# HG changeset patch
# User devteam
# Date 1403298965 14400
# Node ID aaf56858094642e78aaa7b57ac754f1f43f6911b
# Parent e9ebed0c12f663595e900460ef4a2114e574ef48
Uploaded
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
@@ -1,680 +0,0 @@
-
-
-
- freebayes
- samtools
-
- - Bayesian genetic variant detector
-
- ##set up input files
- #set $reference_fasta_filename = "localref.fa"
- #if str( $reference_source.reference_source_selector ) == "history":
- ln -s "${reference_source.ref_file}" "${reference_fasta_filename}" &&
- samtools faidx "${reference_fasta_filename}" 2>&1 || echo "Error running samtools faidx for FreeBayes" >&2 &&
- #else:
- #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path )
- #end if
- #for $bam_count, $input_bam in enumerate( $reference_source.input_bams ):
- ln -s "${input_bam.input_bam}" "localbam_${bam_count}.bam" &&
- ln -s "${input_bam.input_bam.metadata.bam_index}" "localbam_${bam_count}.bam.bai" &&
- #end for
- ##finished setting up inputs
-
- ##start FreeBayes commandline
- freebayes
- #for $bam_count, $input_bam in enumerate( $reference_source.input_bams ):
- --bam "localbam_${bam_count}.bam"
- #end for
- --fasta-reference "${reference_fasta_filename}"
-
- ##outputs
- --vcf "${output_vcf}"
-
- ##advanced options
- #if str( $options_type.options_type_selector ) == "advanced":
- ##additional outputs
- #if $options_type.output_trace_option:
- --trace "${output_trace}"
- #end if
- #if $options_type.output_failed_alleles_option:
- --failed-alleles "${output_failed_alleles_bed}"
- #end if
-
- ##additional inputs
- #if str( $options_type.target_limit_type.target_limit_type_selector ) == "limit_by_target_file":
- --targets "${options_type.target_limit_type.input_target_bed}"
- #elif str( $options_type.target_limit_type.target_limit_type_selector ) == "limit_by_region":
- --region "${options_type.target_limit_type.region_chromosome}:${options_type.target_limit_type.region_start}..${options_type.target_limit_type.region_end}"
- #end if
- #if $options_type.input_sample_file:
- --samples "${options_type.input_sample_file}"
- #end if
- #if $options_type.input_populations_file:
- --populations "${options_type.input_populations_file}"
- #end if
- #if $options_type.input_cnv_map_bed:
- --cnv-map "${options_type.input_cnv_map_bed}"
- #end if
- #if str( $options_type.input_variant_type.input_variant_type_selector ) == "provide_vcf":
- --variant-input "${options_type.input_variant_type.input_variant_vcf}"
- ${options_type.input_variant_type.only_use_input_alleles}
- #end if
- #if $options_type.haplotype_basis_alleles:
- --haplotype-basis-alleles "${options_type.haplotype_basis_alleles}"
- #end if
-
-
- ##reporting
- #if str( $options_type.section_reporting_type.section_reporting_type_selector ) == "set":
- --pvar "${options_type.section_reporting_type.pvar}"
- ${options_type.section_reporting_type.show_reference_repeats}
- #end if
-
- ##population model
- #if str( $options_type.section_population_model_type.section_population_model_type_selector ) == "set":
- --theta "${options_type.section_population_model_type.theta}"
- --ploidy "${options_type.section_population_model_type.ploidy}"
- ${options_type.section_population_model_type.pooled}
- #end if
-
- ##reference allele
- #if str( $options_type.use_reference_allele_type.use_reference_allele_type_selector ) == "include_reference_allele":
- --use-reference-allele
- ${options_type.use_reference_allele_type.diploid_reference}
- --reference-quality "${options_type.use_reference_allele_type.reference_quality_mq},${options_type.use_reference_allele_type.reference_quality_bq}"
- #end if
-
- ##allele scope
- #if str( $options_type.section_allele_scope_type.section_allele_scope_type_selector ) == "set":
- ${options_type.section_allele_scope_type.no_snps}
- ${options_type.section_allele_scope_type.no_indels}
- ${options_type.section_allele_scope_type.no_mnps}
- ${options_type.section_allele_scope_type.no_complex}
- --use-best-n-alleles "${options_type.section_allele_scope_type.use_best_n_alleles}"
- #if $options_type.section_allele_scope_type.max_complex_gap:
- --max-complex-gap "${options_type.section_allele_scope_type.max_complex_gap}"
- #end if
- #end if
-
- ##indel realignment
- ${options_type.left_align_indels}
-
- ##input filters
- #if str( $options_type.section_input_filters_type.section_input_filters_type_selector ) == "set":
- ${options_type.section_input_filters_type.use_duplicate_reads}
