| Previous changeset 11:e9ebed0c12f6 (2014-02-17) Next changeset 13:2dd40b601766 (2014-06-20) |
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Commit message:
Uploaded |
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added:
test-data/freebayes-phix174-test1.vcf test-data/freebayes-phix174.bam test-data/freebayes-phix174.fasta tool-data/sam_fa_indices.loc.sample tool-data/tool_data_table_conf.xml.sample |
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removed:
freebayes.xml sam_fa_indices.loc.sample test-data/fake_phiX_reads_1.bam test-data/freebayes_out_1.output_trace test-data/freebayes_out_1.vcf.contains test-data/phiX.fasta tool_data_table_conf.xml.sample tool_dependencies.xml |
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| diff -r e9ebed0c12f6 -r aaf568580946 freebayes.xml --- a/freebayes.xml Mon Feb 17 10:53:56 2014 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| b'@@ -1,680 +0,0 @@\n-<?xml version="1.0"?>\n-<tool id="freebayes" name="FreeBayes" version="0.0.3">\n- <requirements>\n- <requirement type="package" version="0.9.6_9608597d12e127c847ae03aa03440ab63992fedf">freebayes</requirement>\n- <requirement type="package" version="0.1.18">samtools</requirement>\n- </requirements>\n- <description> - Bayesian genetic variant detector</description>\n- <command>\n- ##set up input files\n- #set $reference_fasta_filename = "localref.fa"\n- #if str( $reference_source.reference_source_selector ) == "history":\n- ln -s "${reference_source.ref_file}" "${reference_fasta_filename}" &&\n- samtools faidx "${reference_fasta_filename}" 2>&1 || echo "Error running samtools faidx for FreeBayes" >&2 &&\n- #else:\n- #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path )\n- #end if\n- #for $bam_count, $input_bam in enumerate( $reference_source.input_bams ):\n- ln -s "${input_bam.input_bam}" "localbam_${bam_count}.bam" &&\n- ln -s "${input_bam.input_bam.metadata.bam_index}" "localbam_${bam_count}.bam.bai" &&\n- #end for\n- ##finished setting up inputs\n- \n- ##start FreeBayes commandline\n- freebayes\n- #for $bam_count, $input_bam in enumerate( $reference_source.input_bams ):\n- --bam "localbam_${bam_count}.bam"\n- #end for\n- --fasta-reference "${reference_fasta_filename}" \n- \n- ##outputs\n- --vcf "${output_vcf}"\n- \n- ##advanced options\n- #if str( $options_type.options_type_selector ) == "advanced":\n- ##additional outputs\n- #if $options_type.output_trace_option:\n- --trace "${output_trace}"\n- #end if\n- #if $options_type.output_failed_alleles_option:\n- --failed-alleles "${output_failed_alleles_bed}"\n- #end if\n- \n- ##additional inputs\n- #if str( $options_type.target_limit_type.target_limit_type_selector ) == "limit_by_target_file":\n- --targets "${options_type.target_limit_type.input_target_bed}"\n- #elif str( $options_type.target_limit_type.target_limit_type_selector ) == "limit_by_region":\n- --region "${options_type.target_limit_type.region_chromosome}:${options_type.target_limit_type.region_start}..${options_type.target_limit_type.region_end}"\n- #end if\n- #if $options_type.input_sample_file:\n- --samples "${options_type.input_sample_file}"\n- #end if\n- #if $options_type.input_populations_file:\n- --populations "${options_type.input_populations_file}"\n- #end if\n- #if $options_type.input_cnv_map_bed:\n- --cnv-map "${options_type.input_cnv_map_bed}"\n- #end if\n- #if str( $options_type.input_variant_type.input_variant_type_selector ) == "provide_vcf":\n- --variant-input "${options_type.input_variant_type.input_variant_vcf}"\n- ${options_type.input_variant_type.only_use_input_alleles}\n- #end if\n- #if $options_type.haplotype_basis_alleles:\n- --haplotype-basis-alleles "${options_type.haplotype_basis_alleles}"\n- #end if\n- \n- \n- ##reporting\n- #if str( $options_type.section_reporting_type.section_reporting_type_selector ) == "set":\n- --pvar "${options_type.section_reporting_type.pvar}"\n- ${options_type.section_reporting_type.show_reference_repeats}\n- #end if\n- \n- ##population model\n- #if str( $options_type.section_population_model_type.section_population_model_type_selector ) == "set":\n- --theta "${options_type.section_population_model_type.theta}"\n- --ploidy "${options_type.section_population_model_type.ploidy}"\n- ${options_type.section_population_model_type.pooled}\n- #end if\n- \n- ##reference allele\n- #if str( $options_type.use_reference_allele_type.use_reference_allele_type_selector ) == "inclu'..b" to evaluate the position. default: 1\n- -3 --min-alternate-qsum N\n- Require at least this sum of quality of observations supporting\n- an alternate allele within a single individual in order\n- to evaluate the position. default: 0\n- -G --min-alternate-total N\n- Require at least this count of observations supporting\n- an alternate allele within the total population in order\n- to use the allele in analysis. default: 1\n- -! --min-coverage N\n- Require at least this coverage to process a site. default: 0\n-\n- bayesian priors:\n-\n- -Y --no-ewens-priors\n- Turns off the Ewens' Sampling Formula component of the priors.\n- -k --no-population-priors\n- Equivalent to --pooled --no-ewens-priors\n- -w --hwe-priors Use the probability of the combination arising under HWE given\n- the allele frequency as estimated by observation frequency.\n-\n- observation prior expectations:\n-\n- -V --binomial-obs-priors\n- Incorporate expectations about osbervations into the priors,\n- Uses read placement probability, strand balance probability,\n- and read position (5'-3') probability.\n- -a --allele-balance-priors\n- Use aggregate probability of observation balance between alleles\n- as a component of the priors. Best for observations with minimal\n- inherent reference bias.\n-\n- algorithmic features:\n-\n- -M --site-selection-max-iterations N\n- Uses hill-climbing algorithm to search posterior space for N\n- iterations to determine if the site should be evaluated. Set to 0\n- to prevent use of this algorithm for site selection, and\n- to a low integer for improvide site selection at a slight\n- performance penalty. default: 5.\n- -B --genotyping-max-iterations N\n- Iterate no more than N times during genotyping step. default: 25.\n- --genotyping-max-banddepth N\n- Integrate no deeper than the Nth best genotype by likelihood when\n- genotyping. default: 6.\n- -W --posterior-integration-limits N,M\n- Integrate all genotype combinations in our posterior space\n- which include no more than N samples with their Mth best\n- data likelihood. default: 1,3.\n- -K --no-permute\n- Do not scale prior probability of genotype combination given allele\n- frequency by the number of permutations of included genotypes.\n- -N --exclude-unobserved-genotypes\n- Skip sample genotypings for which the sample has no supporting reads.\n- -S --genotype-variant-threshold N\n- Limit posterior integration to samples where the second-best\n- genotype likelihood is no more than log(N) from the highest\n- genotype likelihood for the sample. default: ~unbounded\n- -j --use-mapping-quality\n- Use mapping quality of alleles when calculating data likelihoods.\n- -D --read-dependence-factor N\n- Incorporate non-independence of reads by scaling successive\n- observations by this factor during data likelihood\n- calculations. default: 0.9\n- -= --no-marginals\n- Do not calculate the marginal probability of genotypes. Saves\n- time and improves scaling performance in large populations.\n-\n-\n-------\n-\n-**Citation**\n-\n-For the underlying tool, please cite `Erik Garrison and Gabor Marth. Haplotype-based variant detection from short-read sequencing <http://arxiv.org/abs/1207.3907>`_.\n-\n-If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.*\n-\n- </help>\n-</tool>\n" |
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| diff -r e9ebed0c12f6 -r aaf568580946 sam_fa_indices.loc.sample --- a/sam_fa_indices.loc.sample Mon Feb 17 10:53:56 2014 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,28 +0,0 @@ -#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 sam_fa_indices.loc file -#similar to this one (store it in this directory) that points to -#the directories in which those files are stored. The sam_fa_indices.loc -#file has this format (white space characters are TAB characters): -# -#index <seq> <location> -# -#So, for example, if you had hg18 indexed stored in -#/depot/data2/galaxy/sam/, -#then the sam_fa_indices.loc entry would look like this: -# -#index hg18 /depot/data2/galaxy/sam/hg18.fa -# -#and your /depot/data2/galaxy/sam/ directory -#would contain hg18.fa and hg18.fa.fai files: -# -#-rw-r--r-- 1 james universe 830134 2005-09-13 10:12 hg18.fa -#-rw-r--r-- 1 james universe 527388 2005-09-13 10:12 hg18.fa.fai -# -#Your sam_fa_indices.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: -# -#index hg18 /depot/data2/galaxy/sam/hg18.fa -#index hg19 /depot/data2/galaxy/sam/hg19.fa |
