_stats_out1.tab Wed Apr 22 10:29:35 2015 -0400

[

b'@@ -0,0 +1,1137 @@\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+# 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+# Summary Numbers. Use `grep ^SN | cut -f 2-` to extract this part.\n+SN\traw total sequences:\t200\n+SN\tfiltered sequences:\t0\n+SN\tsequences:\t200\n+SN\tis sorted:\t1\n+SN\t1st fragments:\t100\n+SN\tlast fragments:\t100\n+SN\treads mapped:\t25\n+SN\treads mapped and paired:\t0\t# paired-end technology bit set + both mates mapped\n+SN\treads unmapped:\t175\n+SN\treads properly paired:\t0\t# proper-pair bit set\n+SN\treads paired:\t200\t# paired-end technology bit set\n+SN\treads duplicated:\t0\t# PCR or optical duplicate bit set\n+SN\treads MQ0:\t6\t# mapped and MQ=0\n+SN\treads QC failed:\t0\n+SN\tnon-primary alignments:\t0\n+SN\ttotal length:\t50200\t# ignores clipping\n+SN\tbases mapped:\t6275\t# ignores clipping\n+SN\tbases mapped (cigar):\t6275\t# more accurate\n+SN\tbases trimmed:\t0\n+SN\tbases duplicated:\t0\n+SN\tmismatches:\t591\t# from NM fields\n+SN\terror rate:\t9.418327e-02\t# mismatches / bases mapped (cigar)\n+SN\taverage length:\t251\n+SN\tmaximum length:\t251\n+SN\taverage quality:\t34.7\n+SN\tinsert size average:\t0.0\n+SN\tinsert size standard deviation:\t0.0\n+SN\tinward oriented pairs:\t0\n+SN\toutward oriented pairs:\t0\n+SN\tpairs with other orientation:\t0\n+SN\tpairs on different chromosomes:\t0\n+# First Fragment Qualitites. Use `grep ^FFQ | cut -f 2-` to extract this part.\n+# Columns correspond to qualities and rows to cycles. First column is the cycle number.\n+FFQ\t1\t0\t0\t2\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t0\t1\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t3\t2\t0\t20\t38\t32\t1\t0\t0\t0\t0\t0\t0\n+FFQ\t2\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t3\t0\t0\t18\t36\t36\t6\t0\t0\t0\t0\t0\t0\n+FFQ\t3\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t2\t1\t0\t14\t31\t46\t5\t0\t0\t0\t0\t0\t0\n+FFQ\t4\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t1\t0\t8\t36\t42\t11\t0\t0\t0\t0\t0\t0\n+FFQ\t5\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t0\t2\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t0\t0\t12\t35\t43\t6\t0\t0\t0\t0\t0\t0\n+FFQ\t6\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t0\t0\t2\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t7\t8\t0\t0\t81\t0\t0\t0\t0\n+FFQ\t7\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t9\t13\t1\t0\t76\t0\t0\t0\t0\n+FFQ\t8\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t0\t11\t15\t4\t0\t69\t0\t0\t0\t0\n+FFQ\t9\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t0\t0\t1\t6\t20\t3\t0\t68\t0\t0\t0\t0\n+FFQ\t10\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t7\t11\t5\t0\t75\t0\t0\t0\t0\n+FFQ\t11\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t6\t16