- #if str( $options_type.section_input_filters_type.quality_filter_type.quality_filter_type_selector ) == "apply_filters":
- --min-mapping-quality "${options_type.section_input_filters_type.quality_filter_type.min_mapping_quality}"
- --min-base-quality "${options_type.section_input_filters_type.quality_filter_type.min_base_quality}"
- --min-supporting-quality "${options_type.section_input_filters_type.quality_filter_type.min_supporting_quality_mq},${options_type.section_input_filters_type.quality_filter_type.min_supporting_quality_bq}"
- #elif str( $options_type.section_input_filters_type.quality_filter_type.quality_filter_type_selector ) == "standard_filters":
- --standard-filters
- #end if
- --mismatch-base-quality-threshold "${options_type.section_input_filters_type.mismatch_base_quality_threshold}"
- #if $options_type.section_input_filters_type.read_mismatch_limit:
- --read-mismatch-limit "${options_type.section_input_filters_type.read_mismatch_limit}"
- #end if
- --read-max-mismatch-fraction "${options_type.section_input_filters_type.read_max_mismatch_fraction}"
- #if $options_type.section_input_filters_type.read_snp_limit:
- --read-snp-limit "${options_type.section_input_filters_type.read_snp_limit}"
- #end if
- #if $options_type.section_input_filters_type.read_indel_limit:
- --read-indel-limit "${options_type.section_input_filters_type.read_indel_limit}"
- #end if
- --indel-exclusion-window "${options_type.section_input_filters_type.indel_exclusion_window}"
- --min-alternate-fraction "${options_type.section_input_filters_type.min_alternate_fraction}"
- --min-alternate-count "${options_type.section_input_filters_type.min_alternate_count}"
- --min-alternate-qsum "${options_type.section_input_filters_type.min_alternate_qsum}"
- --min-alternate-total "${options_type.section_input_filters_type.min_alternate_total}"
- --min-coverage "${options_type.section_input_filters_type.min_coverage}"
- #end if
-
- ##bayesian priors
- #if str( $options_type.section_bayesian_priors_type.section_bayesian_priors_type_selector ) == "set":
- ${options_type.section_bayesian_priors_type.no_ewens_priors}
- ${options_type.section_bayesian_priors_type.no_population_priors}
- ${options_type.section_bayesian_priors_type.hwe_priors}
- #end if
-
- ##observation prior expectations
- #if str( $options_type.section_observation_prior_expectations_type.section_observation_prior_expectations_type_selector ) == "set":
- ${options_type.section_observation_prior_expectations_type.binomial_obs_priors}
- ${options_type.section_observation_prior_expectations_type.allele_balance_priors}
- #end if
-
- ##algorithmic features
- #if str( $options_type.section_algorithmic_features_type.section_algorithmic_features_type_selector ) == "set":
- --site-selection-max-iterations "${options_type.section_algorithmic_features_type.site_selection_max_iterations}"
- --genotyping-max-iterations "${options_type.section_algorithmic_features_type.genotyping_max_iterations}"
- --genotyping-max-banddepth "${options_type.section_algorithmic_features_type.genotyping_max_banddepth}"
- --posterior-integration-limits "${options_type.section_algorithmic_features_type.posterior_integration_limits_n},${options_type.section_algorithmic_features_type.posterior_integration_limits_m}"
- ${options_type.section_algorithmic_features_type.no_permute}
- ${options_type.section_algorithmic_features_type.exclude_unobserved_genotypes}
- #if $options_type.section_algorithmic_features_type.genotype_variant_threshold:
- --genotype-variant-threshold "${options_type.section_algorithmic_features_type.genotype_variant_threshold}"
- #end if
- ${options_type.section_algorithmic_features_type.use_mapping_quality}
- --read-dependence-factor "${options_type.section_algorithmic_features_type.read_dependence_factor}"
- ${options_type.section_algorithmic_features_type.no_marginals}
- #end if
- #end if
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- options_type['options_type_selector'] == "advanced" and options_type['output_failed_alleles_option'] is True
-
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- options_type['options_type_selector'] == "advanced" and options_type['output_trace_option'] is True
-
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-
-**What it does**
-
-This tool uses FreeBayes to call SNPS given a reference sequence and a BAM alignment file.
-
-FreeBayes is a high-performance, flexible, and open-source Bayesian genetic variant detector. It operates on BAM alignment files, which are produced by most contemporary short-read aligners.
