# HG changeset patch
# User iuc
# Date 1754401678 0
# Node ID 0d8581534009453f7efb6aed03c4f15c355b27e2
# Parent  85dc96ebc7701acebe002687783aeae07b8b7dc3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 48700fed491e8056cddd1ee7d8bc9ca08e19fe8d

diff -r 85dc96ebc770 -r 0d8581534009 freebayes.xml
--- a/freebayes.xml	Tue Jun 10 07:59:51 2025 +0000
+++ b/freebayes.xml	Tue Aug 05 13:47:58 2025 +0000
@@ -1,14 +1,15 @@
-<tool id="freebayes" name="FreeBayes" version="@TOOL_VERSION@+galaxy0">
+<tool id="freebayes" name="FreeBayes" version="@TOOL_VERSION@+galaxy1" profile="23.0">
     <description>bayesian genetic variant detector</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
     <xrefs>
         <xref type="bio.tools">freebayes</xref>
     </xrefs>
-    <macros>
-        <import>macros.xml</import>
-    </macros>
     <expand macro="requirements">
+        <requirement type="package" version="3.11">grep</requirement>
         <requirement type="package" version="5.3.1">gawk</requirement>
-        <requirement type="package" version="20250422">parallel</requirement>
+        <requirement type="package" version="20250622">parallel</requirement>
     </expand>
     <expand macro="version_command" />
     <command detect_errors="exit_code"><![CDATA[
@@ -239,6 +240,18 @@
             #end if
         #end if
 
+        #if str($output_options.flavor) == "gvcf":
+          --gvcf
+        #elif str($output_options.flavor) == "gvcf_custom":
+          --gvcf
+          #if $output_options.gvcf_block_size == 0:
+            ## special-casing the 0 case for performance
+            --gvcf-dont-use-chunk t
+          #else:
+            --gvcf-chunk $output_options.gvcf_block_size
+          #end if
+        #end if
+
         ";
     done > freebayes_commands.sh &&
 
@@ -366,21 +379,21 @@
                             <when value="provide_vcf">
                                 <param name="input_variant_vcf" argument="--variant-input" type="data" format="vcf_bgzip"
                                        label="Use variants reported in this VCF dataset as input to the algorithm"/>
-                                <param name="only_use_input_alleles" argument="--only-use-input-alleles" type="boolean" truevalue="--only-use-input-alleles" falsevalue="" checked="false"
+                                <param argument="--only-use-input-alleles" type="boolean" truevalue="--only-use-input-alleles" falsevalue="" checked="false"
                                        label="Only provide variant calls and genotype likelihoods for sites in VCF" />
                             </when>
                         </conditional>
-                        <param name="haplotype_basis_alleles" argument="--haplotype-basis-alleles" type="data" format="vcf" optional="true"
+                        <param argument="--haplotype-basis-alleles" type="data" format="vcf" optional="true"
                                label="Only use variant alleles provided in this input VCF for the construction of complex or haplotype alleles" />
-                        <param name="report_monomorphic" argument="--report-monomorphic" type="boolean" truevalue="--report-monomorphic" falsevalue="" checked="false"
+                        <param argument="--report-monomorphic" type="boolean" truevalue="--report-monomorphic" falsevalue="" checked="false"
                                label="Report even loci which appear to be monomorphic, and report all considered alleles, even those which are not in called genotypes" />
-                        <param name="observation_bias" argument="--observation-bias" type="data" format="tabular" optional="true"
+                        <param argument="--observation-bias" type="data" format="tabular" optional="true"
                                label="Load read length-dependent allele observation biases from"
                                help="The format is [length] [alignment efficiency relative to reference] where the efficiency is 1 if there is no relative observation bias" />
-                        <param name="contamination_estimates" argument="--contamination-estimates" type="data" format="tabular" optional="true"
+                        <param argument="--contamination-estimates" type="data" format="tabular" optional="true"
                                label="Upload per-sample estimates of contamination from"
                                help="The format should be: sample p(read=R|genotype=AR) p(read=A|genotype=AA) Sample '*' can be used to set default contamination estimates" />
-                        <param name="trim_complex_tail" argument="--trim-complex-tail" type="boolean" truevalue="--trim-complex-tail" falsevalue=""
+                        <param argument="--trim-complex-tail" type="boolean" truevalue="--trim-complex-tail" falsevalue=""
                                label="Trim trailing reference matches" />
                     </when>
                     <when value="do_not_set" />
@@ -432,7 +445,7 @@
                     <when value="set">
                         <param name="Z" argument="--use-reference-allele" type="boolean" truevalue="-Z" falsevalue="" checked="false"
                                label="Include the reference allele in the analysis as if it is another sample from the same population" />
-                        <param name="reference_quality" argument="--reference-quality" type="text" value="100,60"
+                        <param argument="--reference-quality" type="text" value="100,60"
                                label="Assign mapping quality of MQ (100) to the reference allele at each site and base quality of BQ (60)" />
                     </when>
                     <when value="do_not_set" />
@@ -457,13 +470,13 @@
                         <param name="n" argument="--use-best-n-alleles" type="integer" value="0"
                                label="How many best SNP alleles to evaluate"
                                help="Alleles are ranked by the sum of supporting quality scores. Set to 0 to evaluate all" />
-                        <param name="haplotype_length" argument="--haplotype-length" type="integer" value="3"
+                        <param argument="--haplotype-length" type="integer" value="3"
                                label="Allow haplotype calls with contiguous embedded matches of up to (nucleotides)" />
                         <param name="min_repeat_length" argument="--min-repeat-size" type="integer" value="5"
                                label="When assembling observations across repeats, require the total repeat length at least this many bp" />
-                        <param name="min_repeat_entropy" argument="--min-repeat-entropy" type="integer" value="1"
+                        <param argument="--min-repeat-entropy" type="integer" value="1"
                                label="To detect interrupted repeats, build across sequence until it has entropy > (bits per bp)" />