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| diff -r e9ebed0c12f6 -r aaf568580946 test-data/fake_phiX_reads_1.bam |
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| Binary file test-data/fake_phiX_reads_1.bam has changed |
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| diff -r e9ebed0c12f6 -r aaf568580946 test-data/freebayes-phix174-test1.vcf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/freebayes-phix174-test1.vcf Fri Jun 20 17:16:05 2014 -0400 |
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| b'@@ -0,0 +1,27 @@\n+#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tunknown\n+phiX174\t311\t.\tA\tG\t6.48411\t.\tAB=0.222222;ABP=9.04217;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=9;DPB=9;DPRA=0;EPP=7.35324;EPPR=5.80219;GTI=0;LEN=1;MEANALT=1;MQM=25;MQMR=33.5714;NS=1;NUMALT=1;ODDS=1.23853;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=70;QR=478;RO=7;RPP=7.35324;RPPR=3.32051;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=5;SRP=5.80219;SRR=2;TYPE=snp\tGT:DP:RO:QR:AO:QA:GL\t0/1:9:7:478:2:70:-5.49703,0,-10\n+phiX174\t374\t.\tT\tG\t30.6931\t.\tAB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=4;DPB=4;DPRA=0;EPP=7.35324;EPPR=7.35324;GTI=0;LEN=1;MEANALT=1;MQM=37;MQMR=25;NS=1;NUMALT=1;ODDS=7.0665;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=75;QR=141;RO=2;RPP=3.0103;RPPR=7.35324;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=0;SRP=7.35324;SRR=2;TYPE=snp\tGT:DP:RO:QR:AO:QA:GL\t0/1:4:2:141:2:75:-6.69903,0,-10\n+phiX174\t913\t.\tA\tC\t13.1703\t.\tAB=0.4;ABP=3.44459;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=5;DPB=5;DPRA=0;EPP=3.0103;EPPR=3.73412;GTI=0;LEN=1;MEANALT=1;MQM=31;MQMR=29;NS=1;NUMALT=1;ODDS=2.98318;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=58;QR=171;RO=3;RPP=3.0103;RPPR=3.73412;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=3;SRP=9.52472;SRR=0;TYPE=snp\tGT:DP:RO:QR:AO:QA:GL\t0/1:5:3:171:2:58:-5.00485,0,-10\n+phiX174\t1205\t.\tA\tC\t2.30262\t.\tAB=0.2;ABP=10.8276;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=10;DPB=10;DPRA=0;EPP=7.35324;EPPR=7.35324;GTI=0;LEN=1;MEANALT=1;MQM=31;MQMR=34;NS=1;NUMALT=1;ODDS=0.357718;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=67;QR=456;RO=8;RPP=7.35324;RPPR=7.35324;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=2;SRP=7.35324;SRR=6;TYPE=snp\tGT:DP:RO:QR:AO:QA:GL\t0/1:10:8:456:2:67:-5.00791,0,-10\n+phiX174\t1245\t.\tG\tT\t6.48411\t.\tAB=0.222222;ABP=9.04217;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=9;DPB=9;DPRA=0;EPP=7.35324;EPPR=3.32051;GTI=0;LEN=1;MEANALT=1;MQM=31;MQMR=28.4286;NS=1;NUMALT=1;ODDS=1.23853;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=70;QR=389;RO=7;RPP=7.35324;RPPR=3.32051;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=0;SRP=18.2106;SRR=7;TYPE=snp\tGT:DP:RO:QR:AO:QA:GL\t0/1:9:7:389:2:70:-5.49703,0,-10\n+phiX174\t1249\t.\tT\tG\t15.3287\t.\tAB=0.222222;ABP=9.04217;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=9;DPB=9;DPRA=0;EPP=3.0103;EPPR=3.32051;GTI=0;LEN=1;MEANALT=1;MQM=25;MQMR=30.1429;NS=1;NUMALT=1;ODDS=3.4998;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=74;QR=464;RO=7;RPP=3.0103;RPPR=5.80219;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=2;SRP=5.80219;SRR=5;TYPE=snp\tGT:DP:RO:QR:AO:QA:GL\t0/1:9:7:464:2:74:-5.87703,0,-10\n+phiX174\t1445\t.\tC\tA\t24.4745\t.\tAB=0.285714;ABP=5.80219;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=7;DPB=7;DPRA=0;EPP=7.35324;EPPR=6.91895;GTI=0;LEN=1;MEANALT=1;MQM=25;MQMR=32.2;NS=1;NUMALT=1;ODDS=5.63189;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=76;QR=273;RO=5;RPP=3.0103;RPPR=6.91895;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=2;SRP=3.44459;SRR=3;TYPE=snp\tGT:DP:RO:QR:AO:QA:GL\t0/1:7:5:273:2:76:-6.43501,0,-10\n+phiX174\t1577\t.\tA\tC\t4.06305\t.