-
-In addition to substantial performance improvements over its predecessors (PolyBayes, GigaBayes, and BamBayes), it expands the scope of SNP and small-indel variant calling to populations of individuals with heterogeneous copy number. FreeBayes is currently under active development.
-
-Go `here <http://bioinformatics.bc.edu/marthlab/FreeBayes>`_ for details on FreeBayes.
-
-------
-
-**Inputs**
-
-FreeBayes accepts an input aligned BAM file.
-
-
-**Outputs**
-
-The output is in the VCF format.
-
--------
-
-**Settings**::
-
- input and output:
-
- -b --bam FILE Add FILE to the set of BAM files to be analyzed.
- -c --stdin Read BAM input on stdin.
- -v --vcf FILE Output VCF-format results to FILE.
- -f --fasta-reference FILE
- Use FILE as the reference sequence for analysis.
- An index file (FILE.fai) will be created if none exists.
- If neither --targets nor --region are specified, FreeBayes
- will analyze every position in this reference.
- -t --targets FILE
- Limit analysis to targets listed in the BED-format FILE.
- -r --region <chrom>:<start_position>..<end_position>
- Limit analysis to the specified region, 0-base coordinates,
- end_position not included (same as BED format).
- -s --samples FILE
- Limit analysis to samples listed (one per line) in the FILE.
- By default FreeBayes will analyze all samples in its input
- BAM files.
- --populations FILE
- Each line of FILE should list a sample and a population which
- it is part of. The population-based bayesian inference model
- will then be partitioned on the basis of the populations.
- -A --cnv-map FILE
- Read a copy number map from the BED file FILE, which has
- the format:
- reference sequence, start, end, sample name, copy number
- ... for each region in each sample which does not have the
- default copy number as set by --ploidy.
- -L --trace FILE Output an algorithmic trace to FILE.
- --failed-alleles FILE
- Write a BED file of the analyzed positions which do not
- pass --pvar to FILE.
- -@ --variant-input VCF
- Use variants reported in VCF file as input to the algorithm.
- A report will be generated for every record in the VCF file.
- -l --only-use-input-alleles
- Only provide variant calls and genotype likelihoods for sites
- and alleles which are provided in the VCF input, and provide
- output in the VCF for all input alleles, not just those which
- have support in the data.
- --haplotype-basis-alleles VCF
- When specified, only variant alleles provided in this input
- VCF will be used for the construction of complex or haplotype
- alleles.
-
- reporting:
-
- -P --pvar N Report sites if the probability that there is a polymorphism
- at the site is greater than N. default: 0.0001
- -_ --show-reference-repeats
- Calculate and show information about reference repeats in
- the VCF output.
-
- population model:
-
- -T --theta N The expected mutation rate or pairwise nucleotide diversity
- among the population under analysis. This serves as the
- single parameter to the Ewens Sampling Formula prior model
- default: 0.001
- -p --ploidy N Sets the default ploidy for the analysis to N. default: 2
- -J --pooled Assume that samples result from pooled sequencing.
- When using this flag, set --ploidy to the number of
- alleles in each sample.
-
- reference allele:
-
- -Z --use-reference-allele
- This flag includes the reference allele in the analysis as
- if it is another sample from the same population.
- -H --diploid-reference
- If using the reference sequence as a sample (-Z),
- treat it as diploid. default: false (reference is haploid)
- --reference-quality MQ,BQ
- Assign mapping quality of MQ to the reference allele at each
- site and base quality of BQ. default: 100,60
-
- allele scope:
-
- -I --no-snps Ignore SNP alleles.
- -i --no-indels Ignore insertion and deletion alleles.
- -X --no-mnps Ignore multi-nuceotide polymorphisms, MNPs.
- -u --no-complex Ignore complex events (composites of other classes).
- -n --use-best-n-alleles N
- Evaluate only the best N SNP alleles, ranked by sum of
- supporting quality scores. (Set to 0 to use all; default: all)
- -E --max-complex-gap N
- Allow complex alleles with contiguous embedded matches of up
- to this length.
-
- indel realignment:
-
- -O --left-align-indels
- Left-realign and merge gaps embedded in reads. default: false
-
- input filters:
-
- -4 --use-duplicate-reads
- Include duplicate-marked alignments in the analysis.