\t6\t0\t70\t0\t0\t0\t0\n+FFQ\t12\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t0\t0\t0\t2\t8\t2\t0\t86\t0\t0\t0\t0\n+FFQ\t13\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t0\t0\t1\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t3\t3\t92\t0\t0\t0\n+FFQ\t14\t0\t0\t1\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t2\t2\t2\t1\t0\t3\t89\t0\t0\t0\n+FFQ\t15\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t0\t0\t1\t2\t4\t91\t0\t0\t0\n+FFQ\t16\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t0\t0\t0\t0\t2\t96\t0\t0\t0\n+FFQ\t17\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t1\t0\t0\t3\t94\t0\t0\t0\n+FFQ\t18\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t2\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t0\t2\t0\t0\t2\t93\t0\t0\t0\n+FFQ\t19\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t0\t1\t4\t93\t0\t0\t0\n+FFQ\t20\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t0\t0\t2\t1\t4\t91\t0\t0\t0\n+FFQ\t21\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t2\t0\t0\t3\t94\t0\t0\t0\n+FFQ\t22\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t0\t1\t97\t0\t0\t0\n+FFQ\t23\t0\t0\t1\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t0\t1\t4\t18\t74'..b'.50\n+GCC\t174\t17.50\t23.50\t33.50\t25.50\n+GCC\t175\t33.50\t17.50\t35.50\t13.50\n+GCC\t176\t16.50\t32.50\t28.50\t22.50\n+GCC\t177\t19.00\t22.00\t27.00\t32.00\n+GCC\t178\t16.00\t26.00\t30.00\t28.00\n+GCC\t179\t18.00\t18.00\t22.00\t42.00\n+GCC\t180\t21.00\t22.00\t34.00\t23.00\n+GCC\t181\t20.50\t19.50\t35.50\t24.50\n+GCC\t182\t32.50\t18.50\t22.50\t26.50\n+GCC\t183\t24.50\t13.50\t28.50\t33.50\n+GCC\t184\t15.00\t29.00\t30.00\t26.00\n+GCC\t185\t15.00\t32.00\t33.00\t20.00\n+GCC\t186\t22.50\t23.50\t34.50\t19.50\n+GCC\t187\t19.00\t14.00\t40.00\t27.00\n+GCC\t188\t27.50\t21.50\t27.50\t23.50\n+GCC\t189\t17.00\t22.00\t34.00\t27.00\n+GCC\t190\t23.00\t30.00\t23.00\t24.00\n+GCC\t191\t25.00\t22.00\t28.00\t25.00\n+GCC\t192\t34.50\t24.50\t13.50\t27.50\n+GCC\t193\t18.50\t25.50\t25.50\t30.50\n+GCC\t194\t18.50\t33.50\t24.50\t23.50\n+GCC\t195\t16.00\t26.00\t23.00\t35.00\n+GCC\t196\t21.50\t25.50\t24.50\t28.50\n+GCC\t197\t20.00\t21.00\t23.00\t36.00\n+GCC\t198\t17.00\t21.00\t37.00\t25.00\n+GCC\t199\t20.50\t18.50\t25.50\t35.50\n+GCC\t200\t21.00\t29.00\t21.00\t29.00\n+GCC\t201\t27.00\t21.00\t23.00\t29.00\n+GCC\t202\t21.50\t24.50\t19.50\t34.50\n+GCC\t203\t21.50\t24.50\t26.50\t27.50\n+GCC\t204\t27.00\t29.00\t24.00\t20.00\n+GCC\t205\t19.50\t21.50\t22.50\t36.50\n+GCC\t206\t26.50\t24.50\t21.50\t27.50\n+GCC\t207\t22.50\t21.50\t19.50\t36.50\n+GCC\t208\t14.00\t35.00\t29.00\t22.00\n+GCC\t209\t16.00\t23.00\t12.00\t49.00\n+GCC\t210\t18.50\t19.50\t40.50\t21.50\n+GCC\t211\t26.00\t20.00\t22.00\t32.00\n+GCC\t212\t21.00\t31.00\t18.00\t30.00\n+GCC\t213\t24.00\t15.00\t31.00\t30.00\n+GCC\t214\t17.50\t24.50\t25.50\t32.50\n+GCC\t