# HG changeset patch
# User matthias
# Date 1561032798 14400
# Node ID 56d3555cf5f79c42f42dd317453706307406b1fa
# Parent  c23695f62bdd6f40cd5cfc21590452fcb7740206
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f507c4eaca0fe04e730d7c3bbb9e9d2488239a9f

diff -r c23695f62bdd -r 56d3555cf5f7 macros.xml
--- a/macros.xml	Wed Feb 27 09:52:16 2019 -0500
+++ b/macros.xml	Thu Jun 20 08:13:18 2019 -0400
@@ -7,7 +7,7 @@
         </requirements>
     </xml>
 
-    <token name="@STACKS_VERSION@">2.3c</token>
+    <token name="@STACKS_VERSION@">2.4</token>
     <token name="@WRAPPER_VERSION@">0</token>
     <!-- fix to 18.01 since https://github.com/galaxyproject/galaxy/pull/7032 -->
     <token name="@PROFILE@">18.01</token>
@@ -116,7 +116,7 @@
         #end if
     ]]></token>
     <xml name="in_log">
-        <param name="add_log" type="boolean" checked="false" truevalue="yes" falsevalue="no" label="Add log output as dataset" />
+        <param name="add_log" type="boolean" checked="true" truevalue="yes" falsevalue="no" label="Add log output as dataset" />
     </xml>
     <xml name="out_log">
         <data format="txt" name="output_log" label="${tool.name} on ${on_string} log file">
@@ -138,7 +138,7 @@
         <param name="input_bam" format="bam" type="data" multiple="true" optional="false" label="Aligned data" help="either the matches to the catalog (bam), i.e. tsv2bam, or reads aligned to a reference" />
     </xml>
     <xml name="input_aln_macro">
-        <param name="input_aln" format="tabular,txt" type="data_collection" collection_type="list" label="Assembled contigs and variant sites" help="output from previous Stacks pipeline steps (e.g. gstacks, denovo_map, or refmap)" argument="-P" />
+        <param name="input_aln" format="vcf,fasta.gz" type="data_collection" collection_type="list" label="Assembled contigs and variant sites" help="output from previous Stacks pipeline steps (e.g. gstacks, denovo_map, or refmap)" argument="-P" />
     </xml>
 
     <!-- code for creating links to the data sets from previous pipeline steps
@@ -212,7 +212,7 @@
 
     <xml name="fastq_input_bc_file" token_multiple="false" token_listtype="paired">
         <expand macro="fastq_input_bc" multiple="@MULTIPLE@" listtype="@LISTTYPE@">
-            <param name="barcode" argument="-b" type="data"  format="tabular,txt" label="Barcode file" />
+            <param name="barcode" argument="-b" type="data" format="tabular,txt" label="Barcode file" />
         </expand>
     </xml>
 
@@ -509,6 +509,10 @@
             <filter>populations_output['plink']</filter>
         </data>
 
+		<!--structure populations.hzar-->
+        <data format="tabular" name="out_hzar" label="${tool.name} on ${on_string} hzar format" from_work_dir="stacks_outputs/populations.hzar.csv">
+            <filter>populations_output['hzar']</filter>
+        </data>
         <!--structure populations.structure-->
         <data format="tabular" name="out_structure" label="${tool.name} on ${on_string} Structure format" from_work_dir="stacks_outputs/populations.structure">
             <filter>populations_output['structure']</filter>
@@ -560,9 +564,13 @@
         </expand>
     </xml>
 
-    <!-- variant calling option for use in gstacks and denovomap -->
-    <xml name="variant_calling_options_vg">
-        <param argument="--var-alpha" name="var_alpha" type="float" value="0.01" min="0" label="Alpha threshold for discovering SNPs" />
+	<!-- variant calling option for use in gstacks and denovomap 
+         default for var_alpha is 0.01 if model == marukilow (which is the case in denovomap and refmap)
+         otherwise no default is is available and gstacks will output and error
+         "Error: No value was provided for \-\-var-alpha and there is no default for this model)" 
+	-->
+    <xml name="variant_calling_options_vg" token_varalpha_default="">
+        <param argument="--var-alpha" name="var_alpha" type="float" value="@VARALPHA_DEFAULT@" min="0" label="Alpha threshold for discovering SNPs" help="Default is 0.01 if the marukilow model is used (which is the case in refmap and denovomap), otherwise no default value is available." />
         <param argument="--gt-alpha" name="gt_alpha" type="float" value="0.05" min="0" label="Alpha threshold for calling genotypes" />
     </xml>
 