-                        <param name="no_partial_observations" argument="--no-partial-observations" type="boolean" truevalue="--no-partial-observations" falsevalue="" checked="false"
+                        <param argument="--no-partial-observations" type="boolean" truevalue="--no-partial-observations" falsevalue="" checked="false"
                                label="Exclude observations which do not fully span the dynamically-determined detection window"
                                help="By default, FreeBayes uses all observations, dividing partial support across matching haplotypes when generating haplotypes" />
                     </when>
@@ -508,7 +521,7 @@
                                        help="default=~unbounded" />
                                 <param argument="--read-max-mismatch-fraction" type="float" value="1.0" min="0.0" max="1.0"
                                        label="Exclude reads with more than N [0,1] fraction of mismatches where each mismatch has base quality >= mismatch-base-quality-threshold (second option above)" />
-                                <param name="read_snp_limit" argument="--read-snp-limit" type="integer" value="1000"
+                                <param argument="--read-snp-limit" type="integer" value="1000"
                                        label="Exclude reads with more than N base mismatches, ignoring gaps with quality >= mismatch-base-quality-threshold (third option above)"
                                        help="default=~unbounded" />
                             </when>
@@ -559,12 +572,12 @@
                         <option value="set">Set genotype likelihood options</option>
                     </param>
                     <when value="set">
-                        <param name="base_quality_cap" argument="--base-quality-cap" type="integer" value="0"
+                        <param argument="--base-quality-cap" type="integer" value="0"
                                label="Limit estimated observation quality by capping base quality at" />
-                        <param name="experimental_gls" argument="--experimental-gls" type="boolean" truevalue="--experimental-gls" falsevalue="" checked="false"
+                        <param argument="--experimental-gls" type="boolean" truevalue="--experimental-gls" falsevalue="" checked="false"
                                label="Generate genotype likelihoods using 'effective base depth' metric qual = 1-BaseQual * 1-MapQual"
                                help="Incorporate partial observations. This is the default when contamination estimates are provided. Optimized for diploid samples" />
-                        <param name="prob_contamination" argument="--prob-contamination" type="float" value="10e-9"
+                        <param argument="--prob-contamination" type="float" value="10e-9"
                                label="An estimate of contamination to use for all samples" />
                     </when>
                     <when value="do_not_set" />
@@ -578,17 +591,17 @@
                         <option value="set">Set algorithmic features</option>
                     </param>
                     <when value="set">
-                        <param name="report_genotype_likelihood_max" argument="--report-genotype-likelihood-max" type="boolean" truevalue="--report-genotype-likelihood-max" falsevalue="" checked="false"
+                        <param argument="--report-genotype-likelihood-max" type="boolean" truevalue="--report-genotype-likelihood-max" falsevalue="" checked="false"
                                label="Report genotypes using the maximum-likelihood estimate provided from genotype likelihoods" />
                         <param name="B" argument="--genotyping-max-iterations" type="integer" value="1000"
                                label="Iterate no more than N times during genotyping step" />
-                        <param name="genotyping_max_banddepth" argument="--genotyping-max-banddepth" type="integer" value="6"
+                        <param argument="--genotyping-max-banddepth" type="integer" value="6"
                                label="Integrate no deeper than the Nth best genotype by likelihood when genotyping" />
                         <param name="W" argument="--posterior-integration-limits" type="text" value="1,3"
                                label="Integrate all genotype combinations in our posterior space which include no more than N (1) samples with their Mth (3) best data likelihood" />
                         <param name="N" argument="--exclude-unobserved-genotypes" type="boolean" truevalue="--exclude-unobserved-genotypes" falsevalue="" checked="false"
                                label="Skip sample genotypings for which the sample has no supporting reads" />
-                        <param name="genotype_variant_threshold" argument="--genotype-variant-threshold" type="integer" value="" optional="true"
+                        <param argument="--genotype-variant-threshold" type="integer" value="" optional="true"
                                label="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"
                                help="default=~unbounded" />
                         <param name="j" argument="--use-mapping-quality" type="boolean" truevalue="-j" falsevalue="" checked="false"
@@ -598,7 +611,7 @@
                                help="By default, FreeBayes uses a minimum Base Quality in flanking sequence" />
                         <param name="D" argument="--read-dependence-factor" type="float" value="0.9"
                                label="Incorporate non-independence of reads by scaling successive observations by this factor during data likelihood calculations" />
-                        <param name="genotype_qualities" argument="--genotype-qualities" type="boolean" truevalue="--genotype-qualities" falsevalue="" checked="false"
+                        <param argument="--genotype-qualities" type="boolean" truevalue="--genotype-qualities" falsevalue="" checked="false"
                                label="Calculate the marginal probability of genotypes and report as GQ in each sample field in the VCF output" />
                     </when>
                     <when value="do_not_set" />
@@ -609,6 +622,18 @@
             <when value="naive" />
             <when value="naive_w_filters" />
         </conditional>
+        <conditional name="output_options">
+            <param name="flavor" type="select" label="Type of main output to produce" help="The tool will, by default, produce VCF output with information about sites with called variants. If you want also information (such as depth of coverage) about non-called sites, you can use the gVCF or gVCF with custom block size options. The first collapses the stats of entire blocks of consecutive non-called sites into one non-call record. The second gives you control over how many consecutive non-called sites should be combined into a non-call record.">