215\t26.00\t24.00\t23.00\t27.00\n+GCC\t216\t21.50\t17.50\t25.50\t35.50\n+GCC\t217\t26.00\t29.00\t17.00\t28.00\n+GCC\t218\t20.00\t27.00\t21.00\t32.00\n+GCC\t219\t17.00\t21.00\t21.00\t41.00\n+GCC\t220\t25.50\t23.50\t23.50\t27.50\n+GCC\t221\t21.50\t23.50\t20.50\t34.50\n+GCC\t222\t21.50\t21.50\t18.50\t38.50\n+GCC\t223\t20.00\t27.00\t28.00\t25.00\n+GCC\t224\t22.50\t22.50\t24.50\t30.50\n+GCC\t225\t14.50\t35.50\t30.50\t19.50\n+GCC\t226\t20.00\t23.00\t26.00\t31.00\n+GCC\t227\t20.50\t24.50\t23.50\t31.50\n+GCC\t228\t33.00\t19.00\t26.00\t22.00\n+GCC\t229\t22.50\t24.50\t18.50\t34.50\n+GCC\t230\t21.00\t32.00\t16.00\t31.00\n+GCC\t231\t23.00\t28.00\t30.00\t19.00\n+GCC\t232\t23.50\t21.50\t12.50\t42.50\n+GCC\t233\t21.00\t27.00\t25.00\t27.00\n+GCC\t234\t16.50\t27.50\t22.50\t33.50\n+GCC\t235\t20.00\t15.00\t28.00\t37.00\n+GCC\t236\t28.00\t23.00\t21.00\t28.00\n+GCC\t237\t20.50\t19.50\t22.50\t37.50\n+GCC\t238\t21.50\t29.50\t24.50\t24.50\n+GCC\t239\t20.00\t8.00\t17.00\t55.00\n+GCC\t240\t28.00\t24.00\t16.00\t32.00\n+GCC\t241\t22.50\t22.50\t16.50\t38.50\n+GCC\t242\t29.00\t25.00\t13.00\t33.00\n+GCC\t243\t22.50\t15.50\t23.50\t38.50\n+GCC\t244\t20.50\t23.50\t16.50\t39.50\n+GCC\t245\t28.00\t23.00\t19.00\t30.00\n+GCC\t246\t21.00\t29.00\t25.00\t25.00\n+GCC\t247\t32.00\t14.00\t13.00\t41.00\n+GCC\t248\t18.00\t18.00\t25.00\t39.00\n+GCC\t249\t25.00\t23.00\t21.00\t31.00\n+GCC\t250\t27.50\t22.50\t17.50\t32.50\n+GCC\t251\t13.50\t20.50\t36.50\t29.50\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+# Indel distribution. Use `grep ^ID | cut -f 2-` to extract this part. The columns are: length, number of insertions, number of deletions\n+ID\t1\t1\t0\n+ID\t2\t1\t0\n+ID\t4\t2\t0\n+ID\t10\t5\t0\n+ID\t13\t1\t0\n+ID\t14\t1\t0\n+ID\t15\t1\t0\n+ID\t18\t1\t0\n+ID\t21\t1\t0\n+ID\t22\t1\t0\n+ID\t23\t2\t0\n+ID\t24\t3\t0\n+ID\t29\t1\t0\n+ID\t35\t2\t0\n+ID\t38\t2\t0\n+# Indels per cycle. Use `grep ^IC | cut -f 2-` to extract this part. The columns are: cycle, number of insertions (fwd), .. (rev) , number of deletions (fwd), .. (rev)\n+IC\t2\t1\t0\t0\t0\n+IC\t4\t2\t0\t0\t0\n+IC\t5\t3\t0\t0\t0\n+IC\t210\t2\t0\t0\t0\n+IC\t219\t1\t0\t0\t0\n+IC\t220\t1\t0\t0\t0\n+IC\t224\t2\t0\t0\t0\n+IC\t225\t2\t0\t0\t0\n+IC\t226\t1\t0\t0\t0\n+IC\t228\t1\t0\t0\t0\n+IC\t230\t1\t0\t0\t0\n+IC\t233\t1\t0\t0\t0\n+IC\t234\t1\t0\t0\t0\n+IC\t235\t1\t0\t0\t0\n+IC\t236\t1\t0\t0\t0\n+IC\t239\t1\t0\t0\t0\n+IC\t240\t1\t0\t0\t0\n+IC\t241\t1\t0\t0\t0\n+IC\t247\t1\t0\t0\t0\n+# Coverage distribution. Use `grep ^COV | cut -f 2-` to extract this part.\n+COV\t[1-1]\t1\t1\n+COV\t[7-7]\t7\t1\n+COV\t[18-18]\t18\t1\n+COV\t[24-24]\t24\t1\n+COV\t[25-25]\t25\t249\n+# GC-depth. Use `grep ^GCD | cut -f 2-` to extract this part. The columns are: GC%, unique sequence percentiles, 10th, 25th, 50th, 75th and 90th depth percentile\n+GCD\t0.0\t100.000\t0.000\t0.000\t0.000\t0.000\t0.000\n'