diff -r c23695f62bdd -r 56d3555cf5f7 test-data/.gentest.sh.swp
Binary file test-data/.gentest.sh.swp has changed
diff -r c23695f62bdd -r 56d3555cf5f7 test-data/clonefilter/clonefilter.log
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/clonefilter/clonefilter.log	Thu Jun 20 08:13:18 2019 -0400
@@ -0,0 +1,8 @@
+Processing single-end data.
+Searching for inline oligo on single-end read.
+Found 1 input file(s).
+Processing file 1 of 1 [R1_0001.fastq.gz]
+  Reading data from:
+  stacks_inputs/R1_0001.fastq.gz
+Calculating the distribution of cloned read pairs...
+5 pairs of reads input. 4 pairs of reads output, discarded 0 pairs of reads, 20.00% clone reads.
diff -r c23695f62bdd -r 56d3555cf5f7 test-data/cstacks/catalog.alleles.tsv
--- a/test-data/cstacks/catalog.alleles.tsv	Wed Feb 27 09:52:16 2019 -0500
+++ b/test-data/cstacks/catalog.alleles.tsv	Thu Jun 20 08:13:18 2019 -0400
@@ -1,3 +1,3 @@
-# cstacks version 2.3b; catalog generated on 2019-02-21 19:57:38
+# cstacks version 2.4; catalog generated on 2019-06-18 10:34:45
 0	1	AC	0	0
 0	1	CA	0	0
diff -r c23695f62bdd -r 56d3555cf5f7 test-data/cstacks/catalog.snps.tsv
--- a/test-data/cstacks/catalog.snps.tsv	Wed Feb 27 09:52:16 2019 -0500
+++ b/test-data/cstacks/catalog.snps.tsv	Thu Jun 20 08:13:18 2019 -0400
@@ -1,3 +1,3 @@
-# cstacks version 2.3b; catalog generated on 2019-02-21 19:57:38
+# cstacks version 2.4; catalog generated on 2019-06-18 10:34:45
 0	1	33	E	0	A	C	-	-
 0	1	88	E	0	A	C	-	-
diff -r c23695f62bdd -r 56d3555cf5f7 test-data/cstacks/catalog.tags.tsv
--- a/test-data/cstacks/catalog.tags.tsv	Wed Feb 27 09:52:16 2019 -0500
+++ b/test-data/cstacks/catalog.tags.tsv	Thu Jun 20 08:13:18 2019 -0400
@@ -1,4 +1,4 @@
-# cstacks version 2.3b; catalog generated on 2019-02-21 19:57:38
+# cstacks version 2.4; catalog generated on 2019-06-18 10:34:45
 0	1	consensus	0	1_1,2_1	AATTCGTTTGCTGCTTCAGGAATCTCTCGTATAATCTGAGTATGTGCGTACGTACGCTATTTAGATGGATAACCGACGCTGCCAGACGAGAGAC	0	0	0
-0	2	consensus	0	1_2,2_3	AATTCTCTACACCACAGCATCAATTCTAAAAATGACTACCAGAGAGACAACTCCGCAGTTAAACACTCTGACTGCCACGCCAGCTACCTCTAGA	0	0	0
-0	3	consensus	0	1_3,2_2	AATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT	0	0	0
+0	2	consensus	0	1_2,2_2	AATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT	0	0	0
+0	3	consensus	0	1_3,2_3	AATTCTCTACACCACAGCATCAATTCTAAAAATGACTACCAGAGAGACAACTCCGCAGTTAAACACTCTGACTGCCACGCCAGCTACCTCTAGA	0	0	0
diff -r c23695f62bdd -r 56d3555cf5f7 test-data/denovo_map/denovo_map.log
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/denovo_map/denovo_map.log	Thu Jun 20 08:13:18 2019 -0400
@@ -0,0 +1,309 @@
+denovo_map.pl version 2.4 started at 2019-06-18 10:34:45
+/home/berntm/miniconda3/envs/mulled-v1-2b57e7596f85ebb3b321e6c9681e8fd9250523a80d97945c46ac7743359454e7/bin/denovo_map.pl --samples demultiplexed --popmap denovo_map/popmap_cstacks.tsv -o stacks_outputs --paired
+
+ustacks
+==========
+
+Sample 1 of 2 'PopA_01'
+----------
+ustacks -t fastq -f demultiplexed/PopA_01.1.fq -o stacks_outputs -i 1 --name PopA_01
+ustacks parameters selected:
+  Input file: 'demultiplexed/PopA_01.1.fq'
+  Sample ID: 1
+  Min depth of coverage to create a stack (m): 3
+  Repeat removal algorithm: enabled
+  Max distance allowed between stacks (M): 2
+  Max distance allowed to align secondary reads: 4
+  Max number of stacks allowed per de novo locus: 3
+  Deleveraging algorithm: disabled
+  Gapped assembly: enabled
+  Minimum alignment length: 0.8
+  Model type: SNP
+  Alpha significance level for model: 0.05
+
+Loading RAD-Tags...
+
+Loaded 66 reads; formed:
+  4 stacks representing 63 primary reads (95.5%)
+  3 secondary stacks representing 3 secondary reads (4.5%)
+
+Stack coverage: mean=15.75; stdev=7.46; max=27; n_reads=63(95.5%)
+Removing repetitive stacks: cov > 39 (mean+3*stdev)...
+  Blacklisted 0 stacks.
+Coverage after repeat removal: mean=15.75; stdev=7.46; max=27; n_reads=63(95.5%)
+
+Assembling stacks (max. dist. M=2)...
+  Assembled 4 stacks into 3; blacklisted 0 stacks.
+Coverage after assembling stacks: mean=21.00; stdev=4.24; max=27; n_reads=63(95.5%)
+
+Merging secondary stacks (max. dist. N=4 from consensus)...
+  Merged 3 out of 3 secondary reads (100.0%), 1 merged with gapped alignments.
+Coverage after merging secondary stacks: mean=22.00; stdev=4.32; max=28; n_reads=66(100.0%)
+
+Assembling stacks, allowing for gaps (min. match length 80.0%)...
+  Assembled 3 stacks into 3 stacks.
+Coverage after gapped assembly: mean=22.00; stdev=4.32; max=28; n_reads=66(100.0%)
+
+Merging secondary stacks, allowing for gaps (min. match length 80.0%)...
+  Merged 0 out of 0 secondary reads (-nan%).
+Coverage after merging gapped secondary stacks: mean=22.00; stdev=4.32; max=28; n_reads=66(100.0%)
+
+Final coverage: mean=22.00; stdev=4.32; max=28; n_reads=66(100.0%)
+Calling consensus sequences and haplotypes for catalog assembly...
+Writing tags, SNPs, and alleles files...
+Refetching read IDs...done.
+ustacks is done.
+
+Sample 2 of 2 'PopA_02'
+----------
+ustacks -t fastq -f demultiplexed/PopA_02.1.fq -o stacks_outputs -i 2 --name PopA_02
+ustacks parameters selected:
+  Input file: 'demultiplexed/PopA_02.1.fq'
+  Sample ID: 2
+  Min depth of coverage to create a stack (m): 3
+  Repeat removal algorithm: enabled
+  Max distance allowed between stacks (M): 2
+  Max distance allowed to align secondary reads: 4
+  Max number of stacks allowed per de novo locus: 3
+  Deleveraging algorithm: disabled
+  Gapped assembly: enabled
+  Minimum alignment length: 0.8
+  Model type: SNP
+  Alpha significance level for model: 0.05
+
+Loading RAD-Tags...
+
+Loaded 60 reads; formed:
+  4 stacks representing 55 primary reads (91.7%)
+  5 secondary stacks representing 5 secondary reads (8.3%)
+
+Stack coverage: mean=13.75; stdev=9.12; max=26; n_reads=55(91.7%)
+Removing repetitive stacks: cov > 42 (mean+3*stdev)...
+  Blacklisted 0 stacks.
+Coverage after repeat removal: mean=13.75; stdev=9.12; max=26; n_reads=55(91.7%)
+
+Assembling stacks (max. dist. M=2)...
+  Assembled 4 stacks into 3; blacklisted 0 stacks.
+Coverage after assembling stacks: mean=18.33; stdev=6.55; max=26; n_reads=55(91.7%)
+
+Merging secondary stacks (max. dist. N=4 from consensus)...
+  Merged 5 out of 5 secondary reads (100.0%), 0 merged with gapped alignments.
+Coverage after merging secondary stacks: mean=20.00; stdev=6.53; max=28; n_reads=60(100.0%)
+
+Assembling stacks, allowing for gaps (min. match length 80.0%)...
+  Assembled 3 stacks into 3 stacks.
+Coverage after gapped assembly: mean=20.00; stdev=6.53; max=28; n_reads=60(100.0%)
+
+Merging secondary stacks, allowing for gaps (min. match length 80.0%)...
+  Merged 0 out of 0 secondary reads (-nan%).
+Coverage after merging gapped secondary stacks: mean=20.00; stdev=6.53; max=28; n_reads=60(100.0%)
+
+Final coverage: mean=20.00; stdev=6.53; max=28; n_reads=60(100.0%)
+Calling consensus sequences and haplotypes for catalog assembly...
+Writing tags, SNPs, and alleles files...
+Refetching read IDs...done.
+ustacks is done.
+
+Depths of Coverage for Processed Samples:
+PopA_01: 22.00x
+PopA_02: 20.00x
+
+cstacks
+==========
+cstacks -P stacks_outputs -M denovo_map/popmap_cstacks.tsv
+
+cstacks parameters selected:
+  Loci matched based on sequence identity.
+  Number of mismatches allowed between stacks: 1
+  Gapped alignments: enabled
+Constructing catalog from 2 samples.
+
+Initializing new catalog...
+  Parsing stacks_outputs/PopA_01.tags.tsv
+  Parsing stacks_outputs/PopA_01.snps.tsv
+  Parsing stacks_outputs/PopA_01.alleles.tsv
+  3 loci were newly added to the catalog.
+
+Processing sample stacks_outputs/PopA_02 [2 of 2]
+  Parsing stacks_outputs/PopA_02.tags.tsv
+  Parsing stacks_outputs/PopA_02.snps.tsv
+  Parsing stacks_outputs/PopA_02.alleles.tsv
+Searching for sequence matches...
+  3 loci in the catalog, 184 kmers in the catalog hash.
+Searching for gapped alignments...
+Merging matches into catalog...
+  3 loci were matched to a catalog locus.
+  0 loci were matched to a catalog locus using gapped alignments.
+  0 loci were newly added to the catalog.
+  0 loci matched more than one catalog locus, linking them.
+    0 linked catalog loci were merged into 0 loci.
+
+Writing catalog in directory 'stacks_outputs/'.
+Final catalog contains 3 loci.
+cstacks is done.
+
+sstacks
+==========
+sstacks -P stacks_outputs -M denovo_map/popmap_cstacks.tsv
+
+Searching for matches by sequence identity...
+  Parsing stacks_outputs/catalog.tags.tsv
+  Parsing stacks_outputs/catalog.snps.tsv
+  Parsing stacks_outputs/catalog.alleles.tsv
+Populating kmer dictionary for exact matches...done.
+Populating kmer dictionary for gapped alignments...done.
+
+Processing sample 'stacks_outputs/PopA_01' [1 of 2]
+  Parsing stacks_outputs/PopA_01.tags.tsv
+  Parsing stacks_outputs/PopA_01.snps.tsv
+  Parsing stacks_outputs/PopA_01.alleles.tsv
+Searching for sequence matches...
+3 sample loci compared against the catalog containing 3 loci.
+  3 matching loci, 0 contained no verified haplotypes.
+  0 loci matched more than one catalog locus and were excluded.
+  0 loci contained SNPs unaccounted for in the catalog and were excluded.
+  4 total haplotypes examined from matching loci, 4 verified.
+Searching for gapped alignments...
+Out of 3 query loci, 0 gapped alignments attempted.
+  0 loci matched one catalog locus; 0 total haplotypes examined, 0 verified.
+  0 loci matched no catalog locus;
+    0 loci matched more than one catalog locus and were excluded.
+    0 loci contained SNPs unaccounted for in the catalog and were excluded.
+    0 loci had no verified haplotypes.
+    0 loci had inconsistent alignments to a catalog locus and were excluded.
+Outputing to file stacks_outputs/PopA_01.matches.tsv
+
+Processing sample 'stacks_outputs/PopA_02' [2 of 2]
+  Parsing stacks_outputs/PopA_02.tags.tsv
+  Parsing stacks_outputs/PopA_02.snps.tsv
+  Parsing stacks_outputs/PopA_02.alleles.tsv
+Searching for sequence matches...
+3 sample loci compared against the catalog containing 3 loci.
+  3 matching loci, 0 contained no verified haplotypes.
+  0 loci matched more than one catalog locus and were excluded.
+  0 loci contained SNPs unaccounted for in the catalog and were excluded.
+  4 total haplotypes examined from matching loci, 4 verified.
+Searching for gapped alignments...
+Out of 3 query loci, 0 gapped alignments attempted.
+  0 loci matched one catalog locus; 0 total haplotypes examined, 0 verified.
+  0 loci matched no catalog locus;
+    0 loci matched more than one catalog locus and were excluded.
+    0 loci contained SNPs unaccounted for in the catalog and were excluded.
+    0 loci had no verified haplotypes.
+    0 loci had inconsistent alignments to a catalog locus and were excluded.
+Outputing to file stacks_outputs/PopA_02.matches.tsv
+
+sstacks is done.
+
+tsv2bam
+==========
+tsv2bam -P stacks_outputs  -M denovo_map/popmap_cstacks.tsv -R demultiplexed/
+
+Logging to 'stacks_outputs/tsv2bam.log'.
+Configuration for this run:
+  Stacks directory: 'stacks_outputs/'