- default: exclude duplicates
- -m --min-mapping-quality Q
- Exclude alignments from analysis if they have a mapping
- quality less than Q. default: 30
- -q --min-base-quality Q
- Exclude alleles from analysis if their supporting base
- quality is less than Q. default: 20
- -R --min-supporting-quality MQ,BQ
- In order to consider an alternate allele, at least one supporting
- alignment must have mapping quality MQ, and one supporting
- allele must have base quality BQ. default: 0,0, unset
- -Q --mismatch-base-quality-threshold Q
- Count mismatches toward --read-mismatch-limit if the base
- quality of the mismatch is >= Q. default: 10
- -U --read-mismatch-limit N
- Exclude reads with more than N mismatches where each mismatch
- has base quality >= mismatch-base-quality-threshold.
- default: ~unbounded
- -z --read-max-mismatch-fraction N
- Exclude reads with more than N [0,1] fraction of mismatches where
- each mismatch has base quality >= mismatch-base-quality-threshold
- default: 1.0
- -$ --read-snp-limit N
- Exclude reads with more than N base mismatches, ignoring gaps
- with quality >= mismatch-base-quality-threshold.
- default: ~unbounded
- -e --read-indel-limit N
- Exclude reads with more than N separate gaps.
- default: ~unbounded
- -0 --standard-filters Use stringent input base and mapping quality filters
- Equivalent to -m 30 -q 20 -R 0 -S 0
- -x --indel-exclusion-window
- Ignore portions of alignments this many bases from a
- putative insertion or deletion allele. default: 0
- -F --min-alternate-fraction N
- Require at least this fraction of observations supporting
- an alternate allele within a single individual in the
- in order to evaluate the position. default: 0.0
- -C --min-alternate-count N
- Require at least this count of observations supporting
- an alternate allele within a single individual in order
- to evaluate the position. default: 1
- -3 --min-alternate-qsum N
- Require at least this sum of quality of observations supporting
- an alternate allele within a single individual in order
- to evaluate the position. default: 0
- -G --min-alternate-total N
- Require at least this count of observations supporting
- an alternate allele within the total population in order
- to use the allele in analysis. default: 1
- -! --min-coverage N
- Require at least this coverage to process a site. default: 0
-
- bayesian priors:
-
- -Y --no-ewens-priors
- Turns off the Ewens' Sampling Formula component of the priors.
- -k --no-population-priors
- Equivalent to --pooled --no-ewens-priors
- -w --hwe-priors Use the probability of the combination arising under HWE given
- the allele frequency as estimated by observation frequency.
-
- observation prior expectations:
-
- -V --binomial-obs-priors
- Incorporate expectations about osbervations into the priors,
- Uses read placement probability, strand balance probability,
- and read position (5'-3') probability.
- -a --allele-balance-priors
- Use aggregate probability of observation balance between alleles
- as a component of the priors. Best for observations with minimal
- inherent reference bias.
-
- algorithmic features:
-
- -M --site-selection-max-iterations N
- Uses hill-climbing algorithm to search posterior space for N
- iterations to determine if the site should be evaluated. Set to 0
- to prevent use of this algorithm for site selection, and
- to a low integer for improvide site selection at a slight
- performance penalty. default: 5.
- -B --genotyping-max-iterations N
- Iterate no more than N times during genotyping step. default: 25.
- --genotyping-max-banddepth N
- Integrate no deeper than the Nth best genotype by likelihood when
- genotyping. default: 6.
- -W --posterior-integration-limits N,M
- Integrate all genotype combinations in our posterior space
- which include no more than N samples with their Mth best
- data likelihood. default: 1,3.
- -K --no-permute
- Do not scale prior probability of genotype combination given allele
- frequency by the number of permutations of included genotypes.
- -N --exclude-unobserved-genotypes
- Skip sample genotypings for which the sample has no supporting reads.
- -S --genotype-variant-threshold N
- Limit posterior integration to samples where the second-best
- genotype likelihood is no more than log(N) from the highest
- genotype likelihood for the sample. default: ~unbounded
- -j --use-mapping-quality
- Use mapping quality of alleles when calculating data likelihoods.
- -D --read-dependence-factor N
- Incorporate non-independence of reads by scaling successive
- observations by this factor during data likelihood
- calculations. default: 0.9
- -= --no-marginals
- Do not calculate the marginal probability of genotypes. Saves
- time and improves scaling performance in large populations.
-
-
-------
-
-**Citation**
-
-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>`_.