diff -r 000000000000 -r 0d71d9467847 test-data/samtools_stats_out2.tab
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/samtools_stats_out2.tab Wed Apr 22 10:29:35 2015 -0400

[

diff -r 000000000000 -r 0d71d9467847 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 Wed Apr 22 10:29:35 2015 -0400

@@ -0,0 +1,252 @@
+# 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
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diff -r 000000000000 -r 0d71d9467847 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 Wed Apr 22 10:29:35 2015 -0400

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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diff -r 000000000000 -r 0d71d9467847 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 Wed Apr 22 10:29:35 2015 -0400

@@ -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

diff -r 000000000000 -r 0d71d9467847 test-data/samtools_stats_ref.fa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/samtools_stats_ref.fa Wed Apr 22 10:29:35 2015 -0400

b'@@ -0,0 +1,239 @@\n+>chrM\n+GATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGG\n+GTATGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTC\n+CTGCCTCATCCTATTATTTATCGCACCTACGTTCAATATTACAGGCGAACATACTTACTAAAGTGTGTTA\n+ATTAATTAATGCTTGTAGGACATAATAATAACAATTGAATGTCTGCACAGCCACTTTCCACACAGACATC\n+ATAACAAAAAATTTCCACCAAACCCCCCCTCCCCCGCTTCTGGCCACAGCACTTAAACACATCTCTGCCA\n+AACCCCAAAAACAAAGAACCCTAACACCAGCCTAACCAGATTTCAAATTTTATCTTTTGGCGGTATGCAC\n+TTTTAACAGTCACCCCCCAACTAACACATTATTTTCCCCTCCCACTCCCATACTACTAATCTCATCAATA\n+CAACCCCCGCCCATCCTACCCAGCACACACACACCGCTGCTAACCCCATACCCCGAACCAACCAAACCCC\n+AAAGACACCCCCCACAGTTTATGTAGCTTACCTCCTCAAAGCAATACACTGAAAATGTTTAGACGGGCTC\n+ACATCACCCCATAAACAAATAGGTTTGGTCCTAGCCTTTCTATTAGCTCTTAGTAAGATTACACATGCAA\n+GCATCCCCGTTCCAGTGAGTTCACCCTCTAAATCACCACGATCAAAAGGAACAAGCATCAAGCACGCAGC\n+AATGCAGCTCAAAACGCTTAGCCTAGCCACACCCCCACGGGAAACAGCAGTGATTAACCTTTAGCAATAA\n+ACGAAAGTTTAACTAAGCTATACTAACCCCAGGGTTGGTCAATTTCGTGCCAGCCACCGCGGTCACACGA\n+TTAACCCAAGTCAATAGAAGCCGGCGTAAAGAGTGTTTTAGATCACCCCCTCCCCAATAAAGCTAAAACT\n+CACCTGAGTTGTAAAAAACTCCAGTTGACACAAAATAGACTACGAAAGTGGCTTTAACATATCTGAACAC\n+ACAATAGCTAAGACCCAAACTGGGATTAGATACCCCACTATGCTTAGCCCTAAACCTCAACAGTTAAATC\n+AACAAAACTGCTCGCCAGAACACTACGAGCCACAGCTTAAAACTCAAAGGACCTGGCGGTGCTTCATATC\n+CCTCTAGAGGAGCCTGTTCTGTAATCGATAAACCCCGATCAACCTCACCACCTCTTGCTCAGCCTATATA\n+CCGCCATCTTCAGCAAACCCTGATGAAGGCTACAAAGTAAGCGCAAGTACCCACGTAAAGACGTTAGGTC\n+AAGGTGTAGCCCATGAGGTGGCAAGAAATGGGCTACATTTTCTACCCCAGAAAACTACGATAGCCCTTAT\n+GAAACTTAAGGGTCGAAGGTGGATTTAGCAGTAAACTAAGAGTAGAGTGCTTAGTTGAACAGGGCCCTGA\n+AGCGCGTACACACCGCCCGTCACCCTCCTCAAGTATACTTCAAAGGACATTTAACTAAAACCCCTACGCA\n+TTTATATAGAGGAGACAAGTCGTAACATGGTAAGTGTACTGGAAAGTGCACTTGGACGAACCAGAGTGTA\n+GCTTAACACAAAGCACCCAACTTACACTTAGGAGATTTCAACTTAACTTGACCGCTCTGAGCTAAACCTA\n+GCCCCAAACCCACTCCACCTTACTACCAGACAACCTTAGCCAAACCATTTACCCAAATAAAGTATAGGCG\n+ATAGAAATTGAAACCTGGCGCAATAGATATAGTACCGCAAGGGAAAGATGAAAAATTATAACCAAGCATA\n+ATATAGCAAGGACTAACCCCTATACCTTCTGCATAATGAATTAACTAGAAATAACTTTGCAAGGAGAGCC\n+AAAGCTAAGACCCCCGAAACCAGACGAGCTACCTAAGAACAGCTAAAAGAGCACACCCGTCTATGTAGCA\n+AAATAGTGGGAAGATTTATAGGTAGAGGCGACAAACCTACCGAGCCTGGTGATAGCTGGTTGTCCAAGAT\n+AGAATCTTAGTTCAACTTTAAATTTGCCCACAGAACCCTCTAAATCCCCTTGTAAATTTAACTGTTAGTC\n+CAAAGAGGAACAGCTCTTTGGACACTAGGAAAAAACCTTGTAGAGAGAGTAAAAAATTTAACACCCATAG\n+TAGGCCTAAAAGCAGCCACCAATTAAGAAAGCGTTCAAGCTCAACACCCACTACCTAAAAAATCCCAAAC\n+ATATAACTGAACTCCTCACACCCAATTGGACCAATCTATCACCCTATAGAAGAACTAATGTTAGTATAAG\n+TAACATGAAAACATTCTCCTCCGCATAAGCCTGCGTCAGATTAAAACACTGAACTGACAATTAACAGCCC\n+AATATCTACAATCAACCAACAAGTCATTATTACCCTCACTGTCAACCCAACACAGGCATGCTCATAAGGA\n+AAGGTTAAAAAAAGTAAAAGGAACTCGGCAAATCTTACCCCGCCTGTTTACCAAAAACATCACCTCTAGC\n+ATCACCAGTATTAGAGGCACCGCCTGCCCAGTGACACATGTTTAACGGCCGCGGTACCCTAACCGTGCAA\n+AGGTAGCATAATCACTTGTTCCTTAAATAGGGACCTGTATGAATGGCTCCACGAGGGTTCAGCTGTCTCT\n+TACTTTTAACCAGTGAAATTGACCTGCCCGTGAAGAGGCGGGCATAACACAGCAAGACGAGAAGACCCTA\n+TGGAGCTTTAATTTATTAATGCAAACAGTACCTAACAAACCCACAGGTCCTAAACTACCAAACCTGCATT\n+AAAAATTTCGGTTGGGGCGACCTCGGAGCAGAACCCAACCTCCGAGCAGTACATGCTAAGACTTCACCAG\n+TCAAAGCGAACTACTATACTCAATTGATCCAATAACTTGACCAACGGAACAAGTTACCCTAGGGATAACA\n+GCGCAATCCTATTCTAGAGTCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCG\n+ATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCTACGTGATCTGAGTTCAGACCGG\n+AGTAATCCAGGTCGGTTTCTATCTACNTTCAAATTCCTCCCTGTACGAAAGGACAAGAGAAATAAGGCCT\n+ACTTCACAAAGCGCCTTCCCCCGTAAATGATATCATCTCAACTTAGTATTATACCCACACCCACCCAAGA\n+ACAGGGTTTGTTAAGATGGCAGAGCCCGGTAATCGCATAAAACTTAAAACTTTACAGTCAGAGGTTCAAT\n+TCCTCTTCTTAACAACATACCCATGGCCAACCTCCTACTCCTCATTGTACCCATTCTAATCGCAATGGCA\n+TTCCTAATGCTTACCGAACGAAAAATTCTAGGCTATATACAACTACGCAAAGGCCCCAACGTTGTAGGCC\n+CCTACGGGCTACTACAACCCTTCGCTGACGCCATAAAACTCTTCACCAAAGAGCCCCTAAAACCCGCCAC\n+ATCTACCATCACCCTCTACATCACCGCCCCGACCTTAGCTCTCACCATCGCTCTTCTACTATGAACCCCC\n+CTCCCCATACCCAACCCCCTGGTCAACCTCAACCTAGGCCTCCTATTTATTCTAGCCACCTCTAGCCTAG\n+CCGTTTACTCAATCCTCTGATCAGGGTGAGCATCAAACTCAAACTACGCCCTGATCGGCGCACTGCGAGC\n+AGTAGCCCAAACAATCTCATATGAAGTCACCCTAGCCATCATTCTACTATCAACATTACTAATAAGTGGC\n+TCCTTTAACCTCTCCACCCTTATCACAACACAAGAACACCTCTGATTACTCCTGCCATCATGACCCTTGG\n+CCATAATATGATT'..b'GTTCTTCAAATATCTACTCATCTTCCTAATTACCATACTAATCTTAGTTACCGCTAA\n+CAACCTATTCCAACTGTTCATCGGCTGAGAGGGCGTAGGAATTATATCCTTCTTGCTCATCAGTTGATGA\n+TACGCCCGAGCAGATGCCAACACAGCAGCCATTCAAGCAATCCTATACAACCGTATCGGCGATATCGGTT\n+TCATCCTCGCCTTAGCATGATTTATCCTACACTCCAACTCATGAGACCCACAACAAATAGCCCTTCTAAA\n+CGCTAATCCAAGCCTCACCCCACTACTAGGCCTCCTCCTAGCAGCAGCAGGCAAATCAGCCCAATTAGGT\n+CTCCACCCCTGACTCCCCTCAGCCATAGAAGGCCCCACCCCAGTCTCAGCCCTACTCCACTCAAGCACTA\n+TAGTTGTAGCAGGAATCTTCTTACTCATCCGCTTCCACCCCCTAGCAGAAAATAGCCCACTAATCCAAAC\n+TCTAACACTATGCTTAGGCGCTATCACCACTCTGTTCGCAGCAGTCTGCGCCCTTACACAAAATGACATC\n+AAAAAAATCGTAGCCTTCTCCACTTCAAGTCAACTAGGACTCATAATAGTTACAATCGGCATCAACCAAC\n+CACACCTAGCATTCCTGCACATCTGTACCCACGCCTTCTTCAAAGCCATACTATTTATGTGCTCCGGGTC\n+CATCATCCACAACCTTAACAATGAACAAGATATTCGAAAAATAGGAGGACTACTCAAAACCATACCTCTC\n+ACTTCAACCTCCCTCACCATTGGCAGCCTAGCATTAGCAGGAATACCTTTCCTCACAGGTTTCTACTCCA\n+AAGACCACATCATCGAAACCGCAAACATATCATACACAAACGCCTGAGCCCTATCTATTACTCTCATCGC\n+TACCTCCCTGACAAGCGCCTATAGCACTCGAATAATTCTTCTCACCCTAACAGGTCAACCTCGCTTCCCC\n+ACCCTTACTAACATTAACGAAAATAACCCCACCCTACTAAACCCCATTAAACGCCTGGCAGCCGGAAGCC\n+TATTCGCAGGATTTCTCATTACTAACAACATTTCCCCCGCATCCCCCTTCCAAACAACAATCCCCCTCTA\n+CCTAAAACTCACAGCCCTCGCTGTCACTTTCCTAGGACTTCTAACAGCCCTAGACCTCAACTACCTAACC\n+AACAAACTTAAAATAAAATCCCCACTATGCACATTTTATTTCTCCAACATACTCGGATTCTACCCTAGCA\n+TCACACACCGCACAATCCCCTATCTAGGCCTTCTTACGAGCCAAAACCTGCCCCTACTCCTCCTAGACCT\n+AACCTGACTAGAAAAGCTATTACCTAAAACAATTTCACAGCACCAAATCTCCACCTCCATCATCACCTCA\n+ACCCAAAAAGGCATAATTAAACTTTACTTCCTCTCTTTCTTCTTCCCACTCATCCTAACCCTACTCCTAA\n+TCACATAACCTATTCCCCCGAGCAATCTCAATTACAATATATACACCAACAAACAATGTTCAACCAGTAA\n+CTACTACTAATCAACGCCCATAATCATACAAAGCCCCCGCACCAATAGGATCCTCCCGAATCAACCCTGA\n+CCCCTCTCCTTCATAAATTATTCAGCTTCCTACACTATTAAAGTTTACCACAACCACCACCCCATCATAC\n+TCTTTCACCCACAGCACCAATCCTACCTCCATCGCTAACCCCACTAAAACACTCACCAAGACCTCAACCC\n+CTGACCCCCATGCCTCAGGATACTCCTCAATAGCCATCGCTGTAGTATATCCAAAGACAACCATCATTCC\n+CCCTAAATAAATTAAAAAAACTATTAAACCCATATAACCTCCCCCAAAATTCAGAATAATAACACACCCG\n+ACCACACCGCTAACAATCAATACTAAACCCCCATAAATAGGAGAAGGCTTAGAAGAAAACCCCACAAACC\n+CCATTACTAAACCCACACTCAACAGAAACAAAGCATACATCATTATTCTCGCACGGACTACAACCACGAC\n+CAATGATATGAAAAACCATCGTTGTATTTCAACTACAAGAACACCAATGACCCCAATACGCAAAACTAAC\n+CCCCTAATAAAATTAATTAACCACTCATTCATCGACCTCCCCACCCCATCCAACATCTCCGCATGATGAA\n+ACTTCGGCTCACTCCTTGGCGCCTGCCTGATCCTCCAAATCACCACAGGACTATTCCTAGCCATGCACTA\n+CTCACCAGACGCCTCAACCGCCTTTTCATCAATCGCCCACATCACTCGAGACGTAAATTATGGCTGAATC\n+ATCCGCTACCTTCACGCCAATGGCGCCTCAATATTCTTTATCTGCCTCTTCCTACACATCGGGCGAGGCC\n+TATATTACGGATCATTTCTCTACTCAGAAACCTGAAACATCGGCATTATCCTCCTGCTTGCAACTATAGC\n+AACAGCCTTCATAGGCTATGTCCTCCCGTGAGGCCAAATATCATTCTGAGGGGCCACAGTAATTACAAAC\n+TTACTATCCGCCATCCCATACATTGGGACAGACCTAGTTCAATGAATCTGAGGAGGCTACTCAGTAGACA\n+GTCCCACCCTCACACGATTCTTTACCTTTCACTTCATCTTGCCCTTCATTATTGCAGCCCTAGCAACACT\n+CCACCTCCTATTCTTGCACGAAACGGGATCAAACAACCCCCTAGGAATCACCTCCCATTCCGATAAAATC\n+ACCTTCCACCCTTACTACACAATCAAAGACGCCCTCGGCTTACTTCTCTTCCTTCTCTCCTTAATGACAT\n+TAACACTATTCTCACCAGACCTCCTAGGCGACCCAGACAATTATACCCTAGCCAACCCCTTAAACACCCC\n+TCCCCACATCAAGCCCGAATGATATTTCCTATTCGCCTACACAATTCTCCGATCCGTCCCTAACAAACTA\n+GGAGGCGTCCTTGCCCTATTACTATCCATCCTCATCCTAGCAATAATCCCCATCCTCCATATATCCAAAC\n+AACAAAGCATAATATTTCGCCCACTAAGCCAATCACTTTATTGACTCCTAGCCGCAGACCTCCTCATTCT\n+AACCTGAATCGGAGGACAACCAGTAAGCTACCCTTTTACCATCATTGGACAAGTAGCATCCGTACTATAC\n+TTCACAACAATCCTAATCCTAATACCAACTATCTCCCTAATTGAAAACAAAATACTCAAATGGGCCTGTC\n+CTTGTAGTATAAACTAATACACCAGTCTTGTAAACCGGAGATGAAAACCTTTTTCCAAGGACAAATCAGA\n+GAAAAAGTCTTTAACTCCACCATTAGCACCCAAAGCTAAGATTCTAATTTAAACTATTCTCTGTTCTTTC\n+ATGGGGAAGCAGATTTGGGTACCACCCAAGTATTGACTCACCCATCAACAACCGCTATGTATTTCGTACA\n+TTACTGCCAGCCACCATGAATATTGTACGGTACCATAAATACTTGACCACCTGTAGTACATAAAAACCCA\n+ATCCACATCAAAACCCCCTCCCCATGCTTACAAGCAAGTACAGCAATCAACCCTCAACTATCACACATCA\n+ACTGCAACTCCAAAGCCACCCCTCACCCACTAGGATACCAACAAACCTACCCACCCTTAACAGTACATAG\n+TACATAAAGCCATTTACCGTACATAGCACATTACAGTCAAATCCCTTCTCGTCCCCATGGATGACCCCCC\n+TCAGATAGGGGTCCCTTGACCACCATCCTCCGTGAAATCAATATCCCGCACAAGAGTGCTACTCTCCTCG\n+CTCCGGGCCCATAACACTTGGGGGTAGCTAAAGTGAACTGTATCCGACATCTGGTTCCTACTTCAGGGTC\n+ATAAAGCCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATG\n+\n'