\tAB=0.222222;ABP=9.04217;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=9;DPB=9;DPRA=0;EPP=7.35324;EPPR=3.32051;GTI=0;LEN=1;MEANALT=1;MQM=25;MQMR=35.2857;NS=1;NUMALT=1;ODDS=0.437365;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=60;QR=460;RO=7;RPP=3.0103;RPPR=10.7656;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=4;SRP=3.32051;SRR=3;TYPE=snp\tGT:DP:RO:QR:AO:QA:GL\t0/1:9:7:460:2:60:-4.54703,0,-10\n+phiX174\t1631\t.\tT\tG\t2.719\t.\tAB=0.2;ABP=10.8276;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=10;DPB=10;DPRA=0;EPP=7.35324;EPPR=4.09604;GTI=0;LEN=1;MEANALT=1;MQM=25;MQMR=28;NS=1;NUMALT=1;ODDS=0.138972;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=68;QR=500;RO=8;RPP=7.35324;RPPR=3.0103;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=3;SRP=4.09604;SRR=5;TYPE=snp\tGT:DP:RO:QR:AO:QA:GL\t0/1:10:8:500:2:68:-5.10291,0,-10\n+phiX174\t1772\t.\tT\tG\t2.16317\t.\tAB=0.2;ABP=10.8276;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=10;DPB=10;DPRA=0;EPP=3.0103;EPPR=3.32051;GTI=0;LEN=1;MEANALT=2;MQM=31;MQMR=31.8571;NS=1;NUMALT=1;ODDS=0.437618;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=59;QR=425;RO=7;RPP=3.0103;RPPR=3.32051;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=1;SRP=10.7656;SRR=6;TYPE=snp\tGT:DP:RO:QR:AO:QA:GL\t0/1:10:7:425:2:59:-4.16703'..b'=1;SRP=8.80089;SRR=5;TYPE=snp\tGT:DP:RO:QR:AO:QA:GL\t0/1:8:6:348:2:100:-8.53892,0,-10\n+phiX174\t2983\t.\tT\tG\t12.2712\t.\tAB=0.4;ABP=3.44459;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=5;DPB=5;DPRA=0;EPP=3.0103;EPPR=3.73412;GTI=0;LEN=1;MEANALT=1;MQM=31;MQMR=33;NS=1;NUMALT=1;ODDS=2.76444;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=57;QR=150;RO=3;RPP=3.0103;RPPR=3.73412;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=2;SRP=3.73412;SRR=1;TYPE=snp\tGT:DP:RO:QR:AO:QA:GL\t0/1:5:3:150:2:57:-4.90985,0,-10\n+phiX174\t3110\t.\tT\tC\t34.4848\t.\tAB=0.333333;ABP=5.18177;AC=1;AF=0.5;AN=2;AO=3;CIGAR=1X;DP=9;DPB=9;DPRA=0;EPP=3.73412;EPPR=4.45795;GTI=0;LEN=1;MEANALT=1;MQM=25;MQMR=35;NS=1;NUMALT=1;ODDS=7.94006;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=94;QR=361;RO=6;RPP=9.52472;RPPR=3.0103;RUN=1;SAF=1;SAP=3.73412;SAR=2;SRF=1;SRP=8.80089;SRR=5;TYPE=snp\tGT:DP:RO:QR:AO:QA:GL\t0/1:9:6:361:3:94:-7.98834,0,-10\n+phiX174\t3155\t.\tT\tG\t23.5283\t.\tAB=0.285714;ABP=5.80219;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=7;DPB=7;DPRA=0;EPP=3.0103;EPPR=3.44459;GTI=0;LEN=1;MEANALT=1;MQM=37;MQMR=29.8;NS=1;NUMALT=1;ODDS=5.41314;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=75;QR=299;RO=5;RPP=3.0103;RPPR=3.44459;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=4;SRP=6.91895;SRR=1;TYPE=snp\tGT:DP:RO:QR:AO:QA:GL\t0/1:7:5:299:2:75:-6.34001,0,-10\n+phiX174\t3325\t.\tA\tC\t5.77196\t.\tAB=0.333333;ABP=4.45795;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=6;DPB=6;DPRA=0;EPP=7.35324;EPPR=5.18177;GTI=0;LEN=1;MEANALT=1;MQM=25;MQMR=31;NS=1;NUMALT=1;ODDS=1.02152;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=58;QR=284;RO=4;RPP=7.35324;RPPR=3.0103;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=3;SRP=5.18177;SRR=1;TYPE=snp\tGT:DP:RO:QR:AO:QA:GL\t0/1:6:4:284:2:58:-4.87991,0,-10\n+phiX174\t3418\t.\tA\tC\t0.61163\t.\tAB=0.2;ABP=10.8276;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=10;DPB=10;DPRA=0;EPP=7.35324;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=25;MQMR=34;NS=1;NUMALT=1;ODDS=1.88894;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=60;QR=526;RO=8;RPP=7.35324;RPPR=4.09604;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=5;SRP=4.09604;SRR=3;TYPE=snp\tGT:DP:RO:QR:AO:QA:GL\t0/1:10:8:526:2:60:-4.34291,0,-10\n+phiX174\t3729\t.\tC\tT\t8.03017\t.\tAB=0.333333;ABP=4.45795;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=6;DPB=6;DPRA=0;EPP=7.35324;EPPR=5.18177;GTI=0;LEN=1;MEANALT=1;MQM=31;MQMR=37;NS=1;NUMALT=1;ODDS=1.67776;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=61;QR=232;RO=4;RPP=7.35324;RPPR=5.18177;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=0;SRP=11.6962;SRR=4;TYPE=snp\tGT:DP:RO:QR:AO:QA:GL\t0/1:6:4:232:2:61:-5.16491,0,-10\n+phiX174\t4031\t.\tT\tG\t23.4861\t.