+                <option value="vcf">VCF (default)</option>
+                <option value="gvcf">gVCF (--gvcf)</option>
+                <option value="gvcf_custom">gVCF with custom block size</option>
+            </param>
+            <when value="vcf" />
+            <when value="gvcf" />
+            <when value="gvcf_custom">
+                <param name="gvcf_block_size" type="integer" value="0" min="0" max="2147483647" label="Maximal block size for consecutive non-called sites" help="Consolidate data from any non-called site together with the N next non-called sites into one gVCF record, i.e. produce gVCF block records of maximally N+1 sites. Blocks can be shorter if terminated by the end of a chromosome or a site with a called variant. Setting this parameter to 0 produces a separate record for every non-called site, but can result in very large output." />
+            </when>
+        </conditional>
     </inputs>
     <outputs>
         <data format="vcf" name="output_vcf" label="${tool.name} on ${on_string} (variants)" />
@@ -620,7 +645,7 @@
         </data>
     </outputs>
     <tests>
-        <test>
+        <test expect_num_outputs="1">
             <param name="reference_source_selector" value="history" />
             <param name="processmode" value="individual" />
             <param name="ref_file" ftype="fasta" value="freebayes-phix174.fasta"/>
@@ -628,7 +653,31 @@
             <param name="options_type_selector" value="simple"/>
             <output name="output_vcf" file="freebayes-phix174-test1.vcf" lines_diff="4" />
         </test>
-        <test>
+        <test expect_num_outputs="1">
+            <param name="reference_source_selector" value="history" />
+            <param name="processmode" value="individual" />
+            <param name="ref_file" ftype="fasta" value="freebayes-phix174.fasta" />
+            <param name="input_bams" ftype="bam" value="freebayes-phix174.bam" />
+            <param name="options_type_selector" value="simple" />
+            <conditional name="output_options">
+                <param name="flavor" value="gvcf" />
+            </conditional>
+            <output name="output_vcf" file="freebayes-phix174.gvcf" lines_diff="4" />
+        </test>
+        <test expect_num_outputs="1">
+            <param name="reference_source_selector" value="history" />
+            <param name="processmode" value="individual" />
+            <param name="ref_file" ftype="fasta" value="freebayes-phix174.fasta" />
+            <param name="input_bams" ftype="bam" value="freebayes-phix174.bam" />
+            <param name="options_type_selector" value="simple" />
+            <conditional name="output_options">
+                <param name="flavor" value="gvcf_custom" />
+            </conditional>
+            <!-- This test produces one record per reference position
+            so the test file only contains the first part of the expected output up to the second variant site -->
+            <output name="output_vcf" file="freebayes-phix174.full.sample.gvcf" compare="contains" lines_diff="2" />
+        </test>
+        <test expect_num_outputs="1">
             <param name="reference_source_selector" value="history" />
             <param name="processmode" value="individual" />
             <param name="ref_file" ftype="fasta" value="freebayes-phix174.fasta"/>
@@ -639,7 +688,7 @@
             <output name="output_vcf" file="freebayes-phix174-test2.vcf" lines_diff="4" />
         </test>
         <!-- Test that user-provided (variant-input option) sites are included in output -->
-        <test>
+        <test expect_num_outputs="1">
             <param name="reference_source_selector" value="history" />
             <param name="processmode" value="individual" />
             <param name="ref_file" ftype="fasta" value="freebayes-phix174.fasta"/>
@@ -658,7 +707,7 @@
                 </assert_contents>
             </output>
         </test>
-        <test>
+        <test expect_num_outputs="1">
             <param name="reference_source_selector" value="history" />
             <param name="processmode" value="individual" />
             <param name="ref_file" ftype="fasta" value="freebayes-phix174.fasta"/>
@@ -669,7 +718,7 @@
             <param name="trim_complex_tail" value="--trim-complex-tail"/>
             <output name="output_vcf" file="freebayes-phix174-test4.vcf" lines_diff="4" />
         </test>
-        <test>
+        <test expect_num_outputs="1">
             <param name="reference_source_selector" value="history" />
             <param name="processmode" value="individual" />
             <param name="ref_file" ftype="fasta" value="freebayes-hxb2.fasta"/>
@@ -679,7 +728,7 @@
             <param name="min_coverage" value="250" />
             <output name="output_vcf" file="freebayes-hxb2-test5.vcf" lines_diff="4" />
         </test>
-        <test>
+        <test expect_num_outputs="1">
             <param name="reference_source_selector" value="history" />
             <param name="processmode" value="individual" />
             <param name="ref_file" ftype="fasta" value="freebayes-hxb2.fasta"/>
@@ -689,7 +738,7 @@
             <param name="limit_coverage" value="400" />
             <output name="output_vcf" file="freebayes-hxb2-test6.vcf" lines_diff="4" />
         </test>
-        <test>
+        <test expect_num_outputs="1">
             <param name="reference_source_selector" value="history" />
             <param name="processmode" value="individual" />
             <param name="ref_file" ftype="fasta" value="freebayes-hxb2.fasta"/>
@@ -699,7 +748,7 @@
             <param name="skip_coverage" value="100" />
             <output name="output_vcf" file="freebayes-hxb2-test7.vcf" lines_diff="4" />
         </test>
-        <test> <!-- Test with CRAM -->
+        <test expect_num_outputs="1"> <!-- Test with CRAM -->
             <param name="reference_source_selector" value="history" />
             <param name="processmode" value="individual" />
             <param name="ref_file" ftype="fasta" value="freebayes-phix174.fasta"/>
diff -r 85dc96ebc770 -r 0d8581534009 leftalign.xml
--- a/leftalign.xml	Tue Jun 10 07:59:51 2025 +0000
+++ b/leftalign.xml	Tue Aug 05 13:47:58 2025 +0000
@@ -1,12 +1,12 @@
 <?xml version="1.0"?>
 <tool id="bamleftalign" name="BamLeftAlign" version="@TOOL_VERSION@+galaxy0">
     <description> indels in BAM datasets</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
     <xrefs>
         <xref type="bio.tools">freebayes</xref>
     </xrefs>
-    <macros>
-        <import>macros.xml</import>
-    </macros>
     <expand macro="requirements" />
     <expand macro="version_command" />
     <command detect_errors="exit_code"><![CDATA[
diff -r 85dc96ebc770 -r 0d8581534009 macros.xml
--- a/macros.xml	Tue Jun 10 07:59:51 2025 +0000