+  Population map: 'denovo_map/popmap_cstacks.tsv'
+  Num. samples: 2
+  Paired-end reads directory: 'demultiplexed/'
+
+Paired-end reads files found, e.g. 'demultiplexed/PopA_01.2.fq'.
+Loading the catalog...
+Processing sample 'PopA_01'...
+Processing sample 'PopA_02'...
+
+Sample 'PopA_01': matched 3 sample loci to 3 catalog loci; found a paired-end read for 66 (100.0%) of the assembled forward reads; wrote 132 records.
+Sample 'PopA_02': matched 3 sample loci to 3 catalog loci; found a paired-end read for 60 (100.0%) of the assembled forward reads; wrote 120 records.
+
+tsv2bam is done.
+
+gstacks
+==========
+gstacks -P stacks_outputs -M denovo_map/popmap_cstacks.tsv
+
+Logging to 'stacks_outputs/gstacks.log'.
+Locus/sample distributions will be written to 'stacks_outputs/gstacks.log.distribs'.
+
+Configuration for this run:
+  Input mode: denovo
+  Population map: 'denovo_map/popmap_cstacks.tsv'
+  Input files: 2, e.g. 'stacks_outputs/PopA_01.matches.bam'
+  Output to: 'stacks_outputs/'
+  Model: marukilow (var_alpha: 0.01, gt_alpha: 0.05)
+
+Reading BAM headers...
+Processing all loci...
+20%...
+50%...
+100%
+
+Attempted to assemble and align paired-end reads for 3 loci:
+  0 loci had no or almost no paired-end reads (0.0%);
+  0 loci had paired-end reads that couldn't be assembled into a contig (0.0%);
+  For the remaining 3 loci (100.0%), a paired-end contig was assembled;
+    Average contig size was 204.3 bp;
+  0 paired-end contigs overlapped the forward region (0.0%)
+    Mean overlap: -nanbp; mean size of overlapped loci after merging: -nan;
+  Out of 252 paired-end reads in these loci (mean 84.0 reads per locus),
+    252 were successfuly aligned (100.0%);
+  Mean insert length was -nan, stdev: nan (based on aligned reads in overlapped loci).
+
+Genotyped 3 loci:
+  effective per-sample coverage: mean=31.0x, stdev=1.0x, min=30.0x, max=32.0x
+  mean number of sites per locus: 194.3
+  a consistent phasing was found for 5 of out 5 (100.0%) diploid loci needing phasing
+
+gstacks is done.
+
+populations
+==========
+populations -P stacks_outputs -M denovo_map/popmap_cstacks.tsv
+
+Logging to 'stacks_outputs/populations.log'.
+Locus/sample distributions will be written to 'stacks_outputs/populations.log.distribs'.
+populations parameters selected:
+  Percent samples limit per population: 0
+  Locus Population limit: 1
+  Percent samples overall: 0
+  Minor allele frequency cutoff: 0
+  Maximum observed heterozygosity cutoff: 1
+  Applying Fst correction: none.
+  Pi/Fis kernel smoothing: off
+  Fstats kernel smoothing: off
+  Bootstrap resampling: off
+
+Parsing population map...
+The population map contained 2 samples, 1 population(s), 1 group(s).
+Working on 2 samples.
+Working on 1 population(s):
+    1: PopA_01, PopA_02
+Working on 1 group(s) of populations:
+    defaultgrp: 1
+
+Genotyping markers will be written to 'stacks_outputs/populations.markers.tsv'
+Raw Genotypes/Haplotypes will be written to 'stacks_outputs/populations.haplotypes.tsv'
+Population-level summary statistics will be written to 'stacks_outputs/populations.sumstats.tsv'
+Population-level haplotype summary statistics will be written to 'stacks_outputs/populations.hapstats.tsv'
+
+Processing data in batches:
+  * load a batch of catalog loci and apply filters
+  * compute SNP- and haplotype-wise per-population statistics
+  * write the above statistics in the output files
+  * export the genotypes/haplotypes in specified format(s)
+More details in 'stacks_outputs/populations.log.distribs'.
+Now processing...
+Batch 1 
+
+Removed 0 loci that did not pass sample/population constraints from 3 loci.
+Kept 3 loci, composed of 613 sites; 0 of those sites were filtered, 6 variant sites remained.
+Number of loci with PE contig: 3.00 (100.0%);
+  Mean length of loci: 194.33bp (stderr 0.33);
+Number of loci with SE/PE overlap: 0.00 (0.0%);
+  Mean length of overlapping loci: -nanbp (stderr -0.00); mean overlap: -nanbp (stderr -0.00);
+Mean genotyped sites per locus: 194.33bp (stderr 0.33).
+
+Population summary statistics (more detail in populations.sumstats_summary.tsv):
+  1: 2 samples per locus; pi: 0.61111; all/variant/polymorphic sites: 583/6/6; private alleles: 0
+Populations is done.
+denovo_map.pl is done.
+
+denovo_map.pl completed at 2019-06-18 10:34:45
diff -r c23695f62bdd -r 56d3555cf5f7 test-data/gentest.sh
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/gentest.sh	Thu Jun 20 08:13:18 2019 -0400
@@ -0,0 +1,19 @@
+#!/usr/bin/env bash
+
+mkdir stacks_outputs
+
+denovo_map.pl --samples demultiplexed --popmap denovo_map/popmap_cstacks.tsv -o stacks_outputs --paired  && 
+gunzip -c stacks_outputs/catalog.calls > stacks_outputs/catalog.calls.vcf
+rm stacks_outputs/catalog.calls
+
+mv stacks_outputs/PopA_0{1,2}.{tags,snps,alleles}.tsv ustacks/
+mv stacks_outputs/catalog.{tags,snps,alleles}.tsv cstacks/
+mv stacks_outputs/PopA_0{1,2}.matches.tsv sstacks/
+mv stacks_outputs/PopA_0{1,2}.matches.bam tsv2bam/
+mv stacks_outputs/tsv2bam.log tsv2bam/
+mv stacks_outputs/catalog.{calls.vcf,fa.gz} gstacks/
+mv stacks_outputs/gstacks.log* gstacks/
+mv stacks_outputs/populations.* populations/
+mv stacks_outputs/denovo_map.log denovo_map/
+
+rmdir stacks_outputs
diff -r c23695f62bdd -r 56d3555cf5f7 test-data/gstacks/catalog.calls.vcf
--- a/test-data/gstacks/catalog.calls.vcf	Wed Feb 27 09:52:16 2019 -0500
+++ b/test-data/gstacks/catalog.calls.vcf	Thu Jun 20 08:13:18 2019 -0400
@@ -1,6 +1,6 @@
 ##fileformat=VCFv4.2
-##fileDate=20190222
-##source="Stacks v2.3b"
+##fileDate=20190618
+##source="Stacks v2.4"
 ##INFO=<ID=AD,Number=R,Type=Integer,Description="Total Depth for Each Allele">
 ##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency">
 ##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
@@ -106,492 +106,492 @@
 1	92	.	G	.	.	.	DP=30;AD=30	DP	18	12
 1	93	.	A	.	.	.	DP=30;AD=30	DP	18	12
 1	94	.	C	.	.	.	DP=30;AD=30	DP	18	12
-1	105	.	C	.	.	.	DP=22;AD=22	DP	14	8
-1	106	.	G	.	.	.	DP=22;AD=22	DP	14	8
-1	107	.	T	.	.	.	DP=22;AD=22	DP	14	8
-1	108	.	C	.	.	.	DP=22;AD=22	DP	14	8
-1	109	.	A	.	.	.	DP=22;AD=22	DP	14	8
-1	110	.	G	.	.	.	DP=22;AD=22	DP	14	8
-1	111	.	A	.	.	.	DP=22;AD=22	DP	14	8
-1	112	.	G	.	.	.	DP=22;AD=22	DP	14	8
-1	113	.	G	.	.	.	DP=22;AD=22	DP	14	8
-1	114	.	G	.	.	.	DP=22;AD=22	DP	14	8
-1	115	.	C	.	.	.	DP=22;AD=22	DP	14	8
-1	116	.	T	.	.	.	DP=22;AD=22	DP	14	8
-1	117	.	T	.	.	.	DP=22;AD=22	DP	14	8
-1	118	.	A	.	.	.	DP=22;AD=22	DP	14	8
-1	119	.	T	.	.	.	DP=22;AD=22	DP	14	8
-1	120	.	A	.	.	.	DP=22;AD=22	DP	14	8
-1	121	.	T	.	.	.	DP=22;AD=22	DP	14	8
-1	122	.	C	.	.	.	DP=22;AD=22	DP	14	8
-1	123	.	G	.	.	.	DP=22;AD=22	DP	14	8
-1	124	.	T	.	.	.	DP=22;AD=22	DP	14	8
-1	125	.	G	.	.	.	DP=22;AD=22	DP	14	8
-1	126	.	A	.	.	.	DP=22;AD=22	DP	14	8
-1	127	.	G	.	.	.	DP=22;AD=22	DP	14	8
-1	128	.	T	.	.	.	DP=22;AD=22	DP	14	8
-1	129	.	G	.	.	.	DP=22;AD=22	DP	14	8
-1	130	.	A	.	.	.	DP=22;AD=22	DP	14	8
-1	131	.	T	.	.	.	DP=22;AD=22	DP	14	8
-1	132	.	A	.	.	.	DP=22;AD=22	DP	14	8
-1	133	.	G	.	.	.	DP=22;AD=22	DP	14	8
-1	134	.	C	.	.	.	DP=22;AD=22	DP	14	8
-1	135	.	A	.	.	.	DP=22;AD=22	DP	14	8
-1	136	.	G	.	.	.	DP=22;AD=22	DP	14	8
-1	137	.	C	.	.	.	DP=22;AD=22	DP	14	8
-1	138	.	A	.	.	.	DP=22;AD=22	DP	14	8
-1	139	.	G	.	.	.	DP=22;AD=22	DP	14	8
-1	140	.	T	.	.	.	DP=22;AD=22	DP	14	8
-1	141	.	T	.	.	.	DP=22;AD=22	DP	14	8
-1	142	.	T	.	.	.	DP=22;AD=22	DP	14	8
-1	143	.	C	.	.	.	DP=22;AD=22	DP	14	8
-1	144	.	T	.	.	.	DP=22;AD=22	DP	14	8
-1	145	.	C	.	.	.	DP=22;AD=22	DP	14	8
-1	146	.	T	.	.	.	DP=22;AD=22	DP	14	8
-1	147	.	C	.	.	.	DP=22;AD=22	DP	14	8
-1	148	.	T	.	.	.	DP=22;AD=22	DP	14	8
-1	149	.	A	.	.	.	DP=22;AD=22	DP	14	8
-1	150	.	C	.	.	.	DP=22;AD=22	DP	14	8
-1	151	.	C	.	.	.	DP=22;AD=22	DP	14	8
-1	152	.	A	.	.	.	DP=22;AD=22	DP	14	8
-1	153	.	C	.	.	.	DP=22;AD=22	DP	14	8
-1	154	.	A	.	.	.	DP=22;AD=22	DP	14	8
-1	155	.	T	.	.	.	DP=22;AD=22	DP	14	8
-1	156	.	A	.	.	.	DP=22;AD=21	DP	14	8
-1	157	.	G	.	.	.	DP=22;AD=22	DP	14	8
-1	158	.	T	.	.	.	DP=22;AD=22	DP	14	8
-1	159	.	T	.	.	.	DP=22;AD=22	DP	14	8
-1	160	.	A	.	.	.	DP=22;AD=22	DP	14	8
-1	161	.	T	.	.	.	DP=22;AD=22	DP	14	8
-1	162	.	A	.	.	.	DP=22;AD=22	DP	14	8
-1	163	.	C	.	.	.	DP=22;AD=22	DP	14	8
-1	164	.	A	.	.	.	DP=22;AD=22	DP	14	8
-1	165	.	C	.	.	.	DP=22;AD=22	DP	14	8
-1	166	.	C	.	.	.	DP=22;AD=22	DP	14	8
-1	167	.	A	.	.	.	DP=19;AD=19	DP	14	5
-1	168	.	T	.	.	.	DP=22;AD=22	DP	14	8
-1	169	.	T	.	.	.	DP=22;AD=21	DP	14	8
-1	170	.	G	.	.	.	DP=22;AD=19	DP	14	8
-1	171	.	G	.	.	.	DP=22;AD=22	DP	14	8
-1	172	.	G	.	.	.	DP=22;AD=22	DP	14	8
-1	173	.	C	.	.	.	DP=22;AD=22	DP	14	8
-1	174	.	C	.	.	.	DP=22;AD=22	DP	14	8
-1	175	.	A	.	.	.	DP=22;AD=22	DP	14	8
-1	176	.	G	.	.	.	DP=22;AD=22	DP	14	8
-1	177	.	C	.	.	.	DP=22;AD=22	DP	14	8
-1	178	.	T	.	.	.	DP=22;AD=22	DP	14	8
-1	179	.	C	.	.	.	DP=22;AD=22	DP	14	8
-1	180	.	G	.	.	.	DP=22;AD=22	DP	14	8
-1	181	.	T	.	.	.	DP=22;AD=22	DP	14	8
-1	182	.	T	.	.	.	DP=22;AD=22	DP	14	8
-1	183	.	G	.	.	.	DP=22;AD=22	DP	14	8
-1	184	.	A	.	.	.	DP=22;AD=22	DP	14	8
-1	185	.	A	.	.	.	DP=22;AD=22	DP	14	8
-1	186	.	A	.	.	.	DP=22;AD=22	DP	14	8
-1	187	.	A	.	.	.	DP=22;AD=22	DP	14	8
-1	188	.	C	.	.	.	DP=22;AD=22	DP	14	8
-1	189	.	T	.	.	.	DP=22;AD=22	DP	14	8
-1	190	.	A	.	.	.	DP=22;AD=22	DP	14	8
-1	191	.	C	.	.	.	DP=22;AD=21	DP	14	8
-1	192	.	T	.	.	.	DP=22;AD=22	DP	14	8
-1	193	.	G	.	.	.	DP=22;AD=22	DP	14	8
-1	194	.	A	.	.	.	DP=22;AD=22	DP	14	8
-1	195	.	T	.	.	.	DP=22;AD=22	DP	14	8
-1	196	.	G	.	.	.	DP=22;AD=22	DP	14	8
-1	197	.	C	.	.	.	DP=22;AD=22	DP	14	8
-1	198	.	T	.	.	.	DP=22;AD=22	DP	14	8
-1	199	.	G	.	.	.	DP=22;AD=22	DP	14	8
-1	200	.	A	.	.	.	DP=22;AD=22	DP	14	8
-1	201	.	T	.	.	.	DP=22;AD=22	DP	14	8
-1	202	.	C	.	.	.	DP=22;AD=22	DP	14	8
-1	203	.	G	.	.	.	DP=22;AD=22	DP	14	8
-1	204	.	G	.	.	.	DP=22;AD=22	DP	14	8
-2	1	.	A	.	.	.	DP=40;AD=40	DP	20	20
-2	2	.	A	.	.	.	DP=40;AD=40	DP	20	20
-2	3	.	T	.	.	.	DP=40;AD=40	DP	20	20
-2	4	.	T	.	.	.	DP=40;AD=40	DP	20	20
-2	5	.	C	.	.	.	DP=40;AD=40	DP	20	20
-2	6	.	T	.	.	.	DP=40;AD=40	DP	20	20
-2	7	.	C	.	.	.	DP=40;AD=40	DP	20	20
-2	8	.	T	.	.	.	DP=40;AD=40	DP	20	20
-2	9	.	A	.	.	.	DP=40;AD=40	DP	20	20
-2	10	.	C	.	.	.	DP=40;AD=40	DP	20	20
-2	11	.	A	.	.	.	DP=40;AD=40	DP	20	20
-2	12	.	C	.	.	.	DP=40;AD=40	DP	20	20
-2	13	.	C	.	.	.	DP=40;AD=40	DP	20	20
-2	14	.	A	.	.	.	DP=40;AD=40	DP	20	20
-2	15	.	C	.	.	.	DP=40;AD=40	DP	20	20
-2	16	.	A	.	.	.	DP=40;AD=39	DP	20	20
-2	17	.	G	.	.	.	DP=40;AD=40	DP	20	20
-2	18	.	C	.	.	.	DP=40;AD=40	DP	20	20
-2	19	.	A	.	.	.	DP=40;AD=40	DP	20	20
-2	20	.	T	.	.	.	DP=40;AD=40	DP	20	20
-2	21	.	C	.	.	.	DP=40;AD=40	DP	20	20
-2	22	.	A	.	.	.	DP=40;AD=40	DP	20	20
-2	23	.	A	.	.	.	DP=40;AD=40	DP	20	20
-2	24	.	T	.	.	.	DP=40;AD=40	DP	20	20
-2	25	.	T	.	.	.	DP=40;AD=40	DP	20	20
-2	26	.	C	.	.	.	DP=40;AD=40	DP	20	20
-2	27	.	T	.	.	.	DP=40;AD=40	DP	20	20
-2	28	.	A	.	.	.	DP=40;AD=40	DP	20	20
-2	29	.	A	.	.	.	DP=40;AD=40	DP	20	20
-2	30	.	A	.	.	.	DP=40;AD=40	DP	20	20
-2	31	.	A	.	.	.	DP=40;AD=40	DP	20	20
-2	32	.	A	.	.	.	DP=40;AD=40	DP	20	20
-2	33	.	T	.	.	.	DP=40;AD=40	DP	20	20
-2	34	.	G	.	.	.	DP=40;AD=40	DP	20	20
-2	35	.	A	.	.	.	DP=40;AD=40	DP	20	20
-2	36	.	C	.	.	.	DP=40;AD=40	DP	20	20
-2	37	.	T	.	.	.	DP=40;AD=40	DP	20	20
-2	38	.	A	.	.	.	DP=40;AD=40	DP	20	20