\tAB=0.25;ABP=7.35324;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=8;DPB=8;DPRA=0;EPP=7.35324;EPPR=4.45795;GTI=0;LEN=1;MEANALT=1;MQM=31;MQMR=27;NS=1;NUMALT=1;ODDS=5.40338;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=85;QR=322;RO=6;RPP=7.35324;RPPR=8.80089;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=3;SRP=3.0103;SRR=3;TYPE=snp\tGT:DP:RO:QR:AO:QA:GL\t0/1:8:6:322:2:85:-7.11392,0,-10\n+phiX174\t4502\t.\tA\tC\t8.30185\t.\tAB=0.333333;ABP=4.45795;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=6;DPB=6;DPRA=0;EPP=3.0103;EPPR=5.18177;GTI=0;LEN=1;MEANALT=1;MQM=25;MQMR=37;NS=1;NUMALT=1;ODDS=1.75158;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=55;QR=284;RO=4;RPP=3.0103;RPPR=11.6962;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=3;SRP=5.18177;SRR=1;TYPE=snp\tGT:DP:RO:QR:AO:QA:GL\t0/1:6:4:284:2:55:-4.59491,0,-10\n+phiX174\t4558\t.\tC\tG\t6.48999\t.\tAB=0.333333;ABP=4.45795;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=6;DPB=6;DPRA=0;EPP=7.35324;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=25;MQMR=28;NS=1;NUMALT=1;ODDS=1.24027;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=59;QR=204;RO=4;RPP=7.35324;RPPR=11.6962;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=2;SRP=3.0103;SRR=2;TYPE=snp\tGT:DP:RO:QR:AO:QA:GL\t0/1:6:4:204:2:59:-4.97491,0,-10\n+phiX174\t4655\t.\tT\tG\t21.8853\t.\tAB=0.333333;ABP=4.45795;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=6;DPB=6;DPRA=0;EPP=3.0103;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=25;MQMR=37;NS=1;NUMALT=1;ODDS=5.03277;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=70;QR=193;RO=4;RPP=3.0103;RPPR=3.0103;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=0;SRP=11.6962;SRR=4;TYPE=snp\tGT:DP:RO:QR:AO:QA:GL\t0/1:6:4:193:2:70:-6.01991,0,-10\n' |
| b |
| diff -r e9ebed0c12f6 -r aaf568580946 test-data/freebayes-phix174.bam |
| b |
| Binary file test-data/freebayes-phix174.bam has changed |
| b |
| diff -r e9ebed0c12f6 -r aaf568580946 test-data/freebayes-phix174.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/freebayes-phix174.fasta Fri Jun 20 17:16:05 2014 -0400 |
| b |
| @@ -0,0 +1,2 @@ +>phiX174 +GAGTTTTATCGCTTCCATGACGCAGAAGTTAACACTTTCGGATATTTCTGATGAGTCGAAAAATTATCTTGATAAAGCAGGAATTACTACTGCTTGTTTACGAATTAAATCGAAGTGGACTGCTGGCGGAAAATGAGAAAATTCGACCTATCCTTGCGCAGCTCGAGAAGCTCTTACTTTGCGACCTTTCGCCATCAACTAACGATTCTGTCAAAAACTGACGCGTTGGATGAGGAGAAGTGGCTTAATATGCTTGGCACGTTCGTCAAGGACTGGTTTAGATATGAGTCACATTTTGTTCATGGTAGAGATTCTCTTGTTGACATTTTAAAAGAGCGTGGATTACTATCTGAGTCCGATGCTGTTCAACCACTAATAGGTAAGAAATCATGAGTCAAGTTACTGAACAATCCGTACGTTTCCAGACCGCTTTGGCCTCTATTAAGCTCATTCAGGCTTCTGCCGTTTTGGATTTAACCGAAGATGATTTCGATTTTCTGACGAGTAACAAAGTTTGGATTGCTACTGACCGCTCTCGTGCTCGTCGCTGCGTTGAGGCTTGCGTTTATGGTACGCTGGACTTTGTGGGATACCCTCGCTTTCCTGCTCCTGTTGAGTTTATTGCTGCCGTCATTGCTTATTATGTTCATCCCGTCAACATTCAAACGGCCTGTCTCATCATGGAAGGCGCTGAATTTACGGAAAACATTATTAATGGCGTCGAGCGTCCGGTTAAAGCCGCTGAATTGTTCGCGTTTACCTTGCGTGTACGCGCAGGAAACACTGACGTTCTTACTGACGCAGAAGAAAACGTGCGTCAAAAATTACGTGCaGAAGGAGTGATGTAATGTCTAAAGGTAAAAAACGTTCTGGCGCTCGCCCTGGTCGTCCGCAGCCGTTGCGAGGTACTAAAGGCAAGCGTAAAGGCGCTCGTCTTTGGTATGTAGGTGGTCAACAATTTTAATTGCAGGGGCTTCGGCCCCTTACTTGAGGATAAATTATGTCTAATATTCAAACTGGCGCCGAGCGTATGCCGCATGACCTTTCCCATCTTGGCTTCCTTGCTGGTCAGATTGGTCGTCTTATTACCATTTCAACTACTCCGGTTATCGCTGGCGACTCCTTCGAGATGGACGCCGTTGGCGCTCTCCGTCTTTCTCCATTGCGTCGTGGCCTTGCTATTGACTCTACTGTAGACATTTTTACTTTTTATGTCCCTCATCGTCACGTTTATGGTGAACAGTGGATTAAGTTCATGAAGGATGGTGTTAATGCCACTCCTCTCCCGACTGTTAACACTACTGGTTATATTGACCATGCCGCTTTTCTTGGCACGATTAACCCTGATACCAATAAAATCCCTAAGCATTTGTTTCAGGGTTATTTGAATATCTATAACAACTATTTTAAAGCGCCGTGGATGCCTGACCGTACCGAGGCTAACCCTAATGAGCTTAATCAAGATGATGCTCGTTATGGTTTCCGTTGCTGCCATCTCAAAAACATTTGGACTGCTCCGCTTCCTCCTGAGACTGAGCTTTCTCGCCAAATGACGACTTCTACCACATCTATTGACATTATGGGTCTGCAAGCTGCTTATGCTAATTTGCATACTGACCAAGAACGTGATTACTTCATGCAGCGTTACCgTGATGTTATTTCTTCATTTGGAGGTAAAACCTCTTATGACGCTGACAACCGTCCTTTACTTGTCATGCGCTCTAATCTCTGGGCATCTGGCTATGATGTTGATGGAACTGACCAAACGTCGTTAGGCCAGTTTTCTGGTCGTGTTCAACAGACCTATAAACATTCTGTGCCGCGTTTCTTTGTTCCTGAGCATGGCACTATGTTTACTCTTGCGCTTGTTCGTTTTCCGCCTACTGCGACTAAAGAGATTCAGTACCTTAACGCTAAAGGTGCTTTGACTTATACCGATATTGCTGGCGACCCTGTTTTGTATGGCAACTTGCCGCCGCGTGAAATTTCTATGAAGGATGTTTTCCGTTCTGGTGATTCGTCTAAGAAGTTTAAGATTGCTGAGGGTCAGTGGTATCGTTATGCGCCTTCGTATGTTTCTCCTGCTTATCACCTTCTTGAAGGCTTCCCATTCATTCAGGAACCGCCTTCTGGTGATTTGCAAGAACGCGTACTTATTCGCCACCATGATTATGACCAGTGTTTCCAGTCCGTTCAGTTGTTGCAGTGGAATAGTCAGGTTAAATTTAATGTGACCGTTTATCGCAATCTGCCGACCACTCGCGATTCAATCATGACTTCGTGATAAAAGATTGAGTGTGAGGTTATAACGCCGAAGCGGTAAAAATTTTAATTTTTGCCGCTGAGGGGTTGACCAAGCGAAGCGCGGTAGGTTTTCTGCTTAGGAGTTTAATCATGTTTCAGACTTTTATTTCTCGCCATAATTCAAACTTTTTTTCTGATAAGCTGGTTCTCACTTCTGTTACTCCAGCTTCTTCGGCACCTGTTTTACAGACACCTAAAGCTACATCGTCAACGTTATATTTTGATAGTTTGACGGTTAATGCTGGTAATGGTGGTTTTCTTCATTGCATTCAGATGGATACATCTGTCAACGCCGCTAATCAGGTTGTTTCTGTTGGTGCTGATATTGCTTTTGATGCCGACCCTAAATTTTTTGCCTGTTTGGTTCGCTTTGAGTCTTCTTCGGTTCCGACTACCCTCCCGACTGCCTATGATGTTTATCCTTTGAATGGTCGCCATGATGGTGGTTATTATACCGTCAAGGACTGTGTGACTATTGACGTCCTTCCCCGTACGCCGGGCAATAAtGTTTATGTTGGTTTCATGGTTTGGTCTAACTTTACCGCTACTAAATGCCGCGGATTGGTTTCGCTGAATCAGGTTATTAAAGAGATTATTTGTCTCCAGCCACTTAAGTGAGGTGATTTATGTTTGGTGCTATTGCTGGCGGTATTGCTTCTGCTCTTGCTGGTGGCGCCATGTCTAAATTGTTTGGAGGCGGTCAAAAAGCCGCCTCCGGTGGCATTCAAGGTGATGTGCTTGCTACCGATAACAATACTGTAGGCATGGGTGATGCTGGTATTAAATCTGCCATTCAAGGCTCTAATGTTCCTAACCCTGATGAGGCCGCCCCTAGTTTTGTTTCTGGTGCTATGGCTAAAGCTGGTAAAGGACTTCTTGAAGGTACGTTGCAGGCTGGCACTTCTGCCGTTTCTGATAAGTTGCTTGATTTGGTTGGACTTGGTGGCAAGTCTGCCGCTGATAAAGGAAAGGATACTCGTGATTATCTTGCTGCTGCATTTCCTGAGCTTAATGCTTGGGAGCGTGCTGGTGCTGATGCTTCCTCTGCTGGTATGGTTGACGCCGGATTTGAGAATCAAAAAGAGCTTACTAAAATGCAACTGGACAATCAGAAAGAGATTGCCGAGATGCAAAATGAGACTCAAAAAGAGATTGCTGGCATTCAGTCGGCGACTTCACGCCAGAATACGAAAGACCAGGTATATGCACAAAATGAGATGCTTGCTTATCAACAGAAGGAGTCTACTGCTCGCGTTGCGTCTATTATGGAAAACACCAATCTTTCCAAGCAACAGCAGGTTTCCGAGATTATGCGCCAAATGCTTACTCAAGCTCAAACGGCTGGTCAGTATTTTACCAATGACCAAATCAAAGAAATGACTCGCAAGGTTAGTGCTGAGGTTGACTTAGTTCATCAGCAAACGCAGAATCAGCGGTATGGCTCTTCTCATATTGGCGCTACTGCAAAGGATATTTCTAATGTCGTCACTGATGCTGCTTCTGGTGTGGTTGATATTTTTCATGGTATTGATAAAGCTGTTGCCGATACTTGGAACAATTTCTGGAAAGACGGTAAAGCTGATGGTATTGGCTCTAATTTGTCTAGGAAATAACCGTCAGGATTGACACCCTCCCAATTGTATGTTTTCATGCCTCCAAATCTTGGAGGCTTTTTTATGGTTCGTTCTTATTACCCTTCTGAATGTCACGCTGATTATTTTGACTTTGAGCGTATCGAGGCTCTTAAACCTGCTATTGAGGCTTGTGGCATTTCTACTCTTTCTCAATCCCCAATGCTTGGCTTCCATAAGCAGATGGATAACCGCATCAAGCTCTTGGAAGAGATTCTGTCTTTTCGTATGCAGGGCGTTGAGTTCGATAATGGTGATATGTATGTTGACGGCCATAAGGCTGCTTCTGACGTTCGTGATGAGTTTGTATCTGTTACTGAGAAGTTAATGGATGAATTGGCACAATGCTACAATGTGCTCCCCCAACTTGATATTAATAACACTATAGACCACCGCCCCGAAGGGGACGAAAAATGGTTTTTAGAGAACGAGAAGACGGTTACGCAGTTTTGCCGCAAGCTGGCTGCTGAACGCCCTCTTAAGGATATTCGCGATGAGTATAATTACCCCAAAAAGAAAGGTATTAAGGATGAGTGTTCAAGATTGCTGGAGGCCTCCACTATGAAATCGCGTAGAGGCTTTaCTATTCAGCGTTTGATGAATGCAATGCGACAGGCTCATGCTGATGGTTGGTTTATCGTTTTTGACACTCTCACGTTGGCTGACGACCGATTAGAGGCGTTTTATGATAATCCCAATGCTTTGCGTGACTATTTTCGTGATATTGGTCGTATGGTTCTTGCTGCCGAGGGTCGCAAGGCTAATGATTCACACGCCGACTGCTATCAGTATTTTTGTGTGCCTGAGTATGGTACAGCTAATGGCCGTCTTCATTTCCATGCGGTGCAtTTTATGCGGACACTTCCTACAGGTAGCGTTGACCCTAATTTTGGTCGTCGGGTACGCAATCGCCGCCAGTTAAATAGCTTGCAAAATACGTGGCCTTATGGTTACAGTATGCCCATCGCAGTTCGCTACACGCAGGACGCTTTTTCACGTTCTGGTTGGTTGTGGCCTGTTGATGCTAAAGGTGAGCCGCTTAAAGCTACCAGTTATATGGCTGTTGGTTTCTATGTGGCTAAATACGTTAACAAAAAGTCAGATATGGACCTTGCTGCTAAAGGTCTAGGAGCTAAAGAATGGAACAACTCACTAAAAACCAAGCTGTCGCTACTTCCCAAGAAGCTGTTCAGAATCAGAATGAGCCGCAACTTCGGGATGAAAATGCTCACAATGACAAATCTGTCCACGGAGTGCTTAATCCAACTTACCAAGCTGGGTTACGACGCGACGCCGTTCAACCAGATATTGAAGCAGAACGCAAAAAGAGAGATGAGATTGAGGCTGGGAAAAGTTACTGTAGCCGACGTTTTGGCGGCGCAACCTGTGACGACAAATCTGCTCAAATTTATGCGCGCTTCGATAAAAATGATTGGCGTATCCAACCTGCA |
| b |
| diff -r e9ebed0c12f6 -r aaf568580946 test-data/freebayes_out_1.output_trace --- a/test-data/freebayes_out_1.output_trace Mon Feb 17 10:53:56 2014 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,8 +0,0 @@ -phiX174,1411,allele,phiX174,phiX174,A,60,100 -phiX174,1412,allele,phiX174,phiX174,G,60,100 -phiX174,1413,allele,phiX174,phiX174,C,60,100 -phiX174,1414,allele,phiX174,phiX174,G,60,100 -phiX174,1415,allele,phiX174,phiX174,C,60,100 -phiX174,1416,allele,phiX174,phiX174,C,60,100 -phiX174,1417,allele,phiX174,phiX174,G,60,100 -phiX174,1418,allele,phiX174,phiX174,T,60,100 |
| b |
| diff -r e9ebed0c12f6 -r aaf568580946 test-data/freebayes_out_1.vcf.contains --- a/test-data/freebayes_out_1.vcf.contains Mon Feb 17 10:53:56 2014 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,2 +0,0 @@ -#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT A - |
| b |