+++ b/macros.xml	Tue Aug 05 13:47:58 2025 +0000
@@ -4,6 +4,7 @@
         <requirements>
             <requirement type="package" version="@TOOL_VERSION@">freebayes</requirement>
             <requirement type="package" version="1.22">samtools</requirement>
+            <requirement type="package" version="9.5">coreutils</requirement>
             <yield />
         </requirements>
     </xml>
@@ -52,8 +53,8 @@
         --limit-coverage ${coverage_options.limit_coverage}
     </token>
     <xml name="par_min_cov">
-        <param name="min_coverage" argument="--min-coverage" type="integer" value="0" label="Require at least this coverage to process a site" />
-        <param name="limit_coverage" argument="--limit-coverage" type="integer" value="0" label="Downsample per-sample coverage to this level if greater than this coverage" />
-        <param name="skip_coverage" argument="--skip-coverage" type="integer" value="0" label="Skip processing of alignments overlapping positions with coverage greater than this" />
+        <param argument="--min-coverage" type="integer" value="0" label="Require at least this coverage to process a site" />
+        <param argument="--limit-coverage" type="integer" value="0" label="Downsample per-sample coverage to this level if greater than this coverage" />
+        <param argument="--skip-coverage" type="integer" value="0" label="Skip processing of alignments overlapping positions with coverage greater than this" />
     </xml>
 </macros>
diff -r 85dc96ebc770 -r 0d8581534009 test-data/freebayes-phix174.full.sample.gvcf
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/freebayes-phix174.full.sample.gvcf	Tue Aug 05 13:47:58 2025 +0000
@@ -0,0 +1,436 @@
+##fileformat=VCFv4.2
+##fileDate=20250805
+##source=freeBayes v1.3.10
+##reference=localref.fa
+##contig=<ID=phiX174,length=5386>
+##phasing=none
+##commandline="freebayes --region phiX174:0..5386 -f freebayes-phix174.fasta freebayes-phix174.bam --gvcf -& t"
+##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of samples with data">
+##INFO=<ID=DP,Number=1,Type=Integer,Description="Total read depth at the locus">
+##INFO=<ID=DPB,Number=1,Type=Float,Description="Total read depth per bp at the locus; bases in reads overlapping / bases in haplotype">
+##INFO=<ID=AC,Number=A,Type=Integer,Description="Total number of alternate alleles in called genotypes">
+##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
+##INFO=<ID=AF,Number=A,Type=Float,Description="Estimated allele frequency in the range (0,1]">
+##INFO=<ID=RO,Number=1,Type=Integer,Description="Count of full observations of the reference haplotype.">
+##INFO=<ID=AO,Number=A,Type=Integer,Description="Count of full observations of this alternate haplotype.">
+##INFO=<ID=PRO,Number=1,Type=Float,Description="Reference allele observation count, with partial observations recorded fractionally">
+##INFO=<ID=PAO,Number=A,Type=Float,Description="Alternate allele observations, with partial observations recorded fractionally">
+##INFO=<ID=QR,Number=1,Type=Integer,Description="Reference allele quality sum in phred">
+##INFO=<ID=QA,Number=A,Type=Integer,Description="Alternate allele quality sum in phred">
+##INFO=<ID=PQR,Number=1,Type=Float,Description="Reference allele quality sum in phred for partial observations">
+##INFO=<ID=PQA,Number=A,Type=Float,Description="Alternate allele quality sum in phred for partial observations">
+##INFO=<ID=SRF,Number=1,Type=Integer,Description="Number of reference observations on the forward strand">
+##INFO=<ID=SRR,Number=1,Type=Integer,Description="Number of reference observations on the reverse strand">
+##INFO=<ID=SAF,Number=A,Type=Integer,Description="Number of alternate observations on the forward strand">
+##INFO=<ID=SAR,Number=A,Type=Integer,Description="Number of alternate observations on the reverse strand">
+##INFO=<ID=SRP,Number=1,Type=Float,Description="Strand balance probability for the reference allele: Phred-scaled upper-bounds estimate of the probability of observing the deviation between SRF and SRR given E(SRF/SRR) ~ 0.5, derived using Hoeffding's inequality">
+##INFO=<ID=SAP,Number=A,Type=Float,Description="Strand balance probability for the alternate allele: Phred-scaled upper-bounds estimate of the probability of observing the deviation between SAF and SAR given E(SAF/SAR) ~ 0.5, derived using Hoeffding's inequality">
+##INFO=<ID=AB,Number=A,Type=Float,Description="Allele balance at heterozygous sites: a number between 0 and 1 representing the ratio of reads showing the reference allele to all reads, considering only reads from individuals called as heterozygous">
+##INFO=<ID=ABP,Number=A,Type=Float,Description="Allele balance probability at heterozygous sites: Phred-scaled upper-bounds estimate of the probability of observing the deviation between ABR and ABA given E(ABR/ABA) ~ 0.5, derived using Hoeffding's inequality">
+##INFO=<ID=RUN,Number=A,Type=Integer,Description="Run length: the number of consecutive repeats of the alternate allele in the reference genome">
+##INFO=<ID=RPP,Number=A,Type=Float,Description="Read Placement Probability: Phred-scaled upper-bounds estimate of the probability of observing the deviation between RPL and RPR given E(RPL/RPR) ~ 0.5, derived using Hoeffding's inequality">
+##INFO=<ID=RPPR,Number=1,Type=Float,Description="Read Placement Probability for reference observations: Phred-scaled upper-bounds estimate of the probability of observing the deviation between RPL and RPR given E(RPL/RPR) ~ 0.5, derived using Hoeffding's inequality">
+##INFO=<ID=RPL,Number=A,Type=Float,Description="Reads Placed Left: number of reads supporting the alternate balanced to the left (5') of the alternate allele">
+##INFO=<ID=RPR,Number=A,Type=Float,Description="Reads Placed Right: number of reads supporting the alternate balanced to the right (3') of the alternate allele">
+##INFO=<ID=EPP,Number=A,Type=Float,Description="End Placement Probability: Phred-scaled upper-bounds estimate of the probability of observing the deviation between EL and ER given E(EL/ER) ~ 0.5, derived using Hoeffding's inequality">
+##INFO=<ID=EPPR,Number=1,Type=Float,Description="End Placement Probability for reference observations: Phred-scaled upper-bounds estimate of the probability of observing the deviation between EL and ER given E(EL/ER) ~ 0.5, derived using Hoeffding's inequality">
+##INFO=<ID=DPRA,Number=A,Type=Float,Description="Alternate allele depth ratio.  Ratio between depth in samples with each called alternate allele and those without.">
+##INFO=<ID=ODDS,Number=1,Type=Float,Description="The log odds ratio of the best genotype combination to the second-best.">
+##INFO=<ID=GTI,Number=1,Type=Integer,Description="Number of genotyping iterations required to reach convergence or bailout.">
+##INFO=<ID=TYPE,Number=A,Type=String,Description="The type of allele, either snp, mnp, ins, del, or complex.">