-2	39	.	C	.	.	.	DP=40;AD=40	DP	20	20
-2	40	.	C	.	.	.	DP=40;AD=40	DP	20	20
-2	41	.	A	.	.	.	DP=40;AD=40	DP	20	20
-2	42	.	G	.	.	.	DP=40;AD=40	DP	20	20
-2	43	.	A	.	.	.	DP=40;AD=40	DP	20	20
-2	44	.	G	.	.	.	DP=40;AD=40	DP	20	20
-2	45	.	A	.	.	.	DP=40;AD=40	DP	20	20
-2	46	.	G	.	.	.	DP=40;AD=40	DP	20	20
-2	47	.	A	.	.	.	DP=40;AD=40	DP	20	20
-2	48	.	C	.	.	.	DP=40;AD=40	DP	20	20
-2	49	.	A	.	.	.	DP=40;AD=40	DP	20	20
-2	50	.	A	.	.	.	DP=40;AD=40	DP	20	20
-2	51	.	C	.	.	.	DP=40;AD=40	DP	20	20
-2	52	.	T	.	.	.	DP=40;AD=40	DP	20	20
-2	53	.	C	.	.	.	DP=40;AD=40	DP	20	20
-2	54	.	C	.	.	.	DP=40;AD=40	DP	20	20
-2	55	.	G	.	.	.	DP=40;AD=40	DP	20	20
-2	56	.	C	.	.	.	DP=40;AD=40	DP	20	20
-2	57	.	A	.	.	.	DP=40;AD=40	DP	20	20
-2	58	.	G	.	.	.	DP=40;AD=40	DP	20	20
-2	59	.	T	.	.	.	DP=40;AD=40	DP	20	20
-2	60	.	T	.	.	.	DP=40;AD=39	DP	20	20
-2	61	.	A	.	.	.	DP=40;AD=40	DP	20	20
-2	62	.	A	.	.	.	DP=40;AD=40	DP	20	20
-2	63	.	A	.	.	.	DP=40;AD=40	DP	20	20
-2	64	.	C	.	.	.	DP=40;AD=40	DP	20	20
-2	65	.	A	.	.	.	DP=40;AD=40	DP	20	20
-2	66	.	C	.	.	.	DP=40;AD=40	DP	20	20
-2	67	.	T	.	.	.	DP=40;AD=40	DP	20	20
-2	68	.	C	.	.	.	DP=40;AD=40	DP	20	20
-2	69	.	T	.	.	.	DP=40;AD=40	DP	20	20
-2	70	.	G	.	.	.	DP=40;AD=40	DP	20	20
-2	71	.	A	.	.	.	DP=40;AD=40	DP	20	20
-2	72	.	C	.	.	.	DP=40;AD=40	DP	20	20
-2	73	.	T	.	.	.	DP=40;AD=40	DP	20	20
-2	74	.	G	.	.	.	DP=40;AD=40	DP	20	20
-2	75	.	C	.	.	.	DP=40;AD=40	DP	20	20
-2	76	.	C	.	.	.	DP=40;AD=40	DP	20	20
-2	77	.	A	.	.	.	DP=40;AD=40	DP	20	20
-2	78	.	C	.	.	.	DP=40;AD=40	DP	20	20
-2	79	.	G	.	.	.	DP=40;AD=40	DP	20	20
-2	80	.	C	.	.	.	DP=40;AD=40	DP	20	20
-2	81	.	C	.	.	.	DP=40;AD=40	DP	20	20
-2	82	.	A	.	.	.	DP=40;AD=40	DP	20	20
-2	83	.	G	.	.	.	DP=40;AD=40	DP	20	20
-2	84	.	C	.	.	.	DP=40;AD=40	DP	20	20
-2	85	.	T	.	.	.	DP=40;AD=40	DP	20	20
-2	86	.	A	.	.	.	DP=40;AD=40	DP	20	20
-2	87	.	C	.	.	.	DP=40;AD=40	DP	20	20
-2	88	.	C	.	.	.	DP=40;AD=40	DP	20	20
-2	89	.	T	.	.	.	DP=40;AD=40	DP	20	20
-2	90	.	C	.	.	.	DP=40;AD=40	DP	20	20
-2	91	.	T	.	.	.	DP=40;AD=39	DP	20	20
-2	92	.	A	.	.	.	DP=40;AD=40	DP	20	20
-2	93	.	G	.	.	.	DP=40;AD=40	DP	20	20
-2	94	.	A	.	.	.	DP=40;AD=40	DP	20	20
-2	105	.	G	.	.	.	DP=30;AD=30	DP	17	13
-2	106	.	G	.	.	.	DP=30;AD=30	DP	17	13
-2	107	.	C	.	.	.	DP=30;AD=30	DP	17	13
-2	108	.	T	.	.	.	DP=30;AD=30	DP	17	13
-2	109	.	G	.	.	.	DP=30;AD=30	DP	17	13
-2	110	.	C	.	.	.	DP=30;AD=30	DP	17	13
-2	111	.	T	.	.	.	DP=30;AD=30	DP	17	13
-2	112	.	G	.	.	.	DP=30;AD=30	DP	17	13
-2	113	.	G	.	.	.	DP=30;AD=30	DP	17	13
-2	114	.	A	.	.	.	DP=30;AD=30	DP	17	13
-2	115	.	C	.	.	.	DP=30;AD=30	DP	17	13
-2	116	.	G	.	.	.	DP=30;AD=30	DP	17	13
-2	117	.	T	.	.	.	DP=30;AD=30	DP	17	13
-2	118	.	C	.	.	.	DP=30;AD=30	DP	17	13
-2	119	.	C	.	.	.	DP=30;AD=30	DP	17	13
-2	120	.	T	.	.	.	DP=30;AD=30	DP	17	13
-2	121	.	T	.	.	.	DP=30;AD=30	DP	17	13
-2	122	.	C	.	.	.	DP=30;AD=30	DP	17	13
-2	123	.	G	.	.	.	DP=30;AD=30	DP	17	13
-2	124	.	C	.	.	.	DP=30;AD=30	DP	17	13
-2	125	.	T	.	.	.	DP=30;AD=30	DP	17	13
-2	126	.	C	.	.	.	DP=30;AD=30	DP	17	13
-2	127	.	G	.	.	.	DP=30;AD=30	DP	17	13
-2	128	.	G	.	.	.	DP=30;AD=30	DP	17	13
-2	129	.	T	.	.	.	DP=30;AD=30	DP	17	13
-2	130	.	A	.	.	.	DP=30;AD=30	DP	17	13
-2	131	.	C	.	.	.	DP=30;AD=30	DP	17	13
-2	132	.	C	.	.	.	DP=30;AD=29	DP	17	13
-2	133	.	T	.	.	.	DP=30;AD=30	DP	17	13
-2	134	.	T	.	.	.	DP=30;AD=30	DP	17	13
-2	135	.	G	.	.	.	DP=30;AD=30	DP	17	13
-2	136	.	A	.	.	.	DP=30;AD=30	DP	17	13
-2	137	.	C	.	.	.	DP=30;AD=30	DP	17	13
-2	138	.	T	.	.	.	DP=30;AD=30	DP	17	13
-2	139	.	G	.	.	.	DP=30;AD=30	DP	17	13
-2	140	.	G	.	.	.	DP=30;AD=30	DP	17	13
-2	141	.	A	.	.	.	DP=30;AD=30	DP	17	13
-2	142	.	T	.	.	.	DP=30;AD=30	DP	17	13
-2	143	.	T	.	.	.	DP=30;AD=30	DP	17	13
-2	144	.	A	.	.	.	DP=30;AD=30	DP	17	13
-2	145	.	T	C	40	.	DP=30;AD=16,14;AF=0.467	GT:PS:FT:GQ:DP:AD:GL	1|0:145:.:40:17:8,9:-20.29,0.00,-17.57	1|0:145:.:40:13:8,5:-10.39,-0.00,-18.77
-2	146	.	A	.	.	.	DP=30;AD=30	DP	17	13
-2	147	.	T	.	.	.	DP=30;AD=30	DP	17	13
-2	148	.	A	.	.	.	DP=30;AD=30	DP	17	13
-2	149	.	G	.	.	.	DP=30;AD=30	DP	17	13
-2	150	.	C	.	.	.	DP=30;AD=30	DP	17	13
-2	151	.	A	.	.	.	DP=30;AD=30	DP	17	13
-2	152	.	T	.	.	.	DP=30;AD=30	DP	17	13
-2	153	.	T	.	.	.	DP=30;AD=30	DP	17	13
-2	154	.	C	.	.	.	DP=30;AD=30	DP	17	13
-2	155	.	C	.	.	.	DP=30;AD=30	DP	17	13
-2	156	.	T	.	.	.	DP=30;AD=29	DP	17	13
-2	157	.	T	G	40	.	DP=30;AD=16,14;AF=0.467	GT:PS:FT:GQ:DP:AD:GL	1|0:145:.:40:17:8,9:-20.29,0.00,-17.57	1|0:145:.:40:13:8,5:-10.39,-0.00,-18.77
-2	158	.	A	.	.	.	DP=30;AD=30	DP	17	13
-2	159	.	G	.	.	.	DP=30;AD=30	DP	17	13
-2	160	.	T	.	.	.	DP=30;AD=30	DP	17	13
-2	161	.	T	.	.	.	DP=30;AD=30	DP	17	13
-2	162	.	C	.	.	.	DP=30;AD=30	DP	17	13
-2	163	.	A	.	.	.	DP=30;AD=30	DP	17	13
-2	164	.	C	.	.	.	DP=30;AD=30	DP	17	13
-2	165	.	G	.	.	.	DP=30;AD=30	DP	17	13
-2	166	.	G	.	.	.	DP=30;AD=30	DP	17	13
-2	167	.	C	.	.	.	DP=30;AD=30	DP	17	13
-2	168	.	C	.	.	.	DP=30;AD=30	DP	17	13
-2	169	.	A	.	.	.	DP=30;AD=30	DP	17	13
-2	170	.	A	.	.	.	DP=30;AD=30	DP	17	13
-2	171	.	T	.	.	.	DP=30;AD=30	DP	17	13
-2	172	.	A	.	.	.	DP=30;AD=30	DP	17	13
-2	173	.	T	.	.	.	DP=30;AD=30	DP	17	13
-2	174	.	C	.	.	.	DP=30;AD=30	DP	17	13
-2	175	.	G	.	.	.	DP=30;AD=30	DP	17	13
-2	176	.	C	.	.	.	DP=30;AD=30	DP	17	13
-2	177	.	C	.	.	.	DP=30;AD=30	DP	17	13
-2	178	.	A	.	.	.	DP=30;AD=30	DP	17	13
-2	179	.	A	.	.	.	DP=30;AD=30	DP	17	13
-2	180	.	C	.	.	.	DP=30;AD=30	DP	17	13
-2	181	.	C	.	.	.	DP=30;AD=30	DP	17	13
-2	182	.	G	.	.	.	DP=30;AD=30	DP	17	13
-2	183	.	T	.	.	.	DP=30;AD=30	DP	17	13
-2	184	.	T	.	.	.	DP=30;AD=30	DP	17	13
-2	185	.	G	.	.	.	DP=30;AD=30	DP	17	13
-2	186	.	A	.	.	.	DP=30;AD=30	DP	17	13
-2	187	.	G	.	.	.	DP=30;AD=30	DP	17	13
-2	188	.	T	.	.	.	DP=30;AD=30	DP	17	13
-2	189	.	G	.	.	.	DP=30;AD=30	DP	17	13
-2	190	.	A	.	.	.	DP=30;AD=30	DP	17	13
-2	191	.	G	.	.	.	DP=30;AD=30	DP	17	13
-2	192	.	T	.	.	.	DP=30;AD=30	DP	17	13
-2	193	.	T	.	.	.	DP=30;AD=30	DP	17	13
-2	194	.	T	.	.	.	DP=30;AD=30	DP	17	13
-2	195	.	A	.	.	.	DP=30;AD=30	DP	17	13
-2	196	.	G	.	.	.	DP=30;AD=30	DP	17	13
-2	197	.	T	.	.	.	DP=30;AD=30	DP	17	13
-2	198	.	G	.	.	.	DP=30;AD=30	DP	17	13
-2	199	.	A	.	.	.	DP=30;AD=30	DP	17	13
-2	200	.	A	.	.	.	DP=30;AD=30	DP	17	13
-2	201	.	C	.	.	.	DP=30;AD=30	DP	17	13
-2	202	.	C	.	.	.	DP=30;AD=30	DP	17	13
-2	203	.	G	.	.	.	DP=30;AD=30	DP	17	13
-2	204	.	G	.	.	.	DP=30;AD=30	DP	17	13
-3	1	.	A	.	.	.	DP=56;AD=56	DP	28	28
-3	2	.	A	.	.	.	DP=56;AD=56	DP	28	28
-3	3	.	T	.	.	.	DP=56;AD=56	DP	28	28
-3	4	.	T	.	.	.	DP=56;AD=56	DP	28	28
-3	5	.	C	.	.	.	DP=56;AD=56	DP	28	28
-3	6	.	G	.	.	.	DP=56;AD=56	DP	28	28
-3	7	.	G	.	.	.	DP=56;AD=56	DP	28	28
-3	8	.	C	.	.	.	DP=56;AD=56	DP	28	28
-3	9	.	T	.	.	.	DP=56;AD=56	DP	28	28
-3	10	.	T	.	.	.	DP=56;AD=56	DP	28	28
-3	11	.	G	.	.	.	DP=56;AD=56	DP	28	28
-3	12	.	C	.	.	.	DP=56;AD=56	DP	28	28
-3	13	.	A	.	.	.	DP=56;AD=56	DP	28	28
-3	14	.	A	.	.	.	DP=56;AD=56	DP	28	28
-3	15	.	C	.	.	.	DP=56;AD=56	DP	28	28
-3	16	.	G	.	.	.	DP=56;AD=56	DP	28	28
-3	17	.	C	.	.	.	DP=56;AD=56	DP	28	28
-3	18	.	A	.	.	.	DP=56;AD=56	DP	28	28
-3	19	.	A	.	.	.	DP=56;AD=56	DP	28	28
-3	20	.	G	.	.	.	DP=56;AD=56	DP	28	28
-3	21	.	T	.	.	.	DP=56;AD=56	DP	28	28
-3	22	.	G	.	.	.	DP=56;AD=56	DP	28	28
-3	23	.	A	.	.	.	DP=56;AD=56	DP	28	28
-3	24	.	C	.	.	.	DP=56;AD=56	DP	28	28
-3	25	.	G	.	.	.	DP=56;AD=56	DP	28	28
-3	26	.	A	.	.	.	DP=56;AD=56	DP	28	28
-3	27	.	T	.	.	.	DP=56;AD=56	DP	28	28
-3	28	.	T	.	.	.	DP=56;AD=56	DP	28	28
-3	29	.	C	.	.	.	DP=56;AD=56	DP	28	28
-3	30	.	C	.	.	.	DP=56;AD=56	DP	28	28
-3	31	.	C	.	.	.	DP=56;AD=56	DP	28	28
-3	32	.	A	.	.	.	DP=56;AD=55	DP	28	28
-3	33	.	C	.	.	.	DP=56;AD=56	DP	28	28
-3	34	.	G	.	.	.	DP=56;AD=56	DP	28	28
-3	35	.	G	.	.	.	DP=56;AD=56	DP	28	28
-3	36	.	A	.	.	.	DP=56;AD=56	DP	28	28
-3	37	.	C	.	.	.	DP=56;AD=56	DP	28	28
-3	38	.	A	.	.	.	DP=56;AD=56	DP	28	28
-3	39	.	T	.	.	.	DP=56;AD=56	DP	28	28
-3	40	.	A	.	.	.	DP=56;AD=56	DP	28	28
-3	41	.	A	.	.	.	DP=56;AD=56	DP	28	28
-3	42	.	C	.	.	.	DP=56;AD=56	DP	28	28
-3	43	.	T	.	.	.	DP=56;AD=56	DP	28	28
-3	44	.	G	.	.	.	DP=56;AD=56	DP	28	28
-3	45	.	A	.	.	.	DP=56;AD=56	DP	28	28
-3	46	.	T	.	.	.	DP=56;AD=56	DP	28	28
-3	47	.	C	.	.	.	DP=56;AD=56	DP	28	28
-3	48	.	T	.	.	.	DP=56;AD=56	DP	28	28
-3	49	.	A	.	.	.	DP=56;AD=56	DP	28	28
-3	50	.	A	.	.	.	DP=56;AD=56	DP	28	28
-3	51	.	G	.	.	.	DP=56;AD=56	DP	28	28
-3	52	.	T	.	.	.	DP=56;AD=56	DP	28	28
-3	53	.	A	.	.	.	DP=56;AD=56	DP	28	28
-3	54	.	A	.	.	.	DP=56;AD=55	DP	28	28
-3	55	.	C	.	.	.	DP=56;AD=56	DP	28	28
-3	56	.	T	.	.	.	DP=56;AD=56	DP	28	28
-3	57	.	T	.	.	.	DP=56;AD=56	DP	28	28
-3	58	.	C	.	.	.	DP=56;AD=56	DP	28	28
-3	59	.	C	.	.	.	DP=56;AD=56	DP	28	28
-3	60	.	A	.	.	.	DP=56;AD=56	DP	28	28
-3	61	.	A	.	.	.	DP=56;AD=56	DP	28	28
-3	62	.	A	.	.	.	DP=56;AD=55	DP	28	28
-3	63	.	T	.	.	.	DP=56;AD=56	DP	28	28
-3	64	.	C	.	.	.	DP=56;AD=56	DP	28	28
-3	65	.	T	.	.	.	DP=56;AD=56	DP	28	28
-3	66	.	G	.	.	.	DP=56;AD=56	DP	28	28
-3	67	.	G	.	.	.	DP=56;AD=56	DP	28	28
-3	68	.	G	.	.	.	DP=56;AD=56	DP	28	28
-3	69	.	A	.	.	.	DP=56;AD=56	DP	28	28
-3	70	.	A	.	.	.	DP=56;AD=56	DP	28	28
-3	71	.	T	.	.	.	DP=56;AD=56	DP	28	28
-3	72	.	G	.	.	.	DP=56;AD=56	DP	28	28
-3	73	.	G	.	.	.	DP=56;AD=56	DP	28	28
-3	74	.	G	.	.	.	DP=56;AD=56	DP	28	28
-3	75	.	A	.	.	.	DP=56;AD=56	DP	28	28
-3	76	.	T	.	.	.	DP=56;AD=56	DP	28	28
-3	77	.	T	.	.	.	DP=56;AD=56	DP	28	28
-3	78	.	T	.	.	.	DP=56;AD=56	DP	28	28
-3	79	.	C	.	.	.	DP=56;AD=56	DP	28	28
-3	80	.	A	.	.	.	DP=56;AD=56	DP	28	28
-3	81	.	T	.	.	.	DP=56;AD=56	DP	28	28
-3	82	.	A	.	.	.	DP=56;AD=56	DP	28	28
-3	83	.	A	.	.	.	DP=56;AD=56	DP	28	28
-3	84	.	T	.	.	.	DP=56;AD=56	DP	28	28
-3	85	.	T	.	.	.	DP=56;AD=56	DP	28	28
-3	86	.	A	.	.	.	DP=56;AD=56	DP	28	28
-3	87	.	A	.	.	.	DP=56;AD=56	DP	28	28
-3	88	.	G	.	.	.	DP=56;AD=56	DP	28	28
-3	89	.	G	.	.	.	DP=56;AD=56	DP	28	28
-3	90	.	A	.	.	.	DP=56;AD=56	DP	28	28
-3	91	.	C	.	.	.	DP=56;AD=56	DP	28	28
-3	92	.	T	.	.	.	DP=56;AD=56	DP	28	28
-3	93	.	A	.	.	.	DP=56;AD=56	DP	28	28
-3	94	.	T	.	.	.	DP=56;AD=56	DP	28	28
-3	105	.	T	.	.	.	DP=12;AD=12	DP	.	12
-3	106	.	A	.	.	.	DP=46;AD=46	DP	23	23
-3	107	.	C	.	.	.	DP=46;AD=46	DP	23	23
-3	108	.	G	.	.	.	DP=46;AD=46	DP	23	23
-3	109	.	A	.	.	.	DP=46;AD=46	DP	23	23
-3	110	.	C	.	.	.	DP=46;AD=46	DP	23	23
-3	111	.	G	.	.	.	DP=46;AD=46	DP	23	23
-3	112	.	A	.	.	.	DP=46;AD=46	DP	23	23
-3	113	.	G	.	.	.	DP=46;AD=46	DP	23	23
-3	114	.	C	.	.	.	DP=46;AD=46	DP	23	23
-3	115	.	A	.	.	.	DP=46;AD=46	DP	23	23
-3	116	.	A	.	.	.	DP=46;AD=46	DP	23	23
-3	117	.	T	.	.	.	DP=46;AD=46	DP	23	23
-3	118	.	C	.	.	.	DP=46;AD=46	DP	23	23
-3	119	.	C	.	.	.	DP=46;AD=46	DP	23	23
-3	120	.	A	.	.	.	DP=46;AD=46	DP	23	23
-3	121	.	C	.	.	.	DP=46;AD=46	DP	23	23
-3	122	.	A	.	.	.	DP=46;AD=46	DP	23	23
-3	123	.	G	.	.	.	DP=46;AD=46	DP	23	23
-3	124	.	A	.	.	.	DP=46;AD=46	DP	23	23
-3	125	.	C	.	.	.	DP=46;AD=46	DP	23	23
-3	126	.	C	.	.	.	DP=46;AD=45	DP	23	23
-3	127	.	T	.	.	.	DP=46;AD=46	DP	23	23
-3	128	.	A	.	.	.	DP=46;AD=46	DP	23	23
-3	129	.	G	.	.	.	DP=46;AD=46	DP	23	23
-3	130	.	G	.	.	.	DP=46;AD=46	DP	23	23
-3	131	.	C	.	.	.	DP=46;AD=46	DP	23	23
-3	132	.	C	.	.	.	DP=46;AD=46	DP	23	23
-3	133	.	C	.	.	.	DP=46;AD=46	DP	23	23
-3	134	.	A	.	.	.	DP=46;AD=46	DP	23	23
-3	135	.	T	.	.	.	DP=46;AD=46	DP	23	23
-3	136	.	C	.	.	.	DP=46;AD=46	DP	23	23
-3	137	.	G	.	.	.	DP=46;AD=46	DP	23	23
-3	138	.	A	.	.	.	DP=46;AD=46	DP	23	23
-3	139	.	A	.	.	.	DP=46;AD=46	DP	23	23
-3	140	.	G	.	.	.	DP=46;AD=46	DP	23	23
-3	141	.	C	.	.	.	DP=46;AD=46	DP	23	23
-3	142	.	G	.	.	.	DP=46;AD=46	DP	23	23