-
-If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.*
-
-
-
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
@@ -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
-#
-#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
diff -r e9ebed0c12f6 -r aaf568580946 test-data/fake_phiX_reads_1.bam
Binary file test-data/fake_phiX_reads_1.bam has changed
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
@@ -0,0 +1,27 @@
+#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT unknown
+phiX174 311 . A G 6.48411 . AB=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 GT:DP:RO:QR:AO:QA:GL 0/1:9:7:478:2:70:-5.49703,0,-10
+phiX174 374 . T G 30.6931 . AB=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 GT:DP:RO:QR:AO:QA:GL 0/1:4:2:141:2:75:-6.69903,0,-10
+phiX174 913 . A C 13.1703 . AB=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 GT:DP:RO:QR:AO:QA:GL 0/1:5:3:171:2:58:-5.00485,0,-10
+phiX174 1205 . A C 2.30262 . AB=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 GT:DP:RO:QR:AO:QA:GL 0/1:10:8:456:2:67:-5.00791,0,-10
+phiX174 1245 . G T 6.48411 . AB=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 GT:DP:RO:QR:AO:QA:GL 0/1:9:7:389:2:70:-5.49703,0,-10
+phiX174 1249 . T G 15.3287 . AB=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 GT:DP:RO:QR:AO:QA:GL 0/1:9:7:464:2:74:-5.87703,0,-10
+phiX174 1445 . C A 24.4745 . AB=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 GT:DP:RO:QR:AO:QA:GL 0/1:7:5:273:2:76:-6.43501,0,-10
+phiX174 1577 . A C 4.06305 . AB=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 GT:DP:RO:QR:AO:QA:GL 0/1:9:7:460:2:60:-4.54703,0,-10
+phiX174 1631 . T G 2.719 . AB=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 GT:DP:RO:QR:AO:QA:GL 0/1:10:8:500:2:68:-5.10291,0,-10
+phiX174 1772 . T G 2.16317 . AB=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 GT:DP:RO:QR:AO:QA:GL 0/1:10:7:425:2:59:-4.16703,0,-10
+phiX174 1945 . T G 11.7103 . AB=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=31;MQMR=37;NS=1;NUMALT=1;ODDS=2.62656;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=59;QR=263;RO=4;RPP=3.0103;RPPR=5.18177;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=2;SRP=3.0103;SRR=2;TYPE=snp GT:DP:RO:QR:AO:QA:GL 0/1:6:4:263:2:59:-4.97491,0,-10
+phiX174 2230 . T G 1.61813 . AB=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=31;MQMR=35.5;NS=1;NUMALT=1;ODDS=0.795209;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=65;QR=491;RO=8;RPP=7.35324;RPPR=4.09604;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=3;SRP=4.09604;SRR=5;TYPE=snp GT:DP:RO:QR:AO:QA:GL 0/1:10:8:491:2:65:-4.81791,0,-10
+phiX174 2699 . C A 31.6424 . AB=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=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=25;MQMR=37;NS=1;NUMALT=1;ODDS=7.28525;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=76;QR=109;RO=2;RPP=3.0103;RPPR=3.0103;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=0;SRP=7.35324;SRR=2;TYPE=snp GT:DP:RO:QR:AO:QA:GL 0/1:4:2:109:2:76:-6.79403,0,-9.92903