+##INFO=<ID=CIGAR,Number=A,Type=String,Description="The extended CIGAR representation of each alternate allele, with the exception that '=' is replaced by 'M' to ease VCF parsing.  Note that INDEL alleles do not have the first matched base (which is provided by default, per the spec) referred to by the CIGAR.">
+##INFO=<ID=NUMALT,Number=1,Type=Integer,Description="Number of unique non-reference alleles in called genotypes at this position.">
+##INFO=<ID=MEANALT,Number=A,Type=Float,Description="Mean number of unique non-reference allele observations per sample with the corresponding alternate alleles.">
+##INFO=<ID=LEN,Number=A,Type=Integer,Description="allele length">
+##INFO=<ID=MQM,Number=A,Type=Float,Description="Mean mapping quality of observed alternate alleles">
+##INFO=<ID=MQMR,Number=1,Type=Float,Description="Mean mapping quality of observed reference alleles">
+##INFO=<ID=PAIRED,Number=A,Type=Float,Description="Proportion of observed alternate alleles which are supported by properly paired read fragments">
+##INFO=<ID=PAIREDR,Number=1,Type=Float,Description="Proportion of observed reference alleles which are supported by properly paired read fragments">
+##INFO=<ID=MIN_DP,Number=1,Type=Integer,Description="Minimum depth in gVCF output block.">
+##INFO=<ID=END,Number=1,Type=Integer,Description="Last position (inclusive) in gVCF output record.">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=GQ,Number=1,Type=Float,Description="Genotype Quality, the Phred-scaled marginal (or unconditional) probability of the called genotype">
+##FORMAT=<ID=GL,Number=G,Type=Float,Description="Genotype Likelihood, log10-scaled likelihoods of the data given the called genotype for each possible genotype generated from the reference and alternate alleles given the sample ploidy">
+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
+##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Number of observation for each allele">
+##FORMAT=<ID=RO,Number=1,Type=Integer,Description="Reference allele observation count">
+##FORMAT=<ID=QR,Number=1,Type=Float,Description="Sum of quality of the reference observations">
+##FORMAT=<ID=AO,Number=A,Type=Integer,Description="Alternate allele observation count">
+##FORMAT=<ID=QA,Number=A,Type=Float,Description="Sum of quality of the alternate observations">
+##FORMAT=<ID=MIN_DP,Number=1,Type=Integer,Description="Minimum depth in gVCF output block.">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	unknown
+phiX174	1	.	G	<*>	0	.	DP=0;END=1;MIN_DP=0	GQ:DP:MIN_DP:QR:RO:QA:AO	-0:0:0:0:0:0:0
+phiX174	2	.	A	<*>	0	.	DP=0;END=2;MIN_DP=0	GQ:DP:MIN_DP:QR:RO:QA:AO	-0:0:0:0:0:0:0
+phiX174	3	.	G	<*>	0	.	DP=0;END=3;MIN_DP=0	GQ:DP:MIN_DP:QR:RO:QA:AO	-0:0:0:0:0:0:0
+phiX174	4	.	T	<*>	0	.	DP=0;END=4;MIN_DP=0	GQ:DP:MIN_DP:QR:RO:QA:AO	-0:0:0:0:0:0:0
+phiX174	5	.	T	<*>	0	.	DP=0;END=5;MIN_DP=0	GQ:DP:MIN_DP:QR:RO:QA:AO	-0:0:0:0:0:0:0
+phiX174	6	.	T	<*>	0	.	DP=0;END=6;MIN_DP=0	GQ:DP:MIN_DP:QR:RO:QA:AO	-0:0:0:0:0:0:0
+phiX174	7	.	T	<*>	0	.	DP=0;END=7;MIN_DP=0	GQ:DP:MIN_DP:QR:RO:QA:AO	-0:0:0:0:0:0:0
+phiX174	8	.	A	<*>	0	.	DP=0;END=8;MIN_DP=0	GQ:DP:MIN_DP:QR:RO:QA:AO	-0:0:0:0:0:0:0
+phiX174	9	.	T	<*>	0	.	DP=0;END=9;MIN_DP=0	GQ:DP:MIN_DP:QR:RO:QA:AO	-0:0:0:0:0:0:0
+phiX174	10	.	C	<*>	0	.	DP=1;END=10;MIN_DP=1	GQ:DP:MIN_DP:QR:RO:QA:AO	71:1:1:71:1:0:0
+phiX174	11	.	G	<*>	0	.	DP=1;END=11;MIN_DP=1	GQ:DP:MIN_DP:QR:RO:QA:AO	36:1:1:36:1:0:0
+phiX174	12	.	C	<*>	0	.	DP=1;END=12;MIN_DP=1	GQ:DP:MIN_DP:QR:RO:QA:AO	35:1:1:35:1:0:0
+phiX174	13	.	T	<*>	0	.	DP=1;END=13;MIN_DP=1	GQ:DP:MIN_DP:QR:RO:QA:AO	61:1:1:61:1:0:0
+phiX174	14	.	T	<*>	0	.	DP=2;END=14;MIN_DP=2	GQ:DP:MIN_DP:QR:RO:QA:AO	142:2:2:142:2:0:0
+phiX174	15	.	C	<*>	0	.	DP=2;END=15;MIN_DP=2	GQ:DP:MIN_DP:QR:RO:QA:AO	119:2:2:119:2:0:0
+phiX174	16	.	C	<*>	0	.	DP=2;END=16;MIN_DP=2	GQ:DP:MIN_DP:QR:RO:QA:AO	89:2:2:89:2:0:0
+phiX174	17	.	A	<*>	0	.	DP=2;END=17;MIN_DP=2	GQ:DP:MIN_DP:QR:RO:QA:AO	107:2:2:107:2:0:0
+phiX174	18	.	T	<*>	0	.	DP=2;END=18;MIN_DP=2	GQ:DP:MIN_DP:QR:RO:QA:AO	117:2:2:117:2:0:0
+phiX174	19	.	G	<*>	0	.	DP=2;END=19;MIN_DP=2	GQ:DP:MIN_DP:QR:RO:QA:AO	109:2:2:109:2:0:0
+phiX174	20	.	A	<*>	0	.	DP=2;END=20;MIN_DP=2	GQ:DP:MIN_DP:QR:RO:QA:AO	103:2:2:103:2:0:0
+phiX174	21	.	C	<*>	0	.	DP=2;END=21;MIN_DP=2	GQ:DP:MIN_DP:QR:RO:QA:AO	98:2:2:98:2:0:0
+phiX174	22	.	G	<*>	0	.	DP=2;END=22;MIN_DP=2	GQ:DP:MIN_DP:QR:RO:QA:AO	120:2:2:120:2:0:0
+phiX174	23	.	C	<*>	0	.	DP=2;END=23;MIN_DP=2	GQ:DP:MIN_DP:QR:RO:QA:AO	111:2:2:111:2:0:0
+phiX174	24	.	A	<*>	0	.	DP=2;END=24;MIN_DP=2	GQ:DP:MIN_DP:QR:RO:QA:AO	120:2:2:120:2:0:0
+phiX174	25	.	G	<*>	0	.	DP=2;END=25;MIN_DP=2	GQ:DP:MIN_DP:QR:RO:QA:AO	111:2:2:111:2:0:0
+phiX174	26	.	A	<*>	0	.	DP=2;END=26;MIN_DP=2	GQ:DP:MIN_DP:QR:RO:QA:AO	119:2:2:119:2:0:0
+phiX174	27	.	A	<*>	0	.	DP=2;END=27;MIN_DP=2	GQ:DP:MIN_DP:QR:RO:QA:AO	142:2:2:142:2:0:0
+phiX174	28	.	G	<*>	0	.	DP=2;END=28;MIN_DP=2	GQ:DP:MIN_DP:QR:RO:QA:AO	142:2:2:142:2:0:0
+phiX174	29	.	T	<*>	0	.	DP=2;END=29;MIN_DP=2	GQ:DP:MIN_DP:QR:RO:QA:AO	142:2:2:142:2:0:0
+phiX174	30	.	T	<*>	0	.	DP=2;END=30;MIN_DP=2	GQ:DP:MIN_DP:QR:RO:QA:AO	102:2:2:102:2:0:0
+phiX174	31	.	A	<*>	0	.	DP=2;END=31;MIN_DP=2	GQ:DP:MIN_DP:QR:RO:QA:AO	110:2:2:110:2:0:0
+phiX174	32	.	A	<*>	0	.	DP=2;END=32;MIN_DP=2	GQ:DP:MIN_DP:QR:RO:QA:AO	40:2:2:71:1:31:1
+phiX174	33	.	C	<*>	0	.	DP=2;END=33;MIN_DP=2	GQ:DP:MIN_DP:QR:RO:QA:AO	127:2:2:127:2:0:0
+phiX174	34	.	A	<*>	0	.	DP=2;END=34;MIN_DP=2	GQ:DP:MIN_DP:QR:RO:QA:AO	68:2:2:68:2:0:0
+phiX174	35	.	C	<*>	0	.	DP=2;END=35;MIN_DP=2	GQ:DP:MIN_DP:QR:RO:QA:AO	94:2:2:94:2:0:0
+phiX174	36	.	T	<*>	0	.	DP=2;END=36;MIN_DP=2	GQ:DP:MIN_DP:QR:RO:QA:AO	115:2:2:115:2:0:0
+phiX174	37	.	T	<*>	0	.	DP=3;END=37;MIN_DP=3	GQ:DP:MIN_DP:QR:RO:QA:AO	180:3:3:180:3:0:0
+phiX174	38	.	T	<*>	0	.	DP=4;END=38;MIN_DP=4	GQ:DP:MIN_DP:QR:RO:QA:AO	212:4:4:212:4:0:0
+phiX174	39	.	C	<*>	0	.	DP=4;END=39;MIN_DP=4	GQ:DP:MIN_DP:QR:RO:QA:AO	223:4:4:223:4:0:0
+phiX174	40	.	G	<*>	0	.	DP=4;END=40;MIN_DP=4	GQ:DP:MIN_DP:QR:RO:QA:AO	284:4:4:284:4:0:0
+phiX174	41	.	G	<*>	0	.	DP=4;END=41;MIN_DP=4	GQ:DP:MIN_DP:QR:RO:QA:AO	279:4:4:279:4:0:0
+phiX174	42	.	A	<*>	0	.	DP=4;END=42;MIN_DP=4	GQ:DP:MIN_DP:QR:RO:QA:AO	284:4:4:284:4:0:0
+phiX174	43	.	T	<*>	0	.	DP=4;END=43;MIN_DP=4	GQ:DP:MIN_DP:QR:RO:QA:AO	261:4:4:261:4:0:0
+phiX174	44	.	A	<*>	0	.	DP=4;END=44;MIN_DP=4	GQ:DP:MIN_DP:QR:RO:QA:AO	235:4:4:235:4:0:0
+phiX174	45	.	T	<*>	0	.	DP=4;END=45;MIN_DP=4	GQ:DP:MIN_DP:QR:RO:QA:AO	247:4:4:247:4:0:0
+phiX174	46	.	T	<*>	0	.	DP=3;END=46;MIN_DP=3	GQ:DP:MIN_DP:QR:RO:QA:AO	114:3:3:142:2:28:1
+phiX174	47	.	T	<*>	0	.	DP=3;END=47;MIN_DP=3	GQ:DP:MIN_DP:QR:RO:QA:AO	157:3:3:157:3:0:0
+phiX174	48	.	C	<*>	0	.	DP=3;END=48;MIN_DP=3	GQ:DP:MIN_DP:QR:RO:QA:AO	151:3:3:151:3:0:0
+phiX174	49	.	T	<*>	0	.	DP=3;END=49;MIN_DP=3	GQ:DP:MIN_DP:QR:RO:QA:AO	170:3:3:170:3:0:0
+phiX174	50	.	G	<*>	0	.	DP=2;END=50;MIN_DP=2	GQ:DP:MIN_DP:QR:RO:QA:AO	142:2:2:142:2:0:0
+phiX174	51	.	A	<*>	0	.	DP=2;END=51;MIN_DP=2	GQ:DP:MIN_DP:QR:RO:QA:AO	111:2:2:111:2:0:0
+phiX174	52	.	T	<*>	0	.	DP=2;END=52;MIN_DP=2	GQ:DP:MIN_DP:QR:RO:QA:AO	142:2:2:142:2:0:0