-3	143	.	T	.	.	.	DP=46;AD=46	DP	23	23
-3	144	.	C	.	.	.	DP=46;AD=46	DP	23	23
-3	145	.	T	.	.	.	DP=46;AD=46	DP	23	23
-3	146	.	T	.	.	.	DP=46;AD=46	DP	23	23
-3	147	.	A	.	.	.	DP=46;AD=46	DP	23	23
-3	148	.	T	.	.	.	DP=46;AD=46	DP	23	23
-3	149	.	G	.	.	.	DP=46;AD=46	DP	23	23
-3	150	.	A	.	.	.	DP=46;AD=46	DP	23	23
-3	151	.	T	.	.	.	DP=46;AD=46	DP	23	23
-3	152	.	T	.	.	.	DP=46;AD=46	DP	23	23
-3	153	.	G	.	.	.	DP=46;AD=46	DP	23	23
-3	154	.	A	.	.	.	DP=46;AD=46	DP	23	23
-3	155	.	T	.	.	.	DP=46;AD=46	DP	23	23
-3	156	.	A	.	.	.	DP=46;AD=46	DP	23	23
-3	157	.	A	.	.	.	DP=46;AD=46	DP	23	23
-3	158	.	C	.	.	.	DP=46;AD=46	DP	23	23
-3	159	.	A	.	.	.	DP=46;AD=46	DP	23	23
-3	160	.	T	.	.	.	DP=46;AD=46	DP	23	23
-3	161	.	C	.	.	.	DP=46;AD=46	DP	23	23
-3	162	.	A	.	.	.	DP=46;AD=46	DP	23	23
-3	163	.	G	A	40	.	DP=46;AD=34,12;AF=0.261	GT:PS:FT:GQ:DP:AD:GL	0/0:.:.:40:23:23,0:-0.00,-6.89,-68.45	1|0:163:.:40:23:11,12:-28.67,0.00,-25.99
-3	164	.	A	.	.	.	DP=46;AD=46	DP	23	23
-3	165	.	G	.	.	.	DP=46;AD=46	DP	23	23
-3	166	.	G	.	.	.	DP=46;AD=46	DP	23	23
-3	167	.	G	.	.	.	DP=46;AD=46	DP	23	23
-3	168	.	G	.	.	.	DP=46;AD=46	DP	23	23
-3	169	.	G	.	.	.	DP=46;AD=46	DP	23	23
-3	170	.	A	.	.	.	DP=46;AD=46	DP	23	23
-3	171	.	T	.	.	.	DP=46;AD=46	DP	23	23
-3	172	.	G	.	.	.	DP=46;AD=46	DP	23	23
-3	173	.	G	.	.	.	DP=46;AD=46	DP	23	23
-3	174	.	G	.	.	.	DP=46;AD=46	DP	23	23
-3	175	.	A	.	.	.	DP=46;AD=46	DP	23	23
-3	176	.	G	.	.	.	DP=46;AD=45	DP	23	23
-3	177	.	G	.	.	.	DP=46;AD=46	DP	23	23
-3	178	.	T	.	.	.	DP=46;AD=46	DP	23	23
-3	179	.	C	.	.	.	DP=46;AD=46	DP	23	23
-3	180	.	C	.	.	.	DP=46;AD=46	DP	23	23
-3	181	.	T	.	.	.	DP=46;AD=46	DP	23	23
-3	182	.	G	A	40	.	DP=46;AD=34,12;AF=0.261	GT:PS:FT:GQ:DP:AD:GL	0/0:.:.:40:23:23,0:-0.00,-6.89,-68.45	1|0:163:.:40:23:11,12:-28.67,0.00,-25.99
-3	183	.	C	.	.	.	DP=46;AD=46	DP	23	23
-3	184	.	T	.	.	.	DP=46;AD=46	DP	23	23
-3	185	.	G	.	.	.	DP=46;AD=46	DP	23	23
-3	186	.	T	.	.	.	DP=46;AD=45	DP	23	23
-3	187	.	C	.	.	.	DP=46;AD=46	DP	23	23
-3	188	.	G	.	.	.	DP=46;AD=46	DP	23	23
-3	189	.	C	.	.	.	DP=46;AD=46	DP	23	23
-3	190	.	A	.	.	.	DP=46;AD=46	DP	23	23
-3	191	.	T	.	.	.	DP=46;AD=46	DP	23	23
-3	192	.	G	.	.	.	DP=46;AD=46	DP	23	23
-3	193	.	G	.	.	.	DP=46;AD=46	DP	23	23
-3	194	.	G	.	.	.	DP=46;AD=45	DP	23	23
-3	195	.	A	.	.	.	DP=46;AD=46	DP	23	23
-3	196	.	G	.	.	.	DP=46;AD=46	DP	23	23
-3	197	.	A	.	.	.	DP=46;AD=46	DP	23	23
-3	198	.	A	.	.	.	DP=46;AD=46	DP	23	23
-3	199	.	T	.	.	.	DP=46;AD=46	DP	23	23
-3	200	.	A	.	.	.	DP=46;AD=46	DP	23	23
-3	201	.	C	.	.	.	DP=46;AD=46	DP	23	23
-3	202	.	A	.	.	.	DP=34;AD=34	DP	23	11
-3	203	.	C	.	.	.	DP=34;AD=34	DP	23	11
-3	204	.	G	.	.	.	DP=34;AD=34	DP	23	11
-3	205	.	G	.	.	.	DP=34;AD=34	DP	23	11
+1	105	.	C	.	.	.	DP=19;AD=19	DP	11	8
+1	106	.	G	.	.	.	DP=19;AD=19	DP	11	8
+1	107	.	T	.	.	.	DP=19;AD=19	DP	11	8
+1	108	.	C	.	.	.	DP=19;AD=19	DP	11	8
+1	109	.	A	.	.	.	DP=19;AD=19	DP	11	8
+1	110	.	G	.	.	.	DP=19;AD=19	DP	11	8
+1	111	.	A	.	.	.	DP=19;AD=19	DP	11	8
+1	112	.	G	.	.	.	DP=19;AD=19	DP	11	8
+1	113	.	G	.	.	.	DP=19;AD=19	DP	11	8
+1	114	.	G	.	.	.	DP=19;AD=19	DP	11	8
+1	115	.	C	.	.	.	DP=19;AD=19	DP	11	8
+1	116	.	T	.	.	.	DP=19;AD=19	DP	11	8
+1	117	.	T	.	.	.	DP=19;AD=19	DP	11	8
+1	118	.	A	.	.	.	DP=19;AD=19	DP	11	8
+1	119	.	T	.	.	.	DP=19;AD=19	DP	11	8
+1	120	.	A	.	.	.	DP=19;AD=19	DP	11	8
+1	121	.	T	.	.	.	DP=19;AD=19	DP	11	8
+1	122	.	C	.	.	.	DP=19;AD=19	DP	11	8
+1	123	.	G	.	.	.	DP=19;AD=19	DP	11	8
+1	124	.	T	.	.	.	DP=19;AD=19	DP	11	8
+1	125	.	G	.	.	.	DP=19;AD=19	DP	11	8
+1	126	.	A	.	.	.	DP=19;AD=19	DP	11	8
+1	127	.	G	.	.	.	DP=19;AD=19	DP	11	8
+1	128	.	T	.	.	.	DP=19;AD=19	DP	11	8
+1	129	.	G	.	.	.	DP=19;AD=19	DP	11	8
+1	130	.	A	.	.	.	DP=19;AD=19	DP	11	8
+1	131	.	T	.	.	.	DP=19;AD=19	DP	11	8
+1	132	.	A	.	.	.	DP=19;AD=19	DP	11	8
+1	133	.	G	.	.	.	DP=19;AD=19	DP	11	8
+1	134	.	C	.	.	.	DP=19;AD=19	DP	11	8
+1	135	.	A	.	.	.	DP=19;AD=19	DP	11	8
+1	136	.	G	.	.	.	DP=19;AD=19	DP	11	8
+1	137	.	C	.	.	.	DP=19;AD=19	DP	11	8
+1	138	.	A	.	.	.	DP=19;AD=19	DP	11	8
+1	139	.	G	.	.	.	DP=19;AD=19	DP	11	8
+1	140	.	T	.	.	.	DP=19;AD=19	DP	11	8
+1	141	.	T	.	.	.	DP=19;AD=19	DP	11	8
+1	142	.	T	.	.	.	DP=19;AD=19	DP	11	8
+1	143	.	C	.	.	.	DP=19;AD=19	DP	11	8
+1	144	.	T	.	.	.	DP=19;AD=19	DP	11	8
+1	145	.	C	.	.	.	DP=19;AD=19	DP	11	8
+1	146	.	T	.	.	.	DP=19;AD=19	DP	11	8
+1	147	.	C	.	.	.	DP=19;AD=19	DP	11	8
+1	148	.	T	.	.	.	DP=19;AD=19	DP	11	8
+1	149	.	A	.	.	.	DP=19;AD=19	DP	11	8
+1	150	.	C	.	.	.	DP=19;AD=19	DP	11	8
+1	151	.	C	.	.	.	DP=19;AD=19	DP	11	8
+1	152	.	A	.	.	.	DP=19;AD=19	DP	11	8
+1	153	.	C	.	.	.	DP=19;AD=19	DP	11	8
+1	154	.	A	.	.	.	DP=19;AD=19	DP	11	8
+1	155	.	T	.	.	.	DP=19;AD=19	DP	11	8
+1	156	.	A	.	.	.	DP=19;AD=18	DP	11	8
+1	157	.	G	.	.	.	DP=19;AD=19	DP	11	8
+1	158	.	T	.	.	.	DP=19;AD=19	DP	11	8
+1	159	.	T	.	.	.	DP=19;AD=19	DP	11	8
+1	160	.	A	.	.	.	DP=19;AD=19	DP	11	8
+1	161	.	T	.	.	.	DP=19;AD=19	DP	11	8
+1	162	.	A	.	.	.	DP=19;AD=19	DP	11	8
+1	163	.	C	.	.	.	DP=19;AD=19	DP	11	8
+1	164	.	A	.	.	.	DP=19;AD=19	DP	11	8
+1	165	.	C	.	.	.	DP=19;AD=19	DP	11	8
+1	166	.	C	.	.	.	DP=19;AD=19	DP	11	8
+1	167	.	A	.	.	.	DP=16;AD=16	DP	11	5
+1	168	.	T	.	.	.	DP=19;AD=19	DP	11	8
+1	169	.	T	.	.	.	DP=19;AD=18	DP	11	8
+1	170	.	G	.	.	.	DP=19;AD=16	DP	11	8
+1	171	.	G	.	.	.	DP=19;AD=19	DP	11	8
+1	172	.	G	.	.	.	DP=19;AD=19	DP	11	8
+1	173	.	C	.	.	.	DP=19;AD=19	DP	11	8
+1	174	.	C	.	.	.	DP=19;AD=19	DP	11	8
+1	175	.	A	.	.	.	DP=19;AD=19	DP	11	8
+1	176	.	G	.	.	.	DP=19;AD=19	DP	11	8
+1	177	.	C	.	.	.	DP=19;AD=19	DP	11	8
+1	178	.	T	.	.	.	DP=19;AD=19	DP	11	8
+1	179	.	C	.	.	.	DP=19;AD=19	DP	11	8
+1	180	.	G	.	.	.	DP=19;AD=19	DP	11	8
+1	181	.	T	.	.	.	DP=19;AD=19	DP	11	8
+1	182	.	T	.	.	.	DP=19;AD=19	DP	11	8
+1	183	.	G	.	.	.	DP=19;AD=19	DP	11	8
+1	184	.	A	.	.	.	DP=19;AD=19	DP	11	8
+1	185	.	A	.	.	.	DP=19;AD=19	DP	11	8
+1	186	.	A	.	.	.	DP=19;AD=19	DP	11	8
+1	187	.	A	.	.	.	DP=19;AD=19	DP	11	8
+1	188	.	C	.	.	.	DP=19;AD=19	DP	11	8
+1	189	.	T	.	.	.	DP=19;AD=19	DP	11	8
+1	190	.	A	.	.	.	DP=19;AD=19	DP	11	8
+1	191	.	C	.	.	.	DP=19;AD=18	DP	11	8
+1	192	.	T	.	.	.	DP=19;AD=19	DP	11	8
+1	193	.	G	.	.	.	DP=19;AD=19	DP	11	8
+1	194	.	A	.	.	.	DP=19;AD=19	DP	11	8
+1	195	.	T	.	.	.	DP=19;AD=19	DP	11	8
+1	196	.	G	.	.	.	DP=19;AD=19	DP	11	8
+1	197	.	C	.	.	.	DP=19;AD=19	DP	11	8
+1	198	.	T	.	.	.	DP=19;AD=19	DP	11	8
+1	199	.	G	.	.	.	DP=19;AD=19	DP	11	8
+1	200	.	A	.	.	.	DP=19;AD=19	DP	11	8
+1	201	.	T	.	.	.	DP=19;AD=19	DP	11	8
+1	202	.	C	.	.	.	DP=19;AD=19	DP	11	8
+1	203	.	G	.	.	.	DP=19;AD=19	DP	11	8
+1	204	.	G	.	.	.	DP=19;AD=19	DP	11	8
+2	1	.	A	.	.	.	DP=56;AD=56	DP	28	28
+2	2	.	A	.	.	.	DP=56;AD=56	DP	28	28
+2	3	.	T	.	.	.	DP=56;AD=56	DP	28	28
+2	4	.	T	.	.	.	DP=56;AD=56	DP	28	28
+2	5	.	C	.	.	.	DP=56;AD=56	DP	28	28
+2	6	.	G	.	.	.	DP=56;AD=56	DP	28	28
+2	7	.	G	.	.	.	DP=56;AD=56	DP	28	28
+2	8	.	C	.	.	.	DP=56;AD=56	DP	28	28
+2	9	.	T	.	.	.	DP=56;AD=56	DP	28	28
+2	10	.	T	.	.	.	DP=56;AD=56	DP	28	28
+2	11	.	G	.	.	.	DP=56;AD=56	DP	28	28
+2	12	.	C	.	.	.	DP=56;AD=56	DP	28	28
+2	13	.	A	.	.	.	DP=56;AD=56	DP	28	28
+2	14	.	A	.	.	.	DP=56;AD=56	DP	28	28
+2	15	.	C	.	.	.	DP=56;AD=56	DP	28	28
+2	16	.	G	.	.	.	DP=56;AD=56	DP	28	28
+2	17	.	C	.	.	.	DP=56;AD=56	DP	28	28
+2	18	.	A	.	.	.	DP=56;AD=56	DP	28	28
+2	19	.	A	.	.	.	DP=56;AD=56	DP	28	28
+2	20	.	G	.	.	.	DP=56;AD=56	DP	28	28
+2	21	.	T	.	.	.	DP=56;AD=56	DP	28	28
+2	22	.	G	.	.	.	DP=56;AD=56	DP	28	28
+2	23	.	A	.	.	.	DP=56;AD=56	DP	28	28
+2	24	.	C	.	.	.	DP=56;AD=56	DP	28	28
+2	25	.	G	.	.	.	DP=56;AD=56	DP	28	28
+2	26	.	A	.	.	.	DP=56;AD=56	DP	28	28
+2	27	.	T	.	.	.	DP=56;AD=56	DP	28	28
+2	28	.	T	.	.	.	DP=56;AD=56	DP	28	28
+2	29	.	C	.	.	.	DP=56;AD=56	DP	28	28
+2	30	.	C	.	.	.	DP=56;AD=56	DP	28	28
+2	31	.	C	.	.	.	DP=56;AD=56	DP	28	28
+2	32	.	A	.	.	.	DP=56;AD=55	DP	28	28
+2	33	.	C	.	.	.	DP=56;AD=56	DP	28	28
+2	34	.	G	.	.	.	DP=56;AD=56	DP	28	28
+2	35	.	G	.	.	.	DP=56;AD=56	DP	28	28
+2	36	.	A	.	.	.	DP=56;AD=56	DP	28	28
+2	37	.	C	.	.	.	DP=56;AD=56	DP	28	28
+2	38	.	A	.	.	.	DP=56;AD=56	DP	28	28
+2	39	.	T	.	.	.	DP=56;AD=56	DP	28	28
+2	40	.	A	.	.	.	DP=56;AD=56	DP	28	28
+2	41	.	A	.	.	.	DP=56;AD=56	DP	28	28
+2	42	.	C	.	.	.	DP=56;AD=56	DP	28	28
+2	43	.	T	.	.	.	DP=56;AD=56	DP	28	28
+2	44	.	G	.	.	.	DP=56;AD=56	DP	28	28
+2	45	.	A	.	.	.	DP=56;AD=56	DP	28	28
+2	46	.	T	.	.	.	DP=56;AD=56	DP	28	28
+2	47	.	C	.	.	.	DP=56;AD=56	DP	28	28
+2	48	.	T	.	.	.	DP=56;AD=56	DP	28	28
+2	49	.	A	.	.	.	DP=56;AD=56	DP	28	28
+2	50	.	A	.	.	.	DP=56;AD=56	DP	28	28
+2	51	.	G	.	.	.	DP=56;AD=56	DP	28	28
+2	52	.	T	.	.	.	DP=56;AD=56	DP	28	28
+2	53	.	A	.	.	.	DP=56;AD=56	DP	28	28
+2	54	.	A	.	.	.	DP=56;AD=55	DP	28	28
+2	55	.	C	.	.	.	DP=56;AD=56	DP	28	28
+2	56	.	T	.	.	.	DP=56;AD=56	DP	28	28
+2	57	.	T	.	.	.	DP=56;AD=56	DP	28	28
+2	58	.	C	.	.	.	DP=56;AD=56	DP	28	28
+2	59	.	C	.	.	.	DP=56;AD=56	DP	28	28
+2	60	.	A	.	.	.	DP=56;AD=56	DP	28	28
+2	61	.	A	.	.	.	DP=56;AD=56	DP	28	28
+2	62	.	A	.	.	.	DP=56;AD=55	DP	28	28
+2	63	.	T	.	.	.	DP=56;AD=56	DP	28	28
+2	64	.	C	.	.	.	DP=56;AD=56	DP	28	28
+2	65	.	T	.	.	.	DP=56;AD=56	DP	28	28
+2	66	.	G	.	.	.	DP=56;AD=56	DP	28	28
+2	67	.	G	.	.	.	DP=56;AD=56	DP	28	28
+2	68	.	G	.	.	.	DP=56;AD=56	DP	28	28
+2	69	.	A	.	.	.	DP=56;AD=56	DP	28	28
+2	70	.	A	.	.	.	DP=56;AD=56	DP	28	28
+2	71	.	T	.	.	.	DP=56;AD=56	DP	28	28
+2	72	.	G	.	.	.	DP=56;AD=56	DP	28	28
+2	73	.	G	.	.	.	DP=56;AD=56	DP	28	28
+2	74	.	G	.	.	.	DP=56;AD=56	DP	28	28
+2	75	.	A	.	.	.	DP=56;AD=56	DP	28	28
+2	76	.	T	.	.	.	DP=56;AD=56	DP	28	28
+2	77	.	T	.	.	.	DP=56;AD=56	DP	28	28
+2	78	.	T	.	.	.	DP=56;AD=56	DP	28	28
+2	79	.	C	.	.	.	DP=56;AD=56	DP	28	28
+2	80	.	A	.	.	.	DP=56;AD=56	DP	28	28
+2	81	.	T	.	.	.	DP=56;AD=56	DP	28	28
+2	82	.	A	.	.	.	DP=56;AD=56	DP	28	28
+2	83	.	A	.	.	.	DP=56;AD=56	DP	28	28
+2	84	.	T	.	.	.	DP=56;AD=56	DP	28	28
+2	85	.	T	.	.	.	DP=56;AD=56	DP	28	28
+2	86	.	A	.	.	.	DP=56;AD=56	DP	28	28
+2	87	.	A	.	.	.	DP=56;AD=56	DP	28	28
+2	88	.	G	.	.	.	DP=56;AD=56	DP	28	28
+2	89	.	G	.	.	.	DP=56;AD=56	DP	28	28
+2	90	.	A	.	.	.	DP=56;AD=56	DP	28	28
+2	91	.	C	.	.	.	DP=56;AD=56	DP	28	28
+2	92	.	T	.	.	.	DP=56;AD=56	DP	28	28
+2	93	.	A	.	.	.	DP=56;AD=56	DP	28	28
+2	94	.	T	.	.	.	DP=56;AD=56	DP	28	28
+2	105	.	T	.	.	.	DP=12;AD=12	DP	.	12
+2	106	.	A	.	.	.	DP=46;AD=46	DP	23	23
+2	107	.	C	.	.	.	DP=46;AD=46	DP	23	23
+2	108	.	G	.	.	.	DP=46;AD=46	DP	23	23
+2	109	.	A	.	.	.	DP=46;AD=46	DP	23	23
+2	110	.	C	.	.	.	DP=46;AD=46	DP	23	23
+2	111	.	G	.	.	.	DP=46;AD=46	DP	23	23
+2	112	.	A	.	.	.	DP=46;AD=46	DP	23	23
+2	113	.	G	.	.	.	DP=46;AD=46	DP	23	23
+2	114	.	C	.	.	.	DP=46;AD=46	DP	23	23
+2	115	.	A	.	.	.	DP=46;AD=46	DP	23	23
+2	116	.	A	.	.	.	DP=46;AD=46	DP	23	23
+2	117	.	T	.	.	.	DP=46;AD=46	DP	23	23
+2	118	.	C	.	.	.	DP=46;AD=46	DP	23	23
+2	119	.	C	.	.	.	DP=46;AD=46	DP	23	23
+2	120	.	A	.	.	.	DP=46;AD=46	DP	23	23
+2	121	.	C	.	.	.	DP=46;AD=46	DP	23	23
+2	122	.	A	.	.	.	DP=46;AD=46	DP	23	23
+2	123	.	G	.	.	.	DP=46;AD=46	DP	23	23
+2	124	.	A	.	.	.	DP=46;AD=46	DP	23	23
+2	125	.	C	.	.	.	DP=46;AD=46	DP	23	23
+2	126	.	C	.	.	.	DP=46;AD=45	DP	23	23
+2	127	.	T	.	.	.	DP=46;AD=46	DP	23	23
+2	128	.	A	.	.	.	DP=46;AD=46	DP	23	23
+2	129	.	G	.	.	.	DP=46;AD=46	DP	23	23
+2	130	.	G	.	.	.	DP=46;AD=46	DP	23	23
+2	131	.	C	.	.	.	DP=46;AD=46	DP	23	23
+2	132	.	C	.	.	.	DP=46;AD=46	DP	23	23
+2	133	.	C	.	.	.	DP=46;AD=46	DP	23	23
+2	134	.	A	.	.	.	DP=46;AD=46	DP	23	23
+2	135	.	T	.	.	.	DP=46;AD=46	DP	23	23
+2	136	.	C	.	.	.	DP=46;AD=46	DP	23	23
+2	137	.	G	.	.	.	DP=46;AD=46	DP	23	23