+phiX174 2722 . T G 21.5364 . AB=0.4;ABP=3.44459;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=5;DPB=5;DPRA=0;EPP=7.35324;EPPR=3.73412;GTI=0;LEN=1;MEANALT=1;MQM=25;MQMR=33;NS=1;NUMALT=1;ODDS=4.95189;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=67;QR=150;RO=3;RPP=3.0103;RPPR=3.73412;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=0;SRP=9.52472;SRR=3;TYPE=snp GT:DP:RO:QR:AO:QA:GL 0/1:5:3:150:2:67:-5.85985,0,-10
+phiX174 2814 . T G 8.81714 . AB=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=25;MQMR=33;NS=1;NUMALT=1;ODDS=1.88946;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=53;QR=135;RO=3;RPP=3.0103;RPPR=3.73412;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=0;SRP=9.52472;SRR=3;TYPE=snp GT:DP:RO:QR:AO:QA:GL 0/1:5:3:135:2:53:-4.52985,0,-10
+phiX174 2828 . T G 37.7173 . AB=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=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=31;MQMR=31;NS=1;NUMALT=1;ODDS=8.68456;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=100;QR=348;RO=6;RPP=7.35324;RPPR=4.45795;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=1;SRP=8.80089;SRR=5;TYPE=snp GT:DP:RO:QR:AO:QA:GL 0/1:8:6:348:2:100:-8.53892,0,-10
+phiX174 2983 . T G 12.2712 . AB=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 GT:DP:RO:QR:AO:QA:GL 0/1:5:3:150:2:57:-4.90985,0,-10
+phiX174 3110 . T C 34.4848 . AB=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 GT:DP:RO:QR:AO:QA:GL 0/1:9:6:361:3:94:-7.98834,0,-10
+phiX174 3155 . T G 23.5283 . AB=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 GT:DP:RO:QR:AO:QA:GL 0/1:7:5:299:2:75:-6.34001,0,-10
+phiX174 3325 . A C 5.77196 . AB=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 GT:DP:RO:QR:AO:QA:GL 0/1:6:4:284:2:58:-4.87991,0,-10
+phiX174 3418 . A C 0.61163 . AB=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 GT:DP:RO:QR:AO:QA:GL 0/1:10:8:526:2:60:-4.34291,0,-10
+phiX174 3729 . C T 8.03017 . AB=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 GT:DP:RO:QR:AO:QA:GL 0/1:6:4:232:2:61:-5.16491,0,-10
+phiX174 4031 . T G 23.4861 . AB=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 GT:DP:RO:QR:AO:QA:GL 0/1:8:6:322:2:85:-7.11392,0,-10
+phiX174 4502 . A C 8.30185 . AB=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 GT:DP:RO:QR:AO:QA:GL 0/1:6:4:284:2:55:-4.59491,0,-10
+phiX174 4558 . C G 6.48999 . AB=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 GT:DP:RO:QR:AO:QA:GL 0/1:6:4:204:2:59:-4.97491,0,-10
+phiX174 4655 . T G 21.8853 . AB=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 GT:DP:RO:QR:AO:QA:GL 0/1:6:4:193:2:70:-6.01991,0,-10
diff -r e9ebed0c12f6 -r aaf568580946 test-data/freebayes-phix174.bam
Binary file test-data/freebayes-phix174.bam has changed
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
@@ -0,0 +1,2 @@
+>phiX174