diff -r 000000000000 -r 0d71d9467847 tool-data/fasta_indexes.loc.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/fasta_indexes.loc.sample Wed Apr 22 10:29:35 2015 -0400

@@ -0,0 +1,29 @@
+#This is a sample file distributed with Galaxy that enables tools
+#to use a directory of Samtools indexed sequences data files.  You will need
+#to create these data files and then create a fasta_indexes.loc file
+#similar to this one (store it in this directory) that points to
+#the directories in which those files are stored. The fasta_indexes.loc
+#file has this format (white space characters are TAB characters):
+#
+# <unique_build_id> <dbkey> <display_name> <file_base_path>
+#
+#So, for example, if you had hg19 Canonical indexed stored in
+#
+# /depot/data2/galaxy/hg19/sam/,
+#
+#then the fasta_indexes.loc entry would look like this:
+#
+#hg19canon hg19 Human (Homo sapiens): hg19 Canonical /depot/data2/galaxy/hg19/sam/hg19canon.fa
+#
+#and your /depot/data2/galaxy/hg19/sam/ directory
+#would contain hg19canon.fa and hg19canon.fa.fai files.
+#
+#Your fasta_indexes.loc file should include an entry per line for
+#each index set you have stored.  The file in the path does actually
+#exist, but it should never be directly used. Instead, the name serves
+#as a prefix for the index file.  For example:
+#
+#hg18canon hg18 Human (Homo sapiens): hg18 Canonical /depot/data2/galaxy/hg18/sam/hg18canon.fa
+#hg18full hg18 Human (Homo sapiens): hg18 Full /depot/data2/galaxy/hg18/sam/hg18full.fa
+#hg19canon hg19 Human (Homo sapiens): hg19 Canonical /depot/data2/galaxy/hg19/sam/hg19canon.fa
+#hg19full hg19 Human (Homo sapiens): hg19 Full /depot/data2/galaxy/hg19/sam/hg19full.fa

diff -r 000000000000 -r 0d71d9467847 tool_data_table_conf.xml.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample Wed Apr 22 10:29:35 2015 -0400

@@ -0,0 +1,7 @@
+
+<tables>
+    <table name="fasta_indexes" comment_char="#">
+        <columns>value, dbkey, name, path</columns>
+        <file path="tool-data/fasta_indexes.loc" />
+    </table>
+</tables>

diff -r 000000000000 -r 0d71d9467847 tool_dependencies.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml Wed Apr 22 10:29:35 2015 -0400

@@ -0,0 +1,6 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="samtools" version="1.2">
+        <repository changeset_revision="6eea04363026" name="package_samtools_1_2" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
+    </package>
+</tool_dependency>