+2	138	.	A	.	.	.	DP=46;AD=46	DP	23	23
+2	139	.	A	.	.	.	DP=46;AD=46	DP	23	23
+2	140	.	G	.	.	.	DP=46;AD=46	DP	23	23
+2	141	.	C	.	.	.	DP=46;AD=46	DP	23	23
+2	142	.	G	.	.	.	DP=46;AD=46	DP	23	23
+2	143	.	T	.	.	.	DP=46;AD=46	DP	23	23
+2	144	.	C	.	.	.	DP=46;AD=46	DP	23	23
+2	145	.	T	.	.	.	DP=46;AD=46	DP	23	23
+2	146	.	T	.	.	.	DP=46;AD=46	DP	23	23
+2	147	.	A	.	.	.	DP=46;AD=46	DP	23	23
+2	148	.	T	.	.	.	DP=46;AD=46	DP	23	23
+2	149	.	G	.	.	.	DP=46;AD=46	DP	23	23
+2	150	.	A	.	.	.	DP=46;AD=46	DP	23	23
+2	151	.	T	.	.	.	DP=46;AD=46	DP	23	23
+2	152	.	T	.	.	.	DP=46;AD=46	DP	23	23
+2	153	.	G	.	.	.	DP=46;AD=46	DP	23	23
+2	154	.	A	.	.	.	DP=46;AD=46	DP	23	23
+2	155	.	T	.	.	.	DP=46;AD=46	DP	23	23
+2	156	.	A	.	.	.	DP=46;AD=46	DP	23	23
+2	157	.	A	.	.	.	DP=46;AD=46	DP	23	23
+2	158	.	C	.	.	.	DP=46;AD=46	DP	23	23
+2	159	.	A	.	.	.	DP=46;AD=46	DP	23	23
+2	160	.	T	.	.	.	DP=46;AD=46	DP	23	23
+2	161	.	C	.	.	.	DP=46;AD=46	DP	23	23
+2	162	.	A	.	.	.	DP=46;AD=46	DP	23	23
+2	163	.	G	A	40	.	DP=46;AD=34,12;AF=0.261	GT:PS:FT:GQ:DP:AD:GL	0/0:.:.:40:23:23,0:-0.00,-6.89,-68.45	1|0:163:.:40:23:11,12:-28.67,0.00,-25.99
+2	164	.	A	.	.	.	DP=46;AD=46	DP	23	23
+2	165	.	G	.	.	.	DP=46;AD=46	DP	23	23
+2	166	.	G	.	.	.	DP=46;AD=46	DP	23	23
+2	167	.	G	.	.	.	DP=46;AD=46	DP	23	23
+2	168	.	G	.	.	.	DP=46;AD=46	DP	23	23
+2	169	.	G	.	.	.	DP=46;AD=46	DP	23	23
+2	170	.	A	.	.	.	DP=46;AD=46	DP	23	23
+2	171	.	T	.	.	.	DP=46;AD=46	DP	23	23
+2	172	.	G	.	.	.	DP=46;AD=46	DP	23	23
+2	173	.	G	.	.	.	DP=46;AD=46	DP	23	23
+2	174	.	G	.	.	.	DP=46;AD=46	DP	23	23
+2	175	.	A	.	.	.	DP=46;AD=46	DP	23	23
+2	176	.	G	.	.	.	DP=46;AD=45	DP	23	23
+2	177	.	G	.	.	.	DP=46;AD=46	DP	23	23
+2	178	.	T	.	.	.	DP=46;AD=46	DP	23	23
+2	179	.	C	.	.	.	DP=46;AD=46	DP	23	23
+2	180	.	C	.	.	.	DP=46;AD=46	DP	23	23
+2	181	.	T	.	.	.	DP=46;AD=46	DP	23	23
+2	182	.	G	A	40	.	DP=46;AD=34,12;AF=0.261	GT:PS:FT:GQ:DP:AD:GL	0/0:.:.:40:23:23,0:-0.00,-6.89,-68.45	1|0:163:.:40:23:11,12:-28.67,0.00,-25.99
+2	183	.	C	.	.	.	DP=46;AD=46	DP	23	23
+2	184	.	T	.	.	.	DP=46;AD=46	DP	23	23
+2	185	.	G	.	.	.	DP=46;AD=46	DP	23	23
+2	186	.	T	.	.	.	DP=46;AD=45	DP	23	23
+2	187	.	C	.	.	.	DP=46;AD=46	DP	23	23
+2	188	.	G	.	.	.	DP=46;AD=46	DP	23	23
+2	189	.	C	.	.	.	DP=46;AD=46	DP	23	23
+2	190	.	A	.	.	.	DP=46;AD=46	DP	23	23
+2	191	.	T	.	.	.	DP=46;AD=46	DP	23	23
+2	192	.	G	.	.	.	DP=46;AD=46	DP	23	23
+2	193	.	G	.	.	.	DP=46;AD=46	DP	23	23
+2	194	.	G	.	.	.	DP=46;AD=45	DP	23	23
+2	195	.	A	.	.	.	DP=46;AD=46	DP	23	23
+2	196	.	G	.	.	.	DP=46;AD=46	DP	23	23
+2	197	.	A	.	.	.	DP=46;AD=46	DP	23	23
+2	198	.	A	.	.	.	DP=46;AD=46	DP	23	23
+2	199	.	T	.	.	.	DP=46;AD=46	DP	23	23
+2	200	.	A	.	.	.	DP=46;AD=46	DP	23	23
+2	201	.	C	.	.	.	DP=46;AD=46	DP	23	23
+2	202	.	A	.	.	.	DP=34;AD=34	DP	23	11
+2	203	.	C	.	.	.	DP=34;AD=34	DP	23	11
+2	204	.	G	.	.	.	DP=34;AD=34	DP	23	11
+2	205	.	G	.	.	.	DP=34;AD=34	DP	23	11
+3	1	.	A	.	.	.	DP=40;AD=40	DP	20	20
+3	2	.	A	.	.	.	DP=40;AD=40	DP	20	20
+3	3	.	T	.	.	.	DP=40;AD=40	DP	20	20
+3	4	.	T	.	.	.	DP=40;AD=40	DP	20	20
+3	5	.	C	.	.	.	DP=40;AD=40	DP	20	20
+3	6	.	T	.	.	.	DP=40;AD=40	DP	20	20
+3	7	.	C	.	.	.	DP=40;AD=40	DP	20	20
+3	8	.	T	.	.	.	DP=40;AD=40	DP	20	20
+3	9	.	A	.	.	.	DP=40;AD=40	DP	20	20
+3	10	.	C	.	.	.	DP=40;AD=40	DP	20	20
+3	11	.	A	.	.	.	DP=40;AD=40	DP	20	20
+3	12	.	C	.	.	.	DP=40;AD=40	DP	20	20
+3	13	.	C	.	.	.	DP=40;AD=40	DP	20	20
+3	14	.	A	.	.	.	DP=40;AD=40	DP	20	20
+3	15	.	C	.	.	.	DP=40;AD=40	DP	20	20
+3	16	.	A	.	.	.	DP=40;AD=39	DP	20	20
+3	17	.	G	.	.	.	DP=40;AD=40	DP	20	20
+3	18	.	C	.	.	.	DP=40;AD=40	DP	20	20
+3	19	.	A	.	.	.	DP=40;AD=40	DP	20	20
+3	20	.	T	.	.	.	DP=40;AD=40	DP	20	20
+3	21	.	C	.	.	.	DP=40;AD=40	DP	20	20
+3	22	.	A	.	.	.	DP=40;AD=40	DP	20	20
+3	23	.	A	.	.	.	DP=40;AD=40	DP	20	20
+3	24	.	T	.	.	.	DP=40;AD=40	DP	20	20
+3	25	.	T	.	.	.	DP=40;AD=40	DP	20	20
+3	26	.	C	.	.	.	DP=40;AD=40	DP	20	20
+3	27	.	T	.	.	.	DP=40;AD=40	DP	20	20
+3	28	.	A	.	.	.	DP=40;AD=40	DP	20	20
+3	29	.	A	.	.	.	DP=40;AD=40	DP	20	20
+3	30	.	A	.	.	.	DP=40;AD=40	DP	20	20
+3	31	.	A	.	.	.	DP=40;AD=40	DP	20	20
+3	32	.	A	.	.	.	DP=40;AD=40	DP	20	20
+3	33	.	T	.	.	.	DP=40;AD=40	DP	20	20
+3	34	.	G	.	.	.	DP=40;AD=40	DP	20	20
+3	35	.	A	.	.	.	DP=40;AD=40	DP	20	20
+3	36	.	C	.	.	.	DP=40;AD=40	DP	20	20
+3	37	.	T	.	.	.	DP=40;AD=40	DP	20	20
+3	38	.	A	.	.	.	DP=40;AD=40	DP	20	20
+3	39	.	C	.	.	.	DP=40;AD=40	DP	20	20
+3	40	.	C	.	.	.	DP=40;AD=40	DP	20	20
+3	41	.	A	.	.	.	DP=40;AD=40	DP	20	20
+3	42	.	G	.	.	.	DP=40;AD=40	DP	20	20
+3	43	.	A	.	.	.	DP=40;AD=40	DP	20	20
+3	44	.	G	.	.	.	DP=40;AD=40	DP	20	20
+3	45	.	A	.	.	.	DP=40;AD=40	DP	20	20
+3	46	.	G	.	.	.	DP=40;AD=40	DP	20	20
+3	47	.	A	.	.	.	DP=40;AD=40	DP	20	20
+3	48	.	C	.	.	.	DP=40;AD=40	DP	20	20
+3	49	.	A	.	.	.	DP=40;AD=40	DP	20	20
+3	50	.	A	.	.	.	DP=40;AD=40	DP	20	20
+3	51	.	C	.	.	.	DP=40;AD=40	DP	20	20
+3	52	.	T	.	.	.	DP=40;AD=40	DP	20	20
+3	53	.	C	.	.	.	DP=40;AD=40	DP	20	20
+3	54	.	C	.	.	.	DP=40;AD=40	DP	20	20
+3	55	.	G	.	.	.	DP=40;AD=40	DP	20	20
+3	56	.	C	.	.	.	DP=40;AD=40	DP	20	20
+3	57	.	A	.	.	.	DP=40;AD=40	DP	20	20
+3	58	.	G	.	.	.	DP=40;AD=40	DP	20	20
+3	59	.	T	.	.	.	DP=40;AD=40	DP	20	20
+3	60	.	T	.	.	.	DP=40;AD=39	DP	20	20
+3	61	.	A	.	.	.	DP=40;AD=40	DP	20	20
+3	62	.	A	.	.	.	DP=40;AD=40	DP	20	20
+3	63	.	A	.	.	.	DP=40;AD=40	DP	20	20
+3	64	.	C	.	.	.	DP=40;AD=40	DP	20	20
+3	65	.	A	.	.	.	DP=40;AD=40	DP	20	20
+3	66	.	C	.	.	.	DP=40;AD=40	DP	20	20
+3	67	.	T	.	.	.	DP=40;AD=40	DP	20	20
+3	68	.	C	.	.	.	DP=40;AD=40	DP	20	20
+3	69	.	T	.	.	.	DP=40;AD=40	DP	20	20
+3	70	.	G	.	.	.	DP=40;AD=40	DP	20	20
+3	71	.	A	.	.	.	DP=40;AD=40	DP	20	20
+3	72	.	C	.	.	.	DP=40;AD=40	DP	20	20
+3	73	.	T	.	.	.	DP=40;AD=40	DP	20	20
+3	74	.	G	.	.	.	DP=40;AD=40	DP	20	20
+3	75	.	C	.	.	.	DP=40;AD=40	DP	20	20
+3	76	.	C	.	.	.	DP=40;AD=40	DP	20	20
+3	77	.	A	.	.	.	DP=40;AD=40	DP	20	20
+3	78	.	C	.	.	.	DP=40;AD=40	DP	20	20
+3	79	.	G	.	.	.	DP=40;AD=40	DP	20	20
+3	80	.	C	.	.	.	DP=40;AD=40	DP	20	20
+3	81	.	C	.	.	.	DP=40;AD=40	DP	20	20
+3	82	.	A	.	.	.	DP=40;AD=40	DP	20	20
+3	83	.	G	.	.	.	DP=40;AD=40	DP	20	20
+3	84	.	C	.	.	.	DP=40;AD=40	DP	20	20
+3	85	.	T	.	.	.	DP=40;AD=40	DP	20	20
+3	86	.	A	.	.	.	DP=40;AD=40	DP	20	20
+3	87	.	C	.	.	.	DP=40;AD=40	DP	20	20
+3	88	.	C	.	.	.	DP=40;AD=40	DP	20	20
+3	89	.	T	.	.	.	DP=40;AD=40	DP	20	20
+3	90	.	C	.	.	.	DP=40;AD=40	DP	20	20
+3	91	.	T	.	.	.	DP=40;AD=39	DP	20	20
+3	92	.	A	.	.	.	DP=40;AD=40	DP	20	20
+3	93	.	G	.	.	.	DP=40;AD=40	DP	20	20
+3	94	.	A	.	.	.	DP=40;AD=40	DP	20	20
+3	105	.	G	.	.	.	DP=30;AD=30	DP	17	13
+3	106	.	G	.	.	.	DP=30;AD=30	DP	17	13
+3	107	.	C	.	.	.	DP=30;AD=30	DP	17	13
+3	108	.	T	.	.	.	DP=30;AD=30	DP	17	13
+3	109	.	G	.	.	.	DP=30;AD=30	DP	17	13
+3	110	.	C	.	.	.	DP=30;AD=30	DP	17	13
+3	111	.	T	.	.	.	DP=30;AD=30	DP	17	13
+3	112	.	G	.	.	.	DP=30;AD=30	DP	17	13
+3	113	.	G	.	.	.	DP=30;AD=30	DP	17	13
+3	114	.	A	.	.	.	DP=30;AD=30	DP	17	13
+3	115	.	C	.	.	.	DP=30;AD=30	DP	17	13
+3	116	.	G	.	.	.	DP=30;AD=30	DP	17	13
+3	117	.	T	.	.	.	DP=30;AD=30	DP	17	13
+3	118	.	C	.	.	.	DP=30;AD=30	DP	17	13
+3	119	.	C	.	.	.	DP=30;AD=30	DP	17	13
+3	120	.	T	.	.	.	DP=30;AD=30	DP	17	13
+3	121	.	T	.	.	.	DP=30;AD=30	DP	17	13
+3	122	.	C	.	.	.	DP=30;AD=30	DP	17	13
+3	123	.	G	.	.	.	DP=30;AD=30	DP	17	13
+3	124	.	C	.	.	.	DP=30;AD=30	DP	17	13
+3	125	.	T	.	.	.	DP=30;AD=30	DP	17	13
+3	126	.	C	.	.	.	DP=30;AD=30	DP	17	13
+3	127	.	G	.	.	.	DP=30;AD=30	DP	17	13
+3	128	.	G	.	.	.	DP=30;AD=30	DP	17	13
+3	129	.	T	.	.	.	DP=30;AD=30	DP	17	13
+3	130	.	A	.	.	.	DP=30;AD=30	DP	17	13
+3	131	.	C	.	.	.	DP=30;AD=30	DP	17	13
+3	132	.	C	.	.	.	DP=30;AD=29	DP	17	13
+3	133	.	T	.	.	.	DP=30;AD=30	DP	17	13
+3	134	.	T	.	.	.	DP=30;AD=30	DP	17	13
+3	135	.	G	.	.	.	DP=30;AD=30	DP	17	13
+3	136	.	A	.	.	.	DP=30;AD=30	DP	17	13
+3	137	.	C	.	.	.	DP=30;AD=30	DP	17	13
+3	138	.	T	.	.	.	DP=30;AD=30	DP	17	13
+3	139	.	G	.	.	.	DP=30;AD=30	DP	17	13
+3	140	.	G	.	.	.	DP=30;AD=30	DP	17	13
+3	141	.	A	.	.	.	DP=30;AD=30	DP	17	13
+3	142	.	T	.	.	.	DP=30;AD=30	DP	17	13
+3	143	.	T	.	.	.	DP=30;AD=30	DP	17	13
+3	144	.	A	.	.	.	DP=30;AD=30	DP	17	13
+3	145	.	T	C	40	.	DP=30;AD=16,14;AF=0.467	GT:PS:FT:GQ:DP:AD:GL	1|0:145:.:40:17:8,9:-20.29,0.00,-17.57	1|0:145:.:40:13:8,5:-10.39,-0.00,-18.77
+3	146	.	A	.	.	.	DP=30;AD=30	DP	17	13
+3	147	.	T	.	.	.	DP=30;AD=30	DP	17	13
+3	148	.	A	.	.	.	DP=30;AD=30	DP	17	13
+3	149	.	G	.	.	.	DP=30;AD=30	DP	17	13
+3	150	.	C	.	.	.	DP=30;AD=30	DP	17	13
+3	151	.	A	.	.	.	DP=30;AD=30	DP	17	13
+3	152	.	T	.	.	.	DP=30;AD=30	DP	17	13
+3	153	.	T	.	.	.	DP=30;AD=30	DP	17	13
+3	154	.	C	.	.	.	DP=30;AD=30	DP	17	13
+3	155	.	C	.	.	.	DP=30;AD=30	DP	17	13
+3	156	.	T	.	.	.	DP=30;AD=29	DP	17	13
+3	157	.	T	G	40	.	DP=30;AD=16,14;AF=0.467	GT:PS:FT:GQ:DP:AD:GL	1|0:145:.:40:17:8,9:-20.29,0.00,-17.57	1|0:145:.:40:13:8,5:-10.39,-0.00,-18.77
+3	158	.	A	.	.	.	DP=30;AD=30	DP	17	13
+3	159	.	G	.	.	.	DP=30;AD=30	DP	17	13
+3	160	.	T	.	.	.	DP=30;AD=30	DP	17	13
+3	161	.	T	.	.	.	DP=30;AD=30	DP	17	13
+3	162	.	C	.	.	.	DP=30;AD=30	DP	17	13
+3	163	.	A	.	.	.	DP=30;AD=30	DP	17	13
+3	164	.	C	.	.	.	DP=30;AD=30	DP	17	13
+3	165	.	G	.	.	.	DP=30;AD=30	DP	17	13
+3	166	.	G	.	.	.	DP=30;AD=30	DP	17	13
+3	167	.	C	.	.	.	DP=30;AD=30	DP	17	13
+3	168	.	C	.	.	.	DP=30;AD=30	DP	17	13
+3	169	.	A	.	.	.	DP=30;AD=30	DP	17	13
+3	170	.	A	.	.	.	DP=30;AD=30	DP	17	13
+3	171	.	T	.	.	.	DP=30;AD=30	DP	17	13
+3	172	.	A	.	.	.	DP=30;AD=30	DP	17	13
+3	173	.	T	.	.	.	DP=30;AD=30	DP	17	13
+3	174	.	C	.	.	.	DP=30;AD=30	DP	17	13
+3	175	.	G	.	.	.	DP=30;AD=30	DP	17	13
+3	176	.	C	.	.	.	DP=30;AD=30	DP	17	13
+3	177	.	C	.	.	.	DP=30;AD=30	DP	17	13
+3	178	.	A	.	.	.	DP=30;AD=30	DP	17	13
+3	179	.	A	.	.	.	DP=30;AD=30	DP	17	13
+3	180	.	C	.	.	.	DP=30;AD=30	DP	17	13
+3	181	.	C	.	.	.	DP=30;AD=30	DP	17	13
+3	182	.	G	.	.	.	DP=30;AD=30	DP	17	13
+3	183	.	T	.	.	.	DP=30;AD=30	DP	17	13
+3	184	.	T	.	.	.	DP=30;AD=30	DP	17	13
+3	185	.	G	.	.	.	DP=30;AD=30	DP	17	13
+3	186	.	A	.	.	.	DP=30;AD=30	DP	17	13
+3	187	.	G	.	.	.	DP=30;AD=30	DP	17	13
+3	188	.	T	.	.	.	DP=30;AD=30	DP	17	13
+3	189	.	G	.	.	.	DP=30;AD=30	DP	17	13
+3	190	.	A	.	.	.	DP=30;AD=30	DP	17	13
+3	191	.	G	.	.	.	DP=30;AD=30	DP	17	13
+3	192	.	T	.	.	.	DP=30;AD=30	DP	17	13
+3	193	.	T	.	.	.	DP=30;AD=30	DP	17	13
+3	194	.	T	.	.	.	DP=30;AD=30	DP	17	13
+3	195	.	A	.	.	.	DP=30;AD=30	DP	17	13
+3	196	.	G	.	.	.	DP=30;AD=30	DP	17	13
+3	197	.	T	.	.	.	DP=30;AD=30	DP	17	13
+3	198	.	G	.	.	.	DP=30;AD=30	DP	17	13
+3	199	.	A	.	.	.	DP=30;AD=30	DP	17	13
+3	200	.	A	.	.	.	DP=30;AD=30	DP	17	13
+3	201	.	C	.	.	.	DP=30;AD=30	DP	17	13
+3	202	.	C	.	.	.	DP=30;AD=30	DP	17	13
+3	203	.	G	.	.	.	DP=30;AD=30	DP	17	13
+3	204	.	G	.	.	.	DP=30;AD=30	DP	17	13
diff -r c23695f62bdd -r 56d3555cf5f7 test-data/gstacks/catalog.fa.gz
Binary file test-data/gstacks/catalog.fa.gz has changed
diff -r c23695f62bdd -r 56d3555cf5f7 test-data/gstacks/gstacks.log
--- a/test-data/gstacks/gstacks.log	Wed Feb 27 09:52:16 2019 -0500
+++ b/test-data/gstacks/gstacks.log	Thu Jun 20 08:13:18 2019 -0400
@@ -1,11 +1,11 @@
-gstacks v2.3b, executed 2019-02-22 12:51:51
-gstacks -P bam_inputs -M /tmp/tmpZcvUSM/files/000/dataset_3.dat -O stacks_outputs -t 1 --model marukilow --var-alpha 0.01 --gt-alpha 0.05
+gstacks v2.4, executed 2019-06-18 10:34:45 (zlib-1.2.11)
+gstacks -P stacks_outputs -M denovo_map/popmap_cstacks.tsv
 Locus/sample distributions will be written to 'stacks_outputs/gstacks.log.distribs'.
 