+phiX174	53	.	G	<*>	0	.	DP=2;END=53;MIN_DP=2	GQ:DP:MIN_DP:QR:RO:QA:AO	142:2:2:142:2:0:0
+phiX174	54	.	A	<*>	0	.	DP=3;END=54;MIN_DP=3	GQ:DP:MIN_DP:QR:RO:QA:AO	209:3:3:209:3:0:0
+phiX174	55	.	G	<*>	0	.	DP=3;END=55;MIN_DP=3	GQ:DP:MIN_DP:QR:RO:QA:AO	182:3:3:182:3:0:0
+phiX174	56	.	T	<*>	0	.	DP=3;END=56;MIN_DP=3	GQ:DP:MIN_DP:QR:RO:QA:AO	198:3:3:198:3:0:0
+phiX174	57	.	C	<*>	0	.	DP=3;END=57;MIN_DP=3	GQ:DP:MIN_DP:QR:RO:QA:AO	193:3:3:193:3:0:0
+phiX174	58	.	G	<*>	0	.	DP=3;END=58;MIN_DP=3	GQ:DP:MIN_DP:QR:RO:QA:AO	144:3:3:144:3:0:0
+phiX174	59	.	A	<*>	0	.	DP=3;END=59;MIN_DP=3	GQ:DP:MIN_DP:QR:RO:QA:AO	107:3:3:142:2:35:1
+phiX174	60	.	A	<*>	0	.	DP=3;END=60;MIN_DP=3	GQ:DP:MIN_DP:QR:RO:QA:AO	194:3:3:194:3:0:0
+phiX174	61	.	A	<*>	0	.	DP=4;END=61;MIN_DP=4	GQ:DP:MIN_DP:QR:RO:QA:AO	211:4:4:211:4:0:0
+phiX174	62	.	A	<*>	0	.	DP=4;END=62;MIN_DP=4	GQ:DP:MIN_DP:QR:RO:QA:AO	180:4:4:180:4:0:0
+phiX174	63	.	A	<*>	0	.	DP=4;END=63;MIN_DP=4	GQ:DP:MIN_DP:QR:RO:QA:AO	149:4:4:180:3:31:1
+phiX174	64	.	T	<*>	0	.	DP=4;END=64;MIN_DP=4	GQ:DP:MIN_DP:QR:RO:QA:AO	232:4:4:232:4:0:0
+phiX174	65	.	T	<*>	0	.	DP=5;END=65;MIN_DP=5	GQ:DP:MIN_DP:QR:RO:QA:AO	288:5:5:288:5:0:0
+phiX174	66	.	A	<*>	0	.	DP=5;END=66;MIN_DP=5	GQ:DP:MIN_DP:QR:RO:QA:AO	241:5:5:241:5:0:0
+phiX174	67	.	T	<*>	0	.	DP=5;END=67;MIN_DP=5	GQ:DP:MIN_DP:QR:RO:QA:AO	201:5:5:232:4:31:1
+phiX174	68	.	C	<*>	0	.	DP=5;END=68;MIN_DP=5	GQ:DP:MIN_DP:QR:RO:QA:AO	277:5:5:277:5:0:0
+phiX174	69	.	T	<*>	0	.	DP=5;END=69;MIN_DP=5	GQ:DP:MIN_DP:QR:RO:QA:AO	302:5:5:302:5:0:0
+phiX174	70	.	T	<*>	0	.	DP=6;END=70;MIN_DP=6	GQ:DP:MIN_DP:QR:RO:QA:AO	328:6:6:328:6:0:0
+phiX174	71	.	G	<*>	0	.	DP=6;END=71;MIN_DP=6	GQ:DP:MIN_DP:QR:RO:QA:AO	356:6:6:356:6:0:0
+phiX174	72	.	A	<*>	0	.	DP=6;END=72;MIN_DP=6	GQ:DP:MIN_DP:QR:RO:QA:AO	305:6:6:305:6:0:0
+phiX174	73	.	T	<*>	0	.	DP=5;END=73;MIN_DP=5	GQ:DP:MIN_DP:QR:RO:QA:AO	280:5:5:280:5:0:0
+phiX174	74	.	A	<*>	0	.	DP=4;END=74;MIN_DP=4	GQ:DP:MIN_DP:QR:RO:QA:AO	257:4:4:257:4:0:0
+phiX174	75	.	A	<*>	0	.	DP=4;END=75;MIN_DP=4	GQ:DP:MIN_DP:QR:RO:QA:AO	260:4:4:260:4:0:0
+phiX174	76	.	A	<*>	0	.	DP=5;END=76;MIN_DP=5	GQ:DP:MIN_DP:QR:RO:QA:AO	329:5:5:329:5:0:0
+phiX174	77	.	G	<*>	0	.	DP=5;END=77;MIN_DP=5	GQ:DP:MIN_DP:QR:RO:QA:AO	265:5:5:265:5:0:0
+phiX174	78	.	C	<*>	0	.	DP=5;END=78;MIN_DP=5	GQ:DP:MIN_DP:QR:RO:QA:AO	309:5:5:309:5:0:0
+phiX174	79	.	A	<*>	0	.	DP=5;END=79;MIN_DP=5	GQ:DP:MIN_DP:QR:RO:QA:AO	322:5:5:322:5:0:0
+phiX174	80	.	G	<*>	0	.	DP=6;END=80;MIN_DP=6	GQ:DP:MIN_DP:QR:RO:QA:AO	426:6:6:426:6:0:0
+phiX174	81	.	G	<*>	0	.	DP=6;END=81;MIN_DP=6	GQ:DP:MIN_DP:QR:RO:QA:AO	248:6:6:317:5:69:1
+phiX174	82	.	A	<*>	0	.	DP=6;END=82;MIN_DP=6	GQ:DP:MIN_DP:QR:RO:QA:AO	370:6:6:370:6:0:0
+phiX174	83	.	A	<*>	0	.	DP=6;END=83;MIN_DP=6	GQ:DP:MIN_DP:QR:RO:QA:AO	318:6:6:318:6:0:0
+phiX174	84	.	T	<*>	0	.	DP=6;END=84;MIN_DP=6	GQ:DP:MIN_DP:QR:RO:QA:AO	382:6:6:382:6:0:0
+phiX174	85	.	T	<*>	0	.	DP=6;END=85;MIN_DP=6	GQ:DP:MIN_DP:QR:RO:QA:AO	290:6:6:290:6:0:0
+phiX174	86	.	A	<*>	0	.	DP=6;END=86;MIN_DP=6	GQ:DP:MIN_DP:QR:RO:QA:AO	284:6:6:284:6:0:0
+phiX174	87	.	C	<*>	0	.	DP=6;END=87;MIN_DP=6	GQ:DP:MIN_DP:QR:RO:QA:AO	363:6:6:363:6:0:0
+phiX174	88	.	T	<*>	0	.	DP=6;END=88;MIN_DP=6	GQ:DP:MIN_DP:QR:RO:QA:AO	332:6:6:332:6:0:0
+phiX174	89	.	A	<*>	0	.	DP=6;END=89;MIN_DP=6	GQ:DP:MIN_DP:QR:RO:QA:AO	368:6:6:368:6:0:0
+phiX174	90	.	C	<*>	0	.	DP=5;END=90;MIN_DP=5	GQ:DP:MIN_DP:QR:RO:QA:AO	324:5:5:324:5:0:0
+phiX174	91	.	T	<*>	0	.	DP=5;END=91;MIN_DP=5	GQ:DP:MIN_DP:QR:RO:QA:AO	355:5:5:355:5:0:0
+phiX174	92	.	G	<*>	0	.	DP=5;END=92;MIN_DP=5	GQ:DP:MIN_DP:QR:RO:QA:AO	355:5:5:355:5:0:0
+phiX174	93	.	C	<*>	0	.	DP=5;END=93;MIN_DP=5	GQ:DP:MIN_DP:QR:RO:QA:AO	355:5:5:355:5:0:0
+phiX174	94	.	T	<*>	0	.	DP=5;END=94;MIN_DP=5	GQ:DP:MIN_DP:QR:RO:QA:AO	338:5:5:338:5:0:0
+phiX174	95	.	T	<*>	0	.	DP=5;END=95;MIN_DP=5	GQ:DP:MIN_DP:QR:RO:QA:AO	323:5:5:323:5:0:0
+phiX174	96	.	G	<*>	0	.	DP=5;END=96;MIN_DP=5	GQ:DP:MIN_DP:QR:RO:QA:AO	318:5:5:318:5:0:0
+phiX174	97	.	T	<*>	0	.	DP=4;END=97;MIN_DP=4	GQ:DP:MIN_DP:QR:RO:QA:AO	250:4:4:250:4:0:0
+phiX174	98	.	T	<*>	0	.	DP=4;END=98;MIN_DP=4	GQ:DP:MIN_DP:QR:RO:QA:AO	233:4:4:233:4:0:0
+phiX174	99	.	T	<*>	0	.	DP=4;END=99;MIN_DP=4	GQ:DP:MIN_DP:QR:RO:QA:AO	225:4:4:225:4:0:0
+phiX174	100	.	A	<*>	0	.	DP=4;END=100;MIN_DP=4	GQ:DP:MIN_DP:QR:RO:QA:AO	247:4:4:247:4:0:0
+phiX174	101	.	C	<*>	0	.	DP=3;END=101;MIN_DP=3	GQ:DP:MIN_DP:QR:RO:QA:AO	194:3:3:194:3:0:0
+phiX174	102	.	G	<*>	0	.	DP=3;END=102;MIN_DP=3	GQ:DP:MIN_DP:QR:RO:QA:AO	213:3:3:213:3:0:0
+phiX174	103	.	A	<*>	0	.	DP=3;END=103;MIN_DP=3	GQ:DP:MIN_DP:QR:RO:QA:AO	213:3:3:213:3:0:0
+phiX174	104	.	A	<*>	0	.	DP=3;END=104;MIN_DP=3	GQ:DP:MIN_DP:QR:RO:QA:AO	213:3:3:213:3:0:0
+phiX174	105	.	T	<*>	0	.	DP=3;END=105;MIN_DP=3	GQ:DP:MIN_DP:QR:RO:QA:AO	213:3:3:213:3:0:0
+phiX174	106	.	T	<*>	0	.	DP=2;END=106;MIN_DP=2	GQ:DP:MIN_DP:QR:RO:QA:AO	142:2:2:142:2:0:0
+phiX174	107	.	A	<*>	0	.	DP=2;END=107;MIN_DP=2	GQ:DP:MIN_DP:QR:RO:QA:AO	142:2:2:142:2:0:0
+phiX174	108	.	A	<*>	0	.	DP=2;END=108;MIN_DP=2	GQ:DP:MIN_DP:QR:RO:QA:AO	142:2:2:142:2:0:0
+phiX174	109	.	A	<*>	0	.	DP=3;END=109;MIN_DP=3	GQ:DP:MIN_DP:QR:RO:QA:AO	171:3:3:171:3:0:0
+phiX174	110	.	T	<*>	0	.	DP=3;END=110;MIN_DP=3	GQ:DP:MIN_DP:QR:RO:QA:AO	163:3:3:163:3:0:0
+phiX174	111	.	C	<*>	0	.	DP=4;END=111;MIN_DP=4	GQ:DP:MIN_DP:QR:RO:QA:AO	251:4:4:251:4:0:0
+phiX174	112	.	G	<*>	0	.	DP=3;END=112;MIN_DP=3	GQ:DP:MIN_DP:QR:RO:QA:AO	186:3:3:186:3:0:0
+phiX174	113	.	A	<*>	0	.	DP=3;END=113;MIN_DP=3	GQ:DP:MIN_DP:QR:RO:QA:AO	176:3:3:176:3:0:0
+phiX174	114	.	A	<*>	0	.	DP=3;END=114;MIN_DP=3	GQ:DP:MIN_DP:QR:RO:QA:AO	187:3:3:187:3:0:0
+phiX174	115	.	G	<*>	0	.	DP=3;END=115;MIN_DP=3	GQ:DP:MIN_DP:QR:RO:QA:AO	162:3:3:162:3:0:0
+phiX174	116	.	T	<*>	0	.	DP=2;END=116;MIN_DP=2	GQ:DP:MIN_DP:QR:RO:QA:AO	99:2:2:99:2:0:0
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+phiX174	366	.	T	<*>	0	.	DP=6;END=366;MIN_DP=6	GQ:DP:MIN_DP:QR:RO:QA:AO	364:6:6:364:6:0:0
+phiX174	367	.	C	<*>	0	.	DP=6;END=367;MIN_DP=6	GQ:DP:MIN_DP:QR:RO:QA:AO	387:6:6:387:6:0:0
+phiX174	368	.	A	<*>	0	.	DP=6;END=368;MIN_DP=6	GQ:DP:MIN_DP:QR:RO:QA:AO	426:6:6:426:6:0:0
+phiX174	369	.	A	<*>	0	.	DP=6;END=369;MIN_DP=6	GQ:DP:MIN_DP:QR:RO:QA:AO	426:6:6:426:6:0:0
+phiX174	370	.	C	<*>	0	.	DP=5;END=370;MIN_DP=5	GQ:DP:MIN_DP:QR:RO:QA:AO	296:5:5:296:5:0:0
+phiX174	371	.	C	<*>	0	.	DP=5;END=371;MIN_DP=5	GQ:DP:MIN_DP:QR:RO:QA:AO	296:5:5:296:5:0:0
+phiX174	372	.	A	<*>	0	.	DP=5;END=372;MIN_DP=5	GQ:DP:MIN_DP:QR:RO:QA:AO	179:5:5:250:4:71:1
+phiX174	373	.	C	<*>	0	.	DP=5;END=373;MIN_DP=5	GQ:DP:MIN_DP:QR:RO:QA:AO	317:5:5:317:5:0:0
+phiX174	374	.	T	G	23.3387	.	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=1.58025;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=75;QR=141;RO=2;RPL=1;RPP=3.0103;RPPR=7.35324;RPR=1;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=0;SRP=7.35324;SRR=2;TYPE=snp	GT:DP:AD:RO:QR:AO:QA:GL	0/1:4:2,2:2:141:2:75:-5.19433,0,-3.54586
+phiX174	375	.	A	<*>	0	.	DP=4;END=375;MIN_DP=4	GQ:DP:MIN_DP:QR:RO:QA:AO	216:4:4:216:4:0:0
+
diff -r 85dc96ebc770 -r 0d8581534009 test-data/freebayes-phix174.gvcf
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/freebayes-phix174.gvcf	Tue Aug 05 13:47:58 2025 +0000