| diff -r e9ebed0c12f6 -r aaf568580946 test-data/phiX.fasta --- a/test-data/phiX.fasta Mon Feb 17 10:53:56 2014 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,79 +0,0 @@ ->phiX174 -GAGTTTTATCGCTTCCATGACGCAGAAGTTAACACTTTCGGATATTTCTGATGAGTCGAAAAATTATCTT -GATAAAGCAGGAATTACTACTGCTTGTTTACGAATTAAATCGAAGTGGACTGCTGGCGGAAAATGAGAAA -ATTCGACCTATCCTTGCGCAGCTCGAGAAGCTCTTACTTTGCGACCTTTCGCCATCAACTAACGATTCTG -TCAAAAACTGACGCGTTGGATGAGGAGAAGTGGCTTAATATGCTTGGCACGTTCGTCAAGGACTGGTTTA -GATATGAGTCACATTTTGTTCATGGTAGAGATTCTCTTGTTGACATTTTAAAAGAGCGTGGATTACTATC -TGAGTCCGATGCTGTTCAACCACTAATAGGTAAGAAATCATGAGTCAAGTTACTGAACAATCCGTACGTT -TCCAGACCGCTTTGGCCTCTATTAAGCTCATTCAGGCTTCTGCCGTTTTGGATTTAACCGAAGATGATTT -CGATTTTCTGACGAGTAACAAAGTTTGGATTGCTACTGACCGCTCTCGTGCTCGTCGCTGCGTTGAGGCT -TGCGTTTATGGTACGCTGGACTTTGTGGGATACCCTCGCTTTCCTGCTCCTGTTGAGTTTATTGCTGCCG -TCATTGCTTATTATGTTCATCCCGTCAACATTCAAACGGCCTGTCTCATCATGGAAGGCGCTGAATTTAC -GGAAAACATTATTAATGGCGTCGAGCGTCCGGTTAAAGCCGCTGAATTGTTCGCGTTTACCTTGCGTGTA -CGCGCAGGAAACACTGACGTTCTTACTGACGCAGAAGAAAACGTGCGTCAAAAATTACGTGCAGAAGGAG -TGATGTAATGTCTAAAGGTAAAAAACGTTCTGGCGCTCGCCCTGGTCGTCCGCAGCCGTTGCGAGGTACT -AAAGGCAAGCGTAAAGGCGCTCGTCTTTGGTATGTAGGTGGTCAACAATTTTAATTGCAGGGGCTTCGGC -CCCTTACTTGAGGATAAATTATGTCTAATATTCAAACTGGCGCCGAGCGTATGCCGCATGACCTTTCCCA -TCTTGGCTTCCTTGCTGGTCAGATTGGTCGTCTTATTACCATTTCAACTACTCCGGTTATCGCTGGCGAC -TCCTTCGAGATGGACGCCGTTGGCGCTCTCCGTCTTTCTCCATTGCGTCGTGGCCTTGCTATTGACTCTA -CTGTAGACATTTTTACTTTTTATGTCCCTCATCGTCACGTTTATGGTGAACAGTGGATTAAGTTCATGAA -GGATGGTGTTAATGCCACTCCTCTCCCGACTGTTAACACTACTGGTTATATTGACCATGCCGCTTTTCTT -GGCACGATTAACCCTGATACCAATAAAATCCCTAAGCATTTGTTTCAGGGTTATTTGAATATCTATAACA -ACTATTTTAAAGCGCCGTGGATGCCTGACCGTACCGAGGCTAACCCTAATGAGCTTAATCAAGATGATGC -TCGTTATGGTTTCCGTTGCTGCCATCTCAAAAACATTTGGACTGCTCCGCTTCCTCCTGAGACTGAGCTT -TCTCGCCAAATGACGACTTCTACCACATCTATTGACATTATGGGTCTGCAAGCTGCTTATGCTAATTTGC -ATACTGACCAAGAACGTGATTACTTCATGCAGCGTTACCGTGATGTTATTTCTTCATTTGGAGGTAAAAC -CTCTTATGACGCTGACAACCGTCCTTTACTTGTCATGCGCTCTAATCTCTGGGCATCTGGCTATGATGTT -GATGGAACTGACCAAACGTCGTTAGGCCAGTTTTCTGGTCGTGTTCAACAGACCTATAAACATTCTGTGC -CGCGTTTCTTTGTTCCTGAGCATGGCACTATGTTTACTCTTGCGCTTGTTCGTTTTCCGCCTACTGCGAC -TAAAGAGATTCAGTACCTTAACGCTAAAGGTGCTTTGACTTATACCGATATTGCTGGCGACCCTGTTTTG -TATGGCAACTTGCCGCCGCGTGAAATTTCTATGAAGGATGTTTTCCGTTCTGGTGATTCGTCTAAGAAGT -TTAAGATTGCTGAGGGTCAGTGGTATCGTTATGCGCCTTCGTATGTTTCTCCTGCTTATCACCTTCTTGA -AGGCTTCCCATTCATTCAGGAACCGCCTTCTGGTGATTTGCAAGAACGCGTACTTATTCGCCACCATGAT -TATGACCAGTGTTTCCAGTCCGTTCAGTTGTTGCAGTGGAATAGTCAGGTTAAATTTAATGTGACCGTTT -ATCGCAATCTGCCGACCACTCGCGATTCAATCATGACTTCGTGATAAAAGATTGAGTGTGAGGTTATAAC -GCCGAAGCGGTAAAAATTTTAATTTTTGCCGCTGAGGGGTTGACCAAGCGAAGCGCGGTAGGTTTTCTGC -TTAGGAGTTTAATCATGTTTCAGACTTTTATTTCTCGCCATAATTCAAACTTTTTTTCTGATAAGCTGGT -TCTCACTTCTGTTACTCCAGCTTCTTCGGCACCTGTTTTACAGACACCTAAAGCTACATCGTCAACGTTA -TATTTTGATAGTTTGACGGTTAATGCTGGTAATGGTGGTTTTCTTCATTGCATTCAGATGGATACATCTG -TCAACGCCGCTAATCAGGTTGTTTCTGTTGGTGCTGATATTGCTTTTGATGCCGACCCTAAATTTTTTGC -CTGTTTGGTTCGCTTTGAGTCTTCTTCGGTTCCGACTACCCTCCCGACTGCCTATGATGTTTATCCTTTG -AATGGTCGCCATGATGGTGGTTATTATACCGTCAAGGACTGTGTGACTATTGACGTCCTTCCCCGTACGC -CGGGCAATAATGTTTATGTTGGTTTCATGGTTTGGTCTAACTTTACCGCTACTAAATGCCGCGGATTGGT -TTCGCTGAATCAGGTTATTAAAGAGATTATTTGTCTCCAGCCACTTAAGTGAGGTGATTTATGTTTGGTG -CTATTGCTGGCGGTATTGCTTCTGCTCTTGCTGGTGGCGCCATGTCTAAATTGTTTGGAGGCGGTCAAAA -AGCCGCCTCCGGTGGCATTCAAGGTGATGTGCTTGCTACCGATAACAATACTGTAGGCATGGGTGATGCT -GGTATTAAATCTGCCATTCAAGGCTCTAATGTTCCTAACCCTGATGAGGCCGCCCCTAGTTTTGTTTCTG -GTGCTATGGCTAAAGCTGGTAAAGGACTTCTTGAAGGTACGTTGCAGGCTGGCACTTCTGCCGTTTCTGA -TAAGTTGCTTGATTTGGTTGGACTTGGTGGCAAGTCTGCCGCTGATAAAGGAAAGGATACTCGTGATTAT -CTTGCTGCTGCATTTCCTGAGCTTAATGCTTGGGAGCGTGCTGGTGCTGATGCTTCCTCTGCTGGTATGG -TTGACGCCGGATTTGAGAATCAAAAAGAGCTTACTAAAATGCAACTGGACAATCAGAAAGAGATTGCCGA -GATGCAAAATGAGACTCAAAAAGAGATTGCTGGCATTCAGTCGGCGACTTCACGCCAGAATACGAAAGAC -CAGGTATATGCACAAAATGAGATGCTTGCTTATCAACAGAAGGAGTCTACTGCTCGCGTTGCGTCTATTA -TGGAAAACACCAATCTTTCCAAGCAACAGCAGGTTTCCGAGATTATGCGCCAAATGCTTACTCAAGCTCA -AACGGCTGGTCAGTATTTTACCAATGACCAAATCAAAGAAATGACTCGCAAGGTTAGTGCTGAGGTTGAC -TTAGTTCATCAGCAAACGCAGAATCAGCGGTATGGCTCTTCTCATATTGGCGCTACTGCAAAGGATATTT -CTAATGTCGTCACTGATGCTGCTTCTGGTGTGGTTGATATTTTTCATGGTATTGATAAAGCTGTTGCCGA -TACTTGGAACAATTTCTGGAAAGACGGTAAAGCTGATGGTATTGGCTCTAATTTGTCTAGGAAATAACCG -TCAGGATTGACACCCTCCCAATTGTATGTTTTCATGCCTCCAAATCTTGGAGGCTTTTTTATGGTTCGTT -CTTATTACCCTTCTGAATGTCACGCTGATTATTTTGACTTTGAGCGTATCGAGGCTCTTAAACCTGCTAT -TGAGGCTTGTGGCATTTCTACTCTTTCTCAATCCCCAATGCTTGGCTTCCATAAGCAGATGGATAACCGC -ATCAAGCTCTTGGAAGAGATTCTGTCTTTTCGTATGCAGGGCGTTGAGTTCGATAATGGTGATATGTATG -TTGACGGCCATAAGGCTGCTTCTGACGTTCGTGATGAGTTTGTATCTGTTACTGAGAAGTTAATGGATGA -ATTGGCACAATGCTACAATGTGCTCCCCCAACTTGATATTAATAACACTATAGACCACCGCCCCGAAGGG -GACGAAAAATGGTTTTTAGAGAACGAGAAGACGGTTACGCAGTTTTGCCGCAAGCTGGCTGCTGAACGCC -CTCTTAAGGATATTCGCGATGAGTATAATTACCCCAAAAAGAAAGGTATTAAGGATGAGTGTTCAAGATT -GCTGGAGGCCTCCACTATGAAATCGCGTAGAGGCTTTACTATTCAGCGTTTGATGAATGCAATGCGACAG -GCTCATGCTGATGGTTGGTTTATCGTTTTTGACACTCTCACGTTGGCTGACGACCGATTAGAGGCGTTTT -ATGATAATCCCAATGCTTTGCGTGACTATTTTCGTGATATTGGTCGTATGGTTCTTGCTGCCGAGGGTCG -CAAGGCTAATGATTCACACGCCGACTGCTATCAGTATTTTTGTGTGCCTGAGTATGGTACAGCTAATGGC -CGTCTTCATTTCCATGCGGTGCATTTTATGCGGACACTTCCTACAGGTAGCGTTGACCCTAATTTTGGTC -GTCGGGTACGCAATCGCCGCCAGTTAAATAGCTTGCAAAATACGTGGCCTTATGGTTACAGTATGCCCAT -CGCAGTTCGCTACACGCAGGACGCTTTTTCACGTTCTGGTTGGTTGTGGCCTGTTGATGCTAAAGGTGAG -CCGCTTAAAGCTACCAGTTATATGGCTGTTGGTTTCTATGTGGCTAAATACGTTAACAAAAAGTCAGATA -TGGACCTTGCTGCTAAAGGTCTAGGAGCTAAAGAATGGAACAACTCACTAAAAACCAAGCTGTCGCTACT -TCCCAAGAAGCTGTTCAGAATCAGAATGAGCCGCAACTTCGGGATGAAAATGCTCACAATGACAAATCTG -TCCACGGAGTGCTTAATCCAACTTACCAAGCTGGGTTACGACGCGACGCCGTTCAACCAGATATTGAAGC -AGAACGCAAAAAGAGAGATGAGATTGAGGCTGGGAAAAGTTACTGTAGCCGACGTTTTGGCGGCGCAACC -TGTGACGACAAATCTGCTCAAATTTATGCGCGCTTCGATAAAAATGATTGGCGTATCCAACCTGCA - |
| b |
| diff -r e9ebed0c12f6 -r aaf568580946 tool-data/sam_fa_indices.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/sam_fa_indices.loc.sample Fri Jun 20 17:16:05 2014 -0400 |
| b |
| @@ -0,0 +1,28 @@ +#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 sam_fa_indices.loc file +#similar to this one (store it in this directory) that points to +#the directories in which those files are stored. The sam_fa_indices.loc +#file has this format (white space characters are TAB characters): +# +#index <seq> <location> +# +#So, for example, if you had hg18 indexed stored in +#/depot/data2/galaxy/sam/, +#then the sam_fa_indices.loc entry would look like this: +# +#index hg18 /depot/data2/galaxy/sam/hg18.fa +# +#and your /depot/data2/galaxy/sam/ directory +#would contain hg18.fa and hg18.fa.fai files: +# +#-rw-r--r-- 1 james universe 830134 2005-09-13 10:12 hg18.fa +#-rw-r--r-- 1 james universe 527388 2005-09-13 10:12 hg18.fa.fai +# +#Your sam_fa_indices.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: +# +#index hg18 /depot/data2/galaxy/sam/hg18.fa +#index hg19 /depot/data2/galaxy/sam/hg19.fa |
| b |
| diff -r e9ebed0c12f6 -r aaf568580946 tool-data/tool_data_table_conf.xml.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/tool_data_table_conf.xml.sample Fri Jun 20 17:16:05 2014 -0400 |
| b |
| @@ -0,0 +1,8 @@ +<!-- Use the file tool_data_table_conf.xml.oldlocstyle if you don't want to update your loc files as changed in revision 4550:535d276c92bc--> +<tables> + <!-- Location of SAMTools indexes and other files --> + <table name="sam_fa_indexes" comment_char="#"> + <columns>line_type, value, path</columns> + <file path="tool-data/sam_fa_indices.loc" /> + </table> +</tables> |
| b |
| diff -r e9ebed0c12f6 -r aaf568580946 tool_data_table_conf.xml.sample --- a/tool_data_table_conf.xml.sample Mon Feb 17 10:53:56 2014 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,8 +0,0 @@ -<!-- Use the file tool_data_table_conf.xml.oldlocstyle if you don't want to update your loc files as changed in revision 4550:535d276c92bc--> -<tables> - <!-- Location of SAMTools indexes and other files --> - <table name="sam_fa_indexes" comment_char="#"> - <columns>line_type, value, path</columns> - <file path="tool-data/sam_fa_indices.loc" /> - </table> -</tables> |
| b |
| diff -r e9ebed0c12f6 -r aaf568580946 tool_dependencies.xml --- a/tool_dependencies.xml Mon Feb 17 10:53:56 2014 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,9 +0,0 @@ -<?xml version="1.0"?> -<tool_dependency> - <package name="freebayes" version="0.9.6_9608597d12e127c847ae03aa03440ab63992fedf"> - <repository changeset_revision="7615ee9e216d" name="package_freebayes_0_9_6_9608597d" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu" /> - </package> - <package name="samtools" version="0.1.18"> - <repository changeset_revision="171cd8bc208d" name="package_samtools_0_1_18" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu" /> - </package> -</tool_dependency> |