 Configuration for this run:
   Input mode: denovo
-  Population map: '/tmp/tmpZcvUSM/files/000/dataset_3.dat'
-  Input files: 2, e.g. 'bam_inputs/PopA_01.matches.bam'
+  Population map: 'denovo_map/popmap_cstacks.tsv'
+  Input files: 2, e.g. 'stacks_outputs/PopA_01.matches.bam'
   Output to: 'stacks_outputs/'
   Model: marukilow (var_alpha: 0.01, gt_alpha: 0.05)
 
diff -r c23695f62bdd -r 56d3555cf5f7 test-data/gstacks/gstacks.log.distribs
--- a/test-data/gstacks/gstacks.log.distribs	Wed Feb 27 09:52:16 2019 -0500
+++ b/test-data/gstacks/gstacks.log.distribs	Thu Jun 20 08:13:18 2019 -0400
@@ -19,25 +19,25 @@
 Num. threads: 1
 Parallel time: 0.0
 Average thread time spent:
-     0.0  reading (2.9%)
-     0.0  processing (95.7%)
-             0.0 pre-alignments block (69.1%)
-             0.0  reformatting fw-reads (0.2%)
-             0.0  assembling (21.2%)
-             0.0  initializing alignments (4.4%)
-             0.0  aligning (41.3%)
-             0.0  merging read pairs (2.0%)
-             0.0 post-alignments block (25.2%)
+     0.0  reading (3.1%)
+     0.0  processing (95.2%)
+             0.0 pre-alignments block (72.2%)
+             0.0  reformatting fw-reads (0.1%)
+             0.0  assembling (22.2%)
+             0.0  initializing alignments (5.4%)
+             0.0  aligning (42.9%)
+             0.0  merging read pairs (1.5%)
+             0.0 post-alignments block (21.2%)
              0.0  filtering reads (0.0%)
-             0.0  counting nucleotides (4.0%)
+             0.0  counting nucleotides (3.5%)
              0.0  genotyping (1.9%)
-             0.0  haplotyping (1.2%)
+             0.0  haplotyping (1.0%)
              0.0  computing consensus (0.1%)
              0.0  building_fa (0.1%)
-             0.0  building_vcf (17.8%)
+             0.0  building_vcf (14.6%)
      0.0  writing_fa (0.1%)
-     0.0  writing_vcf (1.0%)
+     0.0  writing_vcf (1.3%)
      0.0  clocking (0.2%)
-Total time spent writing vcf: 0.0 (1.0%)
+Total time spent writing vcf: 0.0 (1.3%)
 VCFwrite block size: mean=1.0(n=3); max=1
 END clockings
diff -r c23695f62bdd -r 56d3555cf5f7 test-data/kmerfilter/kmerfilter.log
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/kmerfilter/kmerfilter.log	Thu Jun 20 08:13:18 2019 -0400
@@ -0,0 +1,22 @@
+Using a kmer size of 16
+Filtering out reads by identifying rare kmers: On.
+  A kmer is considered rare when its coverage is at 15% or below the median kmer coverage for the read.
+  A read is dropped when it contains 13 or more rare kmers in a row.
+Filtering out reads by identifying abundant kmers: On.
+  Kmer is considered abundant when it occurs 20000 or more times.
+  A read is dropped when it contains 80% or more abundant kmers.
+Normalizing read depth: Off.
+Found 1 input file(s).
+Found 0 paired input file(s).
+Generating kmer distribution...
+Generating kmers from file 1 of 1 [R1_0001.fastq]
+540 unique k-mers recorded.
+Filtering reads by kmer frequency...
+Processing file 1 of 1 [R1_0001.fastq]
+  5 total reads; -0 rare k-mer reads; -0 abundant k-mer reads; 5 retained reads.
+Outputing details to log: 'stacks_outputs/kmer_filter.log'
+
+5 total sequences;
+  0 rare k-mer reads;
+  0 abundant k-mer reads;
+5 retained reads.
diff -r c23695f62bdd -r 56d3555cf5f7 test-data/populations/.populations.log.distribs.swp
Binary file test-data/populations/.populations.log.distribs.swp has changed
diff -r c23695f62bdd -r 56d3555cf5f7 test-data/populations/populations.fixed.phylip
--- a/test-data/populations/populations.fixed.phylip	Wed Feb 27 09:52:16 2019 -0500
+++ b/test-data/populations/populations.fixed.phylip	Thu Jun 20 08:13:18 2019 -0400
@@ -1,3 +1,3 @@
 1	0
 1
-# Stacks v2.3b;  Phylip sequential; February 25, 2019
+# Stacks v2.4;  Phylip sequential; June 17, 2019
diff -r c23695f62bdd -r 56d3555cf5f7 test-data/populations/populations.fixed.phylip.log
--- a/test-data/populations/populations.fixed.phylip.log	Wed Feb 27 09:52:16 2019 -0500
+++ b/test-data/populations/populations.fixed.phylip.log	Thu Jun 20 08:13:18 2019 -0400
@@ -1,2 +1,2 @@
-# Stacks v2.3b;  Phylip sequential; February 25, 2019
+# Stacks v2.4;  Phylip sequential; June 17, 2019
 # Seq Pos	Locus ID	Column	Population
diff -r c23695f62bdd -r 56d3555cf5f7 test-data/populations/populations.haplotypes.tsv
--- a/test-data/populations/populations.haplotypes.tsv	Wed Feb 27 09:52:16 2019 -0500
+++ b/test-data/populations/populations.haplotypes.tsv	Thu Jun 20 08:13:18 2019 -0400
@@ -1,4 +1,4 @@
 # Catalog Locus ID	Cnt	PopA_01	PopA_02
-1	0	AC/CA	AC/CA
-2	0	CG/TT	CG/TT
-3	0	GG/GG	AA/GG
+1	2	AC/CA	AC/CA
+2	2	GG/GG	AA/GG
+3	2	CG/TT	CG/TT
diff -r c23695f62bdd -r 56d3555cf5f7 test-data/populations/populations.haps.genepop
--- a/test-data/populations/populations.haps.genepop	Wed Feb 27 09:52:16 2019 -0500
+++ b/test-data/populations/populations.haps.genepop	Thu Jun 20 08:13:18 2019 -0400
@@ -1,4 +1,4 @@
-Stacks v2.3b; GenePop v4.1.3; February 25, 2019
+Stacks v2.4; GenePop v4.1.3; June 17, 2019
 1,2,3
 pop
 PopA_01,	0102	0102	0101
diff -r c23695f62bdd -r 56d3555cf5f7 test-data/populations/populations.haps.vcf
--- a/test-data/populations/populations.haps.vcf	Wed Feb 27 09:52:16 2019 -0500
+++ b/test-data/populations/populations.haps.vcf	Thu Jun 20 08:13:18 2019 -0400
@@ -1,6 +1,6 @@
 ##fileformat=VCFv4.2
-##fileDate=20190225
-##source="Stacks v2.3b"
+##fileDate=20190617
+##source="Stacks v2.4"
 ##INFO=<ID=AD,Number=R,Type=Integer,Description="Total Depth for Each Allele">
 ##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency">
 ##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
diff -r c23695f62bdd -r 56d3555cf5f7 test-data/populations/populations.hapstats.tsv
--- a/test-data/populations/populations.hapstats.tsv	Wed Feb 27 09:52:16 2019 -0500
+++ b/test-data/populations/populations.hapstats.tsv	Thu Jun 20 08:13:18 2019 -0400
@@ -1,5 +1,5 @@
 # 1	PopA_01,PopA_02
 # Locus ID	Chr	BP	Pop ID	N	Haplotype Cnt	Gene Diversity	Smoothed Gene Diversity	Smoothed Gene Diversity P-value	Haplotype Diversity	Smoothed Haplotype Diversity	Smoothed Haplotype Diversity P-value	HWE P-value	HWE P-value SE	Haplotypes
-1	un	-201	1	4	2	0.66667	0.00000	0.00000	1.33333	0.00000	0.00000	0.00000	0.00000	AC:2;CA:2
-2	un	3	1	4	2	0.66667	0.00000	0.00000	1.33333	0.00000	0.00000	0.00000	0.00000	CG:2;TT:2
-3	un	206	1	4	2	0.50000	0.00000	0.00000	1.00000	0.00000	0.00000	0.00000	0.00000	AA:1;GG:3
+1	un	1	1	4	2	0.66667	0.00000	0.00000	1.33333	0.00000	0.00000	0.00000	0.00000	AC:2;CA:2
+2	un	205	1	4	2	0.50000	0.00000	0.00000	1.00000	0.00000	0.00000	0.00000	0.00000	AA:1;GG:3
+3	un	410	1	4	2	0.66667	0.00000	0.00000	1.33333	0.00000	0.00000	0.00000	0.00000	CG:2;TT:2
diff -r c23695f62bdd -r 56d3555cf5f7 test-data/populations/populations.hzar.csv
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/populations/populations.hzar.csv	Thu Jun 20 08:13:18 2019 -0400
@@ -0,0 +1,3 @@
+# Stacks v2.4;  HZAR v0.2-5; June 18, 2019
+Population,Distance,1_33.A,1_33.B,1_33.N,1_88.A,1_88.B,1_88.N,2_162.A,2_162.B,2_162.N,2_181.A,2_181.B,2_181.N,3_144.A,3_144.B,3_144.N,3_156.A,3_156.B,3_156.N
+1,0,0.5,0.5,4,0.5,0.5,4,0.75,0.25,4,0.75,0.25,4,0.5,0.5,4,0.5,0.5,4
diff -r c23695f62bdd -r 56d3555cf5f7 test-data/populations/populations.loci.fa
--- a/test-data/populations/populations.loci.fa	Wed Feb 27 09:52:16 2019 -0500
+++ b/test-data/populations/populations.loci.fa	Thu Jun 20 08:13:18 2019 -0400
@@ -1,4 +1,4 @@
-Stacks version 2.3b; February 25, 2019
+# Stacks version 2.4; June 17, 2019
 >CLocus_1
 AATTCGTTTGCTGCTTCAGGAATCTCTCGTATAATCTGAGTATGTGCGTACGTACGCTATTTAGATGGATAACCGACGCTGCCAGACGAGAGACNNNNNNNNNNCGTCAGAGGGCTTATATCGTGAGTGATAGCAGCAGTTTCTCTCTACCACATAGTTATACACCATTGGGCCAGCTCGTTGAAAACTACTGATGCTGATCGG
 >CLocus_2
diff -r c23695f62bdd -r 56d3555cf5f7 test-data/populations/populations.log
--- a/test-data/populations/populations.log	Wed Feb 27 09:52:16 2019 -0500
+++ b/test-data/populations/populations.log	Thu Jun 20 08:13:18 2019 -0400
@@ -1,5 +1,5 @@
-populations v2.3b, executed 2019-02-25 23:06:32
-populations -t 1 -P stacks_inputs -O stacks_outputs -M /tmp/tmp4FNQre/files/000/dataset_3.dat -p 1 -r 0.0 --min_maf 0.0 --min_mac 0 --merge_prune_lim 1.0
+populations v2.4, executed 2019-06-18 10:34:45 (zlib-1.2.11)
+populations -P stacks_outputs -M denovo_map/popmap_cstacks.tsv
 Locus/sample distributions will be written to 'stacks_outputs/populations.log.distribs'.
 populations parameters selected:
   Percent samples limit per population: 0
diff -r c23695f62bdd -r 56d3555cf5f7 test-data/populations/populations.log.distribs
--- a/test-data/populations/populations.log.distribs	Wed Feb 27 09:52:16 2019 -0500
+++ b/test-data/populations/populations.log.distribs	Thu Jun 20 08:13:18 2019 -0400
@@ -8,14 +8,13 @@
 BEGIN samples_per_loc_prefilters
 # Distribution of valid samples matched to a catalog locus prior to filtering.
 n_samples	n_loci
-0	3
+2	3
 END samples_per_loc_prefilters
 