@@ -0,0 +1,126 @@
+##fileformat=VCFv4.2
+##fileDate=20250805
+##source=freeBayes v1.3.10
+##reference=localref.fa
+##contig=<ID=phiX174,length=5386>
+##phasing=none
+##commandline="freebayes --region phiX174:0..5386 -f freebayes-phix174.fasta freebayes-phix174.bam --gvcf"
+##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of samples with data">
+##INFO=<ID=DP,Number=1,Type=Integer,Description="Total read depth at the locus">
+##INFO=<ID=DPB,Number=1,Type=Float,Description="Total read depth per bp at the locus; bases in reads overlapping / bases in haplotype">
+##INFO=<ID=AC,Number=A,Type=Integer,Description="Total number of alternate alleles in called genotypes">
+##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
+##INFO=<ID=AF,Number=A,Type=Float,Description="Estimated allele frequency in the range (0,1]">
+##INFO=<ID=RO,Number=1,Type=Integer,Description="Count of full observations of the reference haplotype.">
+##INFO=<ID=AO,Number=A,Type=Integer,Description="Count of full observations of this alternate haplotype.">
+##INFO=<ID=PRO,Number=1,Type=Float,Description="Reference allele observation count, with partial observations recorded fractionally">
+##INFO=<ID=PAO,Number=A,Type=Float,Description="Alternate allele observations, with partial observations recorded fractionally">
+##INFO=<ID=QR,Number=1,Type=Integer,Description="Reference allele quality sum in phred">
+##INFO=<ID=QA,Number=A,Type=Integer,Description="Alternate allele quality sum in phred">
+##INFO=<ID=PQR,Number=1,Type=Float,Description="Reference allele quality sum in phred for partial observations">
+##INFO=<ID=PQA,Number=A,Type=Float,Description="Alternate allele quality sum in phred for partial observations">
+##INFO=<ID=SRF,Number=1,Type=Integer,Description="Number of reference observations on the forward strand">
+##INFO=<ID=SRR,Number=1,Type=Integer,Description="Number of reference observations on the reverse strand">
+##INFO=<ID=SAF,Number=A,Type=Integer,Description="Number of alternate observations on the forward strand">
+##INFO=<ID=SAR,Number=A,Type=Integer,Description="Number of alternate observations on the reverse strand">
+##INFO=<ID=SRP,Number=1,Type=Float,Description="Strand balance probability for the reference allele: Phred-scaled upper-bounds estimate of the probability of observing the deviation between SRF and SRR given E(SRF/SRR) ~ 0.5, derived using Hoeffding's inequality">
+##INFO=<ID=SAP,Number=A,Type=Float,Description="Strand balance probability for the alternate allele: Phred-scaled upper-bounds estimate of the probability of observing the deviation between SAF and SAR given E(SAF/SAR) ~ 0.5, derived using Hoeffding's inequality">
+##INFO=<ID=AB,Number=A,Type=Float,Description="Allele balance at heterozygous sites: a number between 0 and 1 representing the ratio of reads showing the reference allele to all reads, considering only reads from individuals called as heterozygous">
+##INFO=<ID=ABP,Number=A,Type=Float,Description="Allele balance probability at heterozygous sites: Phred-scaled upper-bounds estimate of the probability of observing the deviation between ABR and ABA given E(ABR/ABA) ~ 0.5, derived using Hoeffding's inequality">
+##INFO=<ID=RUN,Number=A,Type=Integer,Description="Run length: the number of consecutive repeats of the alternate allele in the reference genome">
+##INFO=<ID=RPP,Number=A,Type=Float,Description="Read Placement Probability: Phred-scaled upper-bounds estimate of the probability of observing the deviation between RPL and RPR given E(RPL/RPR) ~ 0.5, derived using Hoeffding's inequality">
+##INFO=<ID=RPPR,Number=1,Type=Float,Description="Read Placement Probability for reference observations: Phred-scaled upper-bounds estimate of the probability of observing the deviation between RPL and RPR given E(RPL/RPR) ~ 0.5, derived using Hoeffding's inequality">
+##INFO=<ID=RPL,Number=A,Type=Float,Description="Reads Placed Left: number of reads supporting the alternate balanced to the left (5') of the alternate allele">
+##INFO=<ID=RPR,Number=A,Type=Float,Description="Reads Placed Right: number of reads supporting the alternate balanced to the right (3') of the alternate allele">
+##INFO=<ID=EPP,Number=A,Type=Float,Description="End Placement Probability: Phred-scaled upper-bounds estimate of the probability of observing the deviation between EL and ER given E(EL/ER) ~ 0.5, derived using Hoeffding's inequality">
+##INFO=<ID=EPPR,Number=1,Type=Float,Description="End Placement Probability for reference observations: Phred-scaled upper-bounds estimate of the probability of observing the deviation between EL and ER given E(EL/ER) ~ 0.5, derived using Hoeffding's inequality">
+##INFO=<ID=DPRA,Number=A,Type=Float,Description="Alternate allele depth ratio.  Ratio between depth in samples with each called alternate allele and those without.">
+##INFO=<ID=ODDS,Number=1,Type=Float,Description="The log odds ratio of the best genotype combination to the second-best.">
+##INFO=<ID=GTI,Number=1,Type=Integer,Description="Number of genotyping iterations required to reach convergence or bailout.">
+##INFO=<ID=TYPE,Number=A,Type=String,Description="The type of allele, either snp, mnp, ins, del, or complex.">
+##INFO=<ID=CIGAR,Number=A,Type=String,Description="The extended CIGAR representation of each alternate allele, with the exception that '=' is replaced by 'M' to ease VCF parsing.  Note that INDEL alleles do not have the first matched base (which is provided by default, per the spec) referred to by the CIGAR.">
+##INFO=<ID=NUMALT,Number=1,Type=Integer,Description="Number of unique non-reference alleles in called genotypes at this position.">
+##INFO=<ID=MEANALT,Number=A,Type=Float,Description="Mean number of unique non-reference allele observations per sample with the corresponding alternate alleles.">
+##INFO=<ID=LEN,Number=A,Type=Integer,Description="allele length">
+##INFO=<ID=MQM,Number=A,Type=Float,Description="Mean mapping quality of observed alternate alleles">
+##INFO=<ID=MQMR,Number=1,Type=Float,Description="Mean mapping quality of observed reference alleles">
+##INFO=<ID=PAIRED,Number=A,Type=Float,Description="Proportion of observed alternate alleles which are supported by properly paired read fragments">
+##INFO=<ID=PAIREDR,Number=1,Type=Float,Description="Proportion of observed reference alleles which are supported by properly paired read fragments">
+##INFO=<ID=MIN_DP,Number=1,Type=Integer,Description="Minimum depth in gVCF output block.">
+##INFO=<ID=END,Number=1,Type=Integer,Description="Last position (inclusive) in gVCF output record.">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=GQ,Number=1,Type=Float,Description="Genotype Quality, the Phred-scaled marginal (or unconditional) probability of the called genotype">
+##FORMAT=<ID=GL,Number=G,Type=Float,Description="Genotype Likelihood, log10-scaled likelihoods of the data given the called genotype for each possible genotype generated from the reference and alternate alleles given the sample ploidy">