+GAGTTTTATCGCTTCCATGACGCAGAAGTTAACACTTTCGGATATTTCTGATGAGTCGAAAAATTATCTTGATAAAGCAGGAATTACTACTGCTTGTTTACGAATTAAATCGAAGTGGACTGCTGGCGGAAAATGAGAAAATTCGACCTATCCTTGCGCAGCTCGAGAAGCTCTTACTTTGCGACCTTTCGCCATCAACTAACGATTCTGTCAAAAACTGACGCGTTGGATGAGGAGAAGTGGCTTAATATGCTTGGCACGTTCGTCAAGGACTGGTTTAGATATGAGTCACATTTTGTTCATGGTAGAGATTCTCTTGTTGACATTTTAAAAGAGCGTGGATTACTATCTGAGTCCGATGCTGTTCAACCACTAATAGGTAAGAAATCATGAGTCAAGTTACTGAACAATCCGTACGTTTCCAGACCGCTTTGGCCTCTATTAAGCTCATTCAGGCTTCTGCCGTTTTGGATTTAACCGAAGATGATTTCGATTTTCTGACGAGTAACAAAGTTTGGATTGCTACTGACCGCTCTCGTGCTCGTCGCTGCGTTGAGGCTTGCGTTTATGGTACGCTGGACTTTGTGGGATACCCTCGCTTTCCTGCTCCTGTTGAGTTTATTGCTGCCGTCATTGCTTATTATGTTCATCCCGTCAACATTCAAACGGCCTGTCTCATCATGGAAGGCGCTGAATTTACGGAAAACATTATTAATGGCGTCGAGCGTCCGGTTAAAGCCGCTGAATTGTTCGCGTTTACCTTGCGTGTACGCGCAGGAAACACTGACGTTCTTACTGACGCAGAAGAAAACGTGCGTCAAAAATTACGTGCaGAAGGAGTGATGTAATGTCTAAAGGTAAAAAACGTTCTGGCGCTCGCCCTGGTCGTCCGCAGCCGTTGCGAGGTACTAAAGGCAAGCGTAAAGGCGCTCGTCTTTGGTATGTAGGTGGTCAACAATTTTAATTGCAGGGGCTTCGGCCCCTTACTTGAGGATAAATTATGTCTAATATTCAAACTGGCGCCGAGCGTATGCCGCATGACCTTTCCCATCTTGGCTTCCTTGCTGGTCAGATTGGTCGTCTTATTACCATTTCAACTACTCCGGTTATCGCTGGCGACTCCTTCGAGATGGACGCCGTTGGCGCTCTCCGTCTTTCTCCATTGCGTCGTGGCCTTGCTATTGACTCTACTGTAGACATTTTTACTTTTTATGTCCCTCATCGTCACGTTTATGGTGAACAGTGGATTAAGTTCATGAAGGATGGTGTTAATGCCACTCCTCTCCCGACTGTTAACACTACTGGTTATATTGACCATGCCGCTTTTCTTGGCACGATTAACCCTGATACCAATAAAATCCCTAAGCATTTGTTTCAGGGTTATTTGAATATCTATAACAACTATTTTAAAGCGCCGTGGATGCCTGACCGTACCGAGGCTAACCCTAATGAGCTTAATCAAGATGATGCTCGTTATGGTTTCCGTTGCTGCCATCTCAAAAACATTTGGACTGCTCCGCTTCCTCCTGAGACTGAGCTTTCTCGCCAAATGACGACTTCTACCACATCTATTGACATTATGGGTCTGCAAGCTGCTTATGCTAATTTGCATACTGACCAAGAACGTGATTACTTCATGCAGCGTTACCgTGATGTTATTTCTTCATTTGGAGGTAAAACCTCTTATGACGCTGACAACCGTCCTTTACTTGTCATGCGCTCTAATCTCTGGGCATCTGGCTATGATGTTGATGGAACTGACCAAACGTCGTTAGGCCAGTTTTCTGGTCGTGTTCAACAGACCTATAAACATTCTGTGCCGCGTTTCTTTGTTCCTGAGCATGGCACTATGTTTACTCTTGCGCTTGTTCGTTTTCCGCCTACTGCGACTAAAGAGATTCAGTACCTTAACGCTAAAGGTGCTTTGACTTATACCGATATTGCTGGCGACCCTGTTTTGTATGGCAACTTGCCGCCGCGTGAAATTTCTATGAAGGATGTTTTCCGTTCTGGTGATTCGTCTAAGAAGTTTAAGATTGCTGAGGGTCAGTGGTATCGTTATGCGCCTTCGTATGTTTCTCCTGCTTATCACCTTCTTGAAGGCTTCCCATTCATTCAGGAACCGCCTTCTGGTGATTTGCAAGAACGCGTACTTATTCGCCACCATGATTATGACCAGTGTTTCCAGTCCGTTCAGTTGTTGCAGTGGAATAGTCAGGTTAAATTTAATGTGACCGTTTATCGCAATCTGCCGACCACTCGCGATTCAATCATGACTTCGTGATAAAAGATTGAGTGTGAGGTTATAACGCCGAAGCGGTAAAAATTTTAATTTTTGCCGCTGAGGGGTTGACCAAGCGAAGCGCGGTAGGTTTTCTGCTTAGGAGTTTAATCATGTTTCAGACTTTTATTTCTCGCCATAATTCAAACTTTTTTTCTGATAAGCTGGTTCTCACTTCTGTTACTCCAGCTTCTTCGGCACCTGTTTTACAGACACCTAAAGCTACATCGTCAACGTTATATTTTGATAGTTTGACGGTTAATGCTGGTAATGGTGGTTTTCTTCATTGCATTCAGATGGATACATCTGTCAACGCCGCTAATCAGGTTGTTTCTGTTGGTGCTGATATTGCTTTTGATGCCGACCCTAAATTTTTTGCCTGTTTGGTTCGCTTTGAGTCTTCTTCGGTTCCGACTACCCTCCCGACTGCCTATGATGTTTATCCTTTGAATGGTCGCCATGATGGTGGTTATTATACCGTCAAGGACTGTGTGACTATTGACGTCCTTCCCCGTACGCCGGGCAATAAtGTTTATGTTGGTTTCATGGTTTGGTCTAACTTTACCGCTACTAAATGCCGCGGATTGGTTTCGCTGAATCAGGTTATTAAAGAGATTATTTGTCTCCAGCCACTTAAGTGAGGTGATTTATGTTTGGTGCTATTGCTGGCGGTATTGCTTCTGCTCTTGCTGGTGGCGCCATGTCTAAATTGTTTGGAGGCGGTCAAAAAGCCGCCTCCGGTGGCATTCAAGGTGATGTGCTTGCTACCGATAACAATACTGTAGGCATGGGTGATGCTGGTATTAAATCTGCCATTCAAGGCTCTAATGTTCCTAACCCTGATGAGGCCGCCCCTAGTTTTGTTTCTGGTGCTATGGCTAAAGCTGGTAAAGGACTTCTTGAAGGTACGTTGCAGGCTGGCACTTCTGCCGTTTCTGATAAGTTGCTTGATTTGGTTGGACTTGGTGGCAAGTCTGCCGCTGATAAAGGAAAGGATACTCGTGATTATCTTGCTGCTGCATTTCCTGAGCTTAATGCTTGGGAGCGTGCTGGTGCTGATGCTTCCTCTGCTGGTATGGTTGACGCCGGATTTGAGAATCAAAAAGAGCTTACTAAAATGCAACTGGACAATCAGAAAGAGATTGCCGAGATGCAAAATGAGACTCAAAAAGAGATTGCTGGCATTCAGTCGGCGACTTCACGCCAGAATACGAAAGACCAGGTATATGCACAAAATGAGATGCTTGCTTATCAACAGAAGGAGTCTACTGCTCGCGTTGCGTCTATTATGGAAAACACCAATCTTTCCAAGCAACAGCAGGTTTCCGAGATTATGCGCCAAATGCTTACTCAAGCTCAAACGGCTGGTCAGTATTTTACCAATGACCAAATCAAAGAAATGACTCGCAAGGTTAGTGCTGAGGTTGACTTAGTTCATCAGCAAACGCAGAATCAGCGGTATGGCTCTTCTCATATTGGCGCTACTGCAAAGGATATTTCTAATGTCGTCACTGATGCTGCTTCTGGTGTGGTTGATATTTTTCATGGTATTGATAAAGCTGTTGCCGATACTTGGAACAATTTCTGGAAAGACGGTAAAGCTGATGGTATTGGCTCTAATTTGTCTAGGAAATAACCGTCAGGATTGACACCCTCCCAATTGTATGTTTTCATGCCTCCAAATCTTGGAGGCTTTTTTATGGTTCGTTCTTATTACCCTTCTGAATGTCACGCTGATTATTTTGACTTTGAGCGTATCGAGGCTCTTAAACCTGCTATTGAGGCTTGTGGCATTTCTACTCTTTCTCAATCCCCAATGCTTGGCTTCCATAAGCAGATGGATAACCGCATCAAGCTCTTGGAAGAGATTCTGTCTTTTCGTATGCAGGGCGTTGAGTTCGATAATGGTGATATGTATGTTGACGGCCATAAGGCTGCTTCTGACGTTCGTGATGAGTTTGTATCTGTTACTGAGAAGTTAATGGATGAATTGGCACAATGCTACAATGTGCTCCCCCAACTTGATATTAATAACACTATAGACCACCGCCCCGAAGGGGACGAAAAATGGTTTTTAGAGAACGAGAAGACGGTTACGCAGTTTTGCCGCAAGCTGGCTGCTGAACGCCCTCTTAAGGATATTCGCGATGAGTATAATTACCCCAAAAAGAAAGGTATTAAGGATGAGTGTTCAAGATTGCTGGAGGCCTCCACTATGAAATCGCGTAGAGGCTTTaCTATTCAGCGTTTGATGAATGCAATGCGACAGGCTCATGCTGATGGTTGGTTTATCGTTTTTGACACTCTCACGTTGGCTGACGACCGATTAGAGGCGTTTTATGATAATCCCAATGCTTTGCGTGACTATTTTCGTGATATTGGTCGTATGGTTCTTGCTGCCGAGGGTCGCAAGGCTAATGATTCACACGCCGACTGCTATCAGTATTTTTGTGTGCCTGAGTATGGTACAGCTAATGGCCGTCTTCATTTCCATGCGGTGCAtTTTATGCGGACACTTCCTACAGGTAGCGTTGACCCTAATTTTGGTCGTCGGGTACGCAATCGCCGCCAGTTAAATAGCTTGCAAAATACGTGGCCTTATGGTTACAGTATGCCCATCGCAGTTCGCTACACGCAGGACGCTTTTTCACGTTCTGGTTGGTTGTGGCCTGTTGATGCTAAAGGTGAGCCGCTTAAAGCTACCAGTTATATGGCTGTTGGTTTCTATGTGGCTAAATACGTTAACAAAAAGTCAGATATGGACCTTGCTGCTAAAGGTCTAGGAGCTAAAGAATGGAACAACTCACTAAAAACCAAGCTGTCGCTACTTCCCAAGAAGCTGTTCAGAATCAGAATGAGCCGCAACTTCGGGATGAAAATGCTCACAATGACAAATCTGTCCACGGAGTGCTTAATCCAACTTACCAAGCTGGGTTACGACGCGACGCCGTTCAACCAGATATTGAAGCAGAACGCAAAAAGAGAGATGAGATTGAGGCTGGGAAAAGTTACTGTAGCCGACGTTTTGGCGGCGCAACCTGTGACGACAAATCTGCTCAAATTTATGCGCGCTTCGATAAAAATGATTGGCGTATCCAACCTGCA
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
@@ -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
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
@@ -1,2 +0,0 @@
-#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT A
-
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
@@ -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
-
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
@@ -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
+#
+#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
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
@@ -0,0 +1,8 @@
+
+
+
+