+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
+##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Number of observation for each allele">
+##FORMAT=<ID=RO,Number=1,Type=Integer,Description="Reference allele observation count">
+##FORMAT=<ID=QR,Number=1,Type=Float,Description="Sum of quality of the reference observations">
+##FORMAT=<ID=AO,Number=A,Type=Integer,Description="Alternate allele observation count">
+##FORMAT=<ID=QA,Number=A,Type=Float,Description="Sum of quality of the alternate observations">
+##FORMAT=<ID=MIN_DP,Number=1,Type=Integer,Description="Minimum depth in gVCF output block.">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	unknown
+phiX174	1	.	G	<*>	0	.	DP=4;END=310;MIN_DP=0	GQ:DP:MIN_DP:QR:RO:QA:AO	86804:4:0:87601:4:797:0
+phiX174	311	.	A	G	0.00392026	.	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=7.0097;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=70;QR=478;RO=7;RPL=0;RPP=7.35324;RPPR=3.32051;RPR=2;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=5;SRP=5.80219;SRR=2;TYPE=snp	GT:DP:AD:RO:QR:AO:QA:GL	0/1:9:7,2:7:478:2:70:-1.91487,0,-18.7749
+phiX174	312	.	T	<*>	0	.	DP=8;END=373;MIN_DP=5	GQ:DP:MIN_DP:QR:RO:QA:AO	31465:8:5:31945:8:480:0
+phiX174	374	.	T	G	23.3387	.	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=1.58025;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=75;QR=141;RO=2;RPL=1;RPP=3.0103;RPPR=7.35324;RPR=1;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=0;SRP=7.35324;SRR=2;TYPE=snp	GT:DP:AD:RO:QR:AO:QA:GL	0/1:4:2,2:2:141:2:75:-5.19433,0,-3.54586
+phiX174	375	.	A	<*>	0	.	DP=6;END=912;MIN_DP=0	GQ:DP:MIN_DP:QR:RO:QA:AO	227000:6:0:229264:6:2264:0
+phiX174	913	.	A	C	2.27318	.	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=0.380296;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=67;QR=171;RO=3;RPL=1;RPP=3.0103;RPPR=3.73412;RPR=1;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=3;SRP=9.52472;SRR=0;TYPE=snp	GT:DP:AD:RO:QR:AO:QA:GL	0/1:5:3,2:3:171:2:67:-3.54411,0,-6.47921
+phiX174	914	.	G	<*>	0	.	DP=7;END=1204;MIN_DP=0	GQ:DP:MIN_DP:QR:RO:QA:AO	129636:7:0:130843:7:1207:0
+phiX174	1205	.	A	C	0.00388031	.	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=7.01995;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=67;QR=456;RO=8;RPL=2;RPP=7.35324;RPPR=7.35324;RPR=0;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=2;SRP=7.35324;SRR=6;TYPE=snp	GT:DP:AD:RO:QR:AO:QA:GL	0/1:10:8,2:8:456:2:67:-2.11454,0,-21.3383
+phiX174	1206	.	C	<*>	0	.	DP=9;END=1244;MIN_DP=0	GQ:DP:MIN_DP:QR:RO:QA:AO	20203:9:0:20483:8:280:0
+phiX174	1245	.	G	T	0.0324554	.	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=4.8927;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=70;QR=389;RO=7;RPL=2;RPP=7.35324;RPPR=3.32051;RPR=0;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=0;SRP=18.2106;SRR=7;TYPE=snp	GT:DP:AD:RO:QR:AO:QA:GL	0/1:9:7,2:7:389:2:70:-2.83427,0,-14.5618
+phiX174	1246	.	G	<*>	0	.	DP=9;END=1248;MIN_DP=9	GQ:DP:MIN_DP:QR:RO:QA:AO	1576:9:9:1576:9:0:0
+phiX174	1249	.	T	G	0.0166698	.	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=5.56079;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=74;QR=464;RO=7;RPL=1;RPP=3.0103;RPPR=5.80219;RPR=1;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=2;SRP=5.80219;SRR=5;TYPE=snp	GT:DP:AD:RO:QR:AO:QA:GL	0/1:9:7,2:7:464:2:74:-1.94207,0,-16.5662
+phiX174	1250	.	A	<*>	0	.	DP=9;END=1444;MIN_DP=0	GQ:DP:MIN_DP:QR:RO:QA:AO	117232:9:0:118408:9:1176:0
+phiX174	1445	.	C	A	0.147157	.	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=3.36782;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=76;QR=273;RO=5;RPL=1;RPP=3.0103;RPPR=6.91895;RPR=1;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=2;SRP=3.44459;SRR=3;TYPE=snp	GT:DP:AD:RO:QR:AO:QA:GL	0/1:7:5,2:5:273:2:76:-2.52649,0,-12.4911
+phiX174	1446	.	C	<*>	0	.	DP=5;END=1576;MIN_DP=1	GQ:DP:MIN_DP:QR:RO:QA:AO	40596:5:1:41046:5:450:0
+phiX174	1577	.	A	C	0.0123232	.	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=5.8634;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=60;QR=460;RO=7;RPL=1;RPP=3.0103;RPPR=10.7656;RPR=1;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=4;SRP=3.32051;SRR=3;TYPE=snp	GT:DP:AD:RO:QR:AO:QA:GL	0/1:9:7,2:7:460:2:60:-1.81064,0,-19.8257
+phiX174	1578	.	T	<*>	0	.	DP=11;END=1630;MIN_DP=0	GQ:DP:MIN_DP:QR:RO:QA:AO	37187:11:0:37576:11:389:0
+phiX174	1631	.	T	G	0.00100612	.	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=8.3701;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=68;QR=500;RO=8;RPL=0;RPP=7.35324;RPPR=3.0103;RPR=2;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=3;SRP=4.09604;SRR=5;TYPE=snp	GT:DP:AD:RO:QR:AO:QA:GL	0/1:10:8,2:8:500:2:68:-1.52818,0,-17.3788
+phiX174	1632	.	A	<*>	0	.	DP=10;END=1664;MIN_DP=0	GQ:DP:MIN_DP:QR:RO:QA:AO	21423:10:0:21616:10:193:0
+phiX174	1665	.	C	A	0.0164128	.	AB=0.166667;ABP=14.5915;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=12;DPB=12;DPRA=0;EPP=7.35324;EPPR=5.18177;GTI=0;LEN=1;MEANALT=2;MQM=37;MQMR=30.3333;NS=1;NUMALT=1;ODDS=5.57635;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=65;QR=587;RO=9;RPL=1;RPP=3.0103;RPPR=5.18177;RPR=1;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=4;SRP=3.25157;SRR=5;TYPE=snp	GT:DP:AD:RO:QR:AO:QA:GL	0/1:12:9,2:9:587:2:65:-2.35331,0,-21.269
+phiX174	1666	.	A	<*>	0	.	DP=10;END=1771;MIN_DP=4	GQ:DP:MIN_DP:QR:RO:QA:AO	62611:10:4:63430:9:819:0
+phiX174	1772	.	T	G	0.0180574	.	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=5.48067;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=59;QR=425;RO=7;RPL=1;RPP=3.0103;RPPR=3.32051;RPR=1;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=1;SRP=10.7656;SRR=6;TYPE=snp	GT:DP:AD:RO:QR:AO:QA:GL	0/1:10:7,2:7:425:2:59:-1.97686,0,-17.3816
+phiX174	1773	.	T	<*>	0	.	DP=11;END=1785;MIN_DP=9	GQ:DP:MIN_DP:QR:RO:QA:AO	8476:11:9:8574:11:98:0
+phiX174	1786	.	T	G	7.94817e-05	.	AB=0.166667;ABP=14.5915;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=12;DPB=12;DPRA=0;EPP=7.35324;EPPR=3.87889;GTI=0;LEN=1;MEANALT=1;MQM=25;MQMR=33.4;NS=1;NUMALT=1;ODDS=10.9085;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=59;QR=537;RO=10;RPL=0;RPP=7.35324;RPPR=6.48466;RPR=2;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=1;SRP=16.9077;SRR=9;TYPE=snp	GT:DP:AD:RO:QR:AO:QA:GL	0/1:12:10,2:10:537:2:59:-0.861483,0,-25.1364
+phiX174	1787	.	G	<*>	0	.	DP=4;END=1944;MIN_DP=1	GQ:DP:MIN_DP:QR:RO:QA:AO	47842:4:1:48427:4:585:0
+phiX174	1945	.	T	G	1.01422	.	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=1.3354;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=59;QR=263;RO=4;RPL=1;RPP=3.0103;RPPR=5.18177;RPR=1;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=2;SRP=3.0103;SRR=2;TYPE=snp	GT:DP:AD:RO:QR:AO:QA:GL	0/1:6:4,2:4:263:2:59:-3.25425,0,-11.8637
+phiX174	1946	.	G	<*>	0	.	DP=6;END=2229;MIN_DP=0	GQ:DP:MIN_DP:QR:RO:QA:AO	106303:6:0:107388:5:1085:0
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