 BEGIN missing_samples_per_loc_prefilters
-
 # Distribution of missing samples for each catalog locus prior to filtering.
 # Absent samples at locus	Count
-2	3
+0	3
 END missing_samples_per_loc_prefilters
 
 BEGIN snps_per_loc_prefilters
@@ -27,14 +26,13 @@
 BEGIN samples_per_loc_postfilters
 # Distribution of valid samples matched to a catalog locus after filtering.
 n_samples	n_loci
-0	3
+2	3
 END samples_per_loc_postfilters
 
 BEGIN missing_samples_per_loc_postfilters
-
 # Distribution of missing samples for each catalog locus after filtering.
 # Absent samples at locus	Count
-2	3
+0	3
 END missing_samples_per_loc_postfilters
 
 BEGIN snps_per_loc_postfilters
diff -r c23695f62bdd -r 56d3555cf5f7 test-data/populations/populations.markers.tsv
--- a/test-data/populations/populations.markers.tsv	Wed Feb 27 09:52:16 2019 -0500
+++ b/test-data/populations/populations.markers.tsv	Thu Jun 20 08:13:18 2019 -0400
@@ -1,4 +1,4 @@
 # Catalog Locus ID		Total Genotypes	Max	Genotype Freqs	F	Mean Log Likelihood	Genotype Map	
 1		2	100.00000	ab:2(100.0%);	0.00000	1.00000	AC:a;CA:b;	
-2		2	100.00000	ab:2(100.0%);	0.00000	1.00000	CG:a;TT:b;	
-3		2	50.00000	aa:1(50.0%);ab:1(50.0%);	0.00000	1.00000	AA:b;GG:a;	
+2		2	50.00000	aa:1(50.0%);ab:1(50.0%);	0.00000	1.00000	AA:b;GG:a;	
+3		2	100.00000	ab:2(100.0%);	0.00000	1.00000	CG:a;TT:b;	
diff -r c23695f62bdd -r 56d3555cf5f7 test-data/populations/populations.plink.map
--- a/test-data/populations/populations.plink.map	Wed Feb 27 09:52:16 2019 -0500
+++ b/test-data/populations/populations.plink.map	Thu Jun 20 08:13:18 2019 -0400
@@ -1,7 +1,7 @@
-# Stacks v2.3b;  PLINK v1.07; February 25, 2019
-un	1_33	0	35
-un	1_88	0	90
-un	2_144	0	350
-un	2_156	0	362
-un	3_162	0	572
-un	3_181	0	591
+# Stacks v2.4;  PLINK v1.07; June 17, 2019
+un	1_33	0	34
+un	1_88	0	89
+un	2_144	0	349
+un	2_156	0	361
+un	3_162	0	571
+un	3_181	0	590
diff -r c23695f62bdd -r 56d3555cf5f7 test-data/populations/populations.plink.ped
--- a/test-data/populations/populations.plink.ped	Wed Feb 27 09:52:16 2019 -0500
+++ b/test-data/populations/populations.plink.ped	Thu Jun 20 08:13:18 2019 -0400
@@ -1,3 +1,3 @@
-# Stacks v2.3b;  PLINK v1.07; February 25, 2019
+# Stacks v2.4;  PLINK v1.07; June 17, 2019
 1	PopA_01	0	0	0	0	A	C	A	C	C	T	G	T	G	G	G	G
 1	PopA_02	0	0	0	0	A	C	A	C	C	T	G	T	A	G	A	G
diff -r c23695f62bdd -r 56d3555cf5f7 test-data/populations/populations.samples-raw.fa
--- a/test-data/populations/populations.samples-raw.fa	Wed Feb 27 09:52:16 2019 -0500
+++ b/test-data/populations/populations.samples-raw.fa	Thu Jun 20 08:13:18 2019 -0400
@@ -1,4 +1,4 @@
-Stacks version 2.3b; February 25, 2019
+# Stacks version 2.4; June 17, 2019
 >CLocus_1_Sample_1_Locus_1_Allele_0 [PopA_01]
 AATTCGTTTGCTGCTTCAGGAATCTCTCGTATAATCTGAGTATGTGCGTACGTACGCTATTTAGATGGATAACCGACGCTGCCAGACGCGAGACNNNNNNNNNNCGTCAGAGGGCTTATATCGTGAGTGATAGCAGCAGTTTCTCTCTACCACATAGTTATACACCATTGGGCCAGCTCGTTGAAAACTACTGATGCTGATCGG
 >CLocus_1_Sample_1_Locus_1_Allele_1 [PopA_01]
diff -r c23695f62bdd -r 56d3555cf5f7 test-data/populations/populations.samples.fa
--- a/test-data/populations/populations.samples.fa	Wed Feb 27 09:52:16 2019 -0500
+++ b/test-data/populations/populations.samples.fa	Thu Jun 20 08:13:18 2019 -0400
@@ -1,4 +1,4 @@
-Stacks version 2.3b; February 25, 2019
+# Stacks version 2.4; June 17, 2019
 >CLocus_1_Sample_1_Locus_1_Allele_0 [PopA_01]
 AATTCGTTTGCTGCTTCAGGAATCTCTCGTATAATCTGAGTATGTGCGTACGTACGCTATTTAGATGGATAACCGACGCTGCCAGACGCGAGACNNNNNNNNNNCGTCAGAGGGCTTATATCGTGAGTGATAGCAGCAGTTTCTCTCTACCACATAGTTATACACCATTGGGCCAGCTCGTTGAAAACTACTGATGCTGATCGG
 >CLocus_1_Sample_1_Locus_1_Allele_1 [PopA_01]
diff -r c23695f62bdd -r 56d3555cf5f7 test-data/populations/populations.snps.genepop
--- a/test-data/populations/populations.snps.genepop	Wed Feb 27 09:52:16 2019 -0500
+++ b/test-data/populations/populations.snps.genepop	Thu Jun 20 08:13:18 2019 -0400
@@ -1,4 +1,4 @@
-# Stacks v2.3b; GenePop v4.1.3; February 25, 2019
+# Stacks v2.4; GenePop v4.1.3; June 17, 2019
 1_33,1_88,2_144,2_156,3_162,3_181
 pop
 PopA_01,	0102	0102	0204	0304	0303	0303
diff -r c23695f62bdd -r 56d3555cf5f7 test-data/populations/populations.snps.vcf
--- a/test-data/populations/populations.snps.vcf	Wed Feb 27 09:52:16 2019 -0500
+++ b/test-data/populations/populations.snps.vcf	Thu Jun 20 08:13:18 2019 -0400
@@ -1,6 +1,6 @@
 ##fileformat=VCFv4.2
-##fileDate=20190225
-##source="Stacks v2.3b"
+##fileDate=20190617
+##source="Stacks v2.4"
 ##INFO=<ID=AD,Number=R,Type=Integer,Description="Total Depth for Each Allele">
 ##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency">
 ##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
diff -r c23695f62bdd -r 56d3555cf5f7 test-data/populations/populations.structure
--- a/test-data/populations/populations.structure	Wed Feb 27 09:52:16 2019 -0500
+++ b/test-data/populations/populations.structure	Thu Jun 20 08:13:18 2019 -0400
@@ -1,4 +1,4 @@
-# Stacks v2.3b;  Structure v2.3; February 25, 2019
+# Stacks v2.4;  Structure v2.3; June 17, 2019
 		1_33	1_88	2_144	2_156	3_162	3_181
 PopA_01	1	1	1	2	3	3	3
 PopA_01	1	2	2	4	4	3	3
diff -r c23695f62bdd -r 56d3555cf5f7 test-data/populations/populations.sumstats.tsv
--- a/test-data/populations/populations.sumstats.tsv	Wed Feb 27 09:52:16 2019 -0500
+++ b/test-data/populations/populations.sumstats.tsv	Thu Jun 20 08:13:18 2019 -0400
@@ -1,8 +1,8 @@
 # 1	PopA_01,PopA_02
 # Locus ID	Chr	BP	Col	Pop ID	P Nuc	Q Nuc	N	P	Obs Het	Obs Hom	Exp Het	Exp Hom	Pi	Smoothed Pi	Smoothed Pi P-value	Fis	Smoothed Fis	Smoothed Fis P-value	HWE P-value	Private
-1	un	35	33	1	A	C	2	0.50000000	1.00000	0.00000	0.50000	0.50000	0.66667	0.00000	0.00000	-0.50000	0.00000	0.00000	0.00000	0
-1	un	90	88	1	A	C	2	0.50000000	1.00000	0.00000	0.50000	0.50000	0.66667	0.00000	0.00000	-0.50000	0.00000	0.00000	0.00000	0
-2	un	350	144	1	C	T	2	0.50000000	1.00000	0.00000	0.50000	0.50000	0.66667	0.00000	0.00000	-0.50000	0.00000	0.00000	0.00000	0
-2	un	362	156	1	G	T	2	0.50000000	1.00000	0.00000	0.50000	0.50000	0.66667	0.00000	0.00000	-0.50000	0.00000	0.00000	0.00000	0
-3	un	572	162	1	G	A	2	0.75000000	0.50000	0.50000	0.37500	0.62500	0.50000	0.00000	0.00000	0.00000	0.00000	0.00000	0.00000	0
-3	un	591	181	1	G	A	2	0.75000000	0.50000	0.50000	0.37500	0.62500	0.50000	0.00000	0.00000	0.00000	0.00000	0.00000	0.00000	0
+1	un	34	33	1	A	C	2	0.50000000	1.00000	0.00000	0.50000	0.50000	0.66667	0.00000	0.00000	-0.50000	0.00000	0.00000	0.00000	0
+1	un	89	88	1	A	C	2	0.50000000	1.00000	0.00000	0.50000	0.50000	0.66667	0.00000	0.00000	-0.50000	0.00000	0.00000	0.00000	0
+2	un	367	162	1	G	A	2	0.75000000	0.50000	0.50000	0.37500	0.62500	0.50000	0.00000	0.00000	0.00000	0.00000	0.00000	0.00000	0
+2	un	386	181	1	G	A	2	0.75000000	0.50000	0.50000	0.37500	0.62500	0.50000	0.00000	0.00000	0.00000	0.00000	0.00000	0.00000	0
+3	un	554	144	1	C	T	2	0.50000000	1.00000	0.00000	0.50000	0.50000	0.66667	0.00000	0.00000	-0.50000	0.00000	0.00000	0.00000	0
+3	un	566	156	1	G	T	2	0.50000000	1.00000	0.00000	0.50000	0.50000	0.66667	0.00000	0.00000	-0.50000	0.00000	0.00000	0.00000	0
diff -r c23695f62bdd -r 56d3555cf5f7 test-data/populations/populations.treemix
--- a/test-data/populations/populations.treemix	Wed Feb 27 09:52:16 2019 -0500
+++ b/test-data/populations/populations.treemix	Thu Jun 20 08:13:18 2019 -0400
@@ -1,3 +1,4 @@
+# Stacks v2.4;  TreeMix v1.1; June 17, 2019
 1
 2,2
 2,2
diff -r c23695f62bdd -r 56d3555cf5f7 test-data/populations/populations.var.phylip
--- a/test-data/populations/populations.var.phylip	Wed Feb 27 09:52:16 2019 -0500
+++ b/test-data/populations/populations.var.phylip	Thu Jun 20 08:13:18 2019 -0400
@@ -1,3 +1,3 @@
 1	6
 1	MMYKRR
-# Stacks v2.3b;  Phylip sequential; February 25, 2019
+# Stacks v2.4;  Phylip sequential; June 17, 2019
diff -r c23695f62bdd -r 56d3555cf5f7 test-data/populations/populations.var.phylip.log
--- a/test-data/populations/populations.var.phylip.log	Wed Feb 27 09:52:16 2019 -0500
+++ b/test-data/populations/populations.var.phylip.log	Thu Jun 20 08:13:18 2019 -0400
@@ -1,4 +1,4 @@
-# Stacks v2.3b;  Phylip sequential; February 25, 2019
+# Stacks v2.4;  Phylip sequential; June 17, 2019
 # Seq Pos	Locus ID	Column	Population
 0	1	33	1:M,
 1	1	88	1:M,
diff -r c23695f62bdd -r 56d3555cf5f7 test-data/refmap/catalog.calls.vcf
--- a/test-data/refmap/catalog.calls.vcf	Wed Feb 27 09:52:16 2019 -0500
+++ b/test-data/refmap/catalog.calls.vcf	Thu Jun 20 08:13:18 2019 -0400
@@ -1,6 +1,6 @@
 ##fileformat=VCFv4.2
-##fileDate=20190225
-##source="Stacks v2.3b"
+##fileDate=20190617
+##source="Stacks v2.4"
 ##INFO=<ID=AD,Number=R,Type=Integer,Description="Total Depth for Each Allele">
 ##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency">
 ##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
diff -r c23695f62bdd -r 56d3555cf5f7 test-data/refmap/populations.haplotypes.tsv
--- a/test-data/refmap/populations.haplotypes.tsv	Wed Feb 27 09:52:16 2019 -0500
+++ b/test-data/refmap/populations.haplotypes.tsv	Thu Jun 20 08:13:18 2019 -0400
@@ -1,14 +1,14 @@
 # Catalog Locus ID	Cnt	PopA_01	PopA_02
-1	0	consensus	consensus
-2	0	consensus	consensus
-3	0	consensus	consensus
-4	0	consensus	consensus
-5	0	consensus	consensus
-6	0	consensus	consensus
-7	0	consensus	consensus
-8	0	consensus	consensus
-9	0	consensus	consensus
-10	0	AC/CA	AC/CA
-11	0	consensus	consensus
-12	0	AC/CA	AC/CA
-13	0	AC/CA	AC/CA
+1	2	consensus	consensus
+2	2	consensus	consensus
+3	2	consensus	consensus
+4	2	consensus	consensus
+5	2	consensus	consensus
+6	2	consensus	consensus
+7	2	consensus	consensus
+8	2	consensus	consensus
+9	2	consensus	consensus
+10	2	AC/CA	AC/CA
+11	2	consensus	consensus
+12	2	AC/CA	AC/CA
+13	2	AC/CA	AC/CA
diff -r c23695f62bdd -r 56d3555cf5f7 test-data/refmap/populations.hapstats.tsv
--- a/test-data/refmap/populations.hapstats.tsv	Wed Feb 27 09:52:16 2019 -0500
+++ b/test-data/refmap/populations.hapstats.tsv	Thu Jun 20 08:13:18 2019 -0400
@@ -1,5 +1,5 @@
 # 1	PopA_01,PopA_02
 # Locus ID	Chr	BP	Pop ID	N	Haplotype Cnt	Gene Diversity	Smoothed Gene Diversity	Smoothed Gene Diversity P-value	Haplotype Diversity	Smoothed Haplotype Diversity	Smoothed Haplotype Diversity P-value	HWE P-value	HWE P-value SE	Haplotypes
-10	Contig_3091	-92	1	4	2	0.66667	0.00000	0.00000	1.33333	0.00000	0.00000	0.00000	0.00000	AC:2;CA:2
-12	Contig_3358	-92	1	4	2	0.66667	0.00000	0.00000	1.33333	0.00000	0.00000	0.00000	0.00000	AC:2;CA:2
-13	Contig_3569	-92	1	4	2	0.66667	0.00000	0.00000	1.33333	0.00000	0.00000	0.00000	0.00000	AC:2;CA:2
+10	Contig_3091	1	1	4	2	0.66667	0.00000	0.00000	1.33333	0.00000	0.00000	0.00000	0.00000	AC:2;CA:2
+12	Contig_3358	1	1	4	2	0.66667	0.00000	0.00000	1.33333	0.00000	0.00000	0.00000	0.00000	AC:2;CA:2
+13	Contig_3569	1	1	4	2	0.66667	0.00000	0.00000	1.33333	0.00000	0.00000	0.00000	0.00000	AC:2;CA:2
diff -r c23695f62bdd -r 56d3555cf5f7 test-data/refmap/populations.log.distribs
--- a/test-data/refmap/populations.log.distribs	Wed Feb 27 09:52:16 2019 -0500
+++ b/test-data/refmap/populations.log.distribs	Thu Jun 20 08:13:18 2019 -0400
@@ -21,14 +21,13 @@
 BEGIN samples_per_loc_prefilters
 # Distribution of valid samples matched to a catalog locus prior to filtering.
 n_samples	n_loci
-0	13
+2	13
 END samples_per_loc_prefilters
 
 BEGIN missing_samples_per_loc_prefilters
-
 # Distribution of missing samples for each catalog locus prior to filtering.
 # Absent samples at locus	Count
-2	13
+0	13
 END missing_samples_per_loc_prefilters
 
 BEGIN snps_per_loc_prefilters
@@ -41,14 +40,13 @@
 BEGIN samples_per_loc_postfilters
 # Distribution of valid samples matched to a catalog locus after filtering.
 n_samples	n_loci
-0	13
+2	13
 END samples_per_loc_postfilters
 
 BEGIN missing_samples_per_loc_postfilters
-
 # Distribution of missing samples for each catalog locus after filtering.
 # Absent samples at locus	Count
-2	13
+0	13
 END missing_samples_per_loc_postfilters
 
 BEGIN snps_per_loc_postfilters
diff -r c23695f62bdd -r 56d3555cf5f7 test-data/sstacks/PopA_01.matches.tsv
--- a/test-data/sstacks/PopA_01.matches.tsv	Wed Feb 27 09:52:16 2019 -0500
+++ b/test-data/sstacks/PopA_01.matches.tsv	Thu Jun 20 08:13:18 2019 -0400
@@ -1,5 +1,5 @@
-# sstacks version 2.3b; generated on 2019-02-21 19:57:38
+# sstacks version 2.4; generated on 2019-06-18 10:34:45
 1	1	1	AC	9	94M
 1	1	1	CA	9	94M
-2	1	2	consensus	20	94M
-3	1	3	consensus	28	94M
+2	1	2	consensus	28	94M
+3	1	3	consensus	20	94M
diff -r c23695f62bdd -r 56d3555cf5f7 test-data/sstacks/PopA_02.matches.tsv
--- a/test-data/sstacks/PopA_02.matches.tsv	Wed Feb 27 09:52:16 2019 -0500
+++ b/test-data/sstacks/PopA_02.matches.tsv	Thu Jun 20 08:13:18 2019 -0400
@@ -1,5 +1,5 @@
-# sstacks version 2.3b; generated on 2019-02-21 19:57:38
+# sstacks version 2.4; generated on 2019-06-18 10:34:45
 1	2	1	AC	6	94M
 1	2	1	CA	6	94M
-3	2	2	consensus	28	94M
-2	2	3	consensus	20	94M
+2	2	2	consensus	28	94M
+3	2	3	consensus	20	94M
diff -r c23695f62bdd -r 56d3555cf5f7 test-data/stacks_outputs/catalog.calls
Binary file test-data/stacks_outputs/catalog.calls has changed
diff -r c23695f62bdd -r 56d3555cf5f7 test-data/stacks_outputs/tsv2bam.log
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/stacks_outputs/tsv2bam.log	Thu Jun 20 08:13:18 2019 -0400
@@ -0,0 +1,17 @@
+tsv2bam v2.4, executed 2019-06-18 10:34:45 (zlib-1.2.11)
+tsv2bam -P stacks_outputs -M denovo_map/popmap_cstacks.tsv -R demultiplexed/
+Configuration for this run:
+  Stacks directory: 'stacks_outputs/'
+  Population map: 'denovo_map/popmap_cstacks.tsv'
+  Num. samples: 2
+  Paired-end reads directory: 'demultiplexed/'
+
+Paired-end reads files found, e.g. 'demultiplexed/PopA_01.2.fq'.
+Loading the catalog...
+Processing sample 'PopA_01'...
+Processing sample 'PopA_02'...
+
+Sample 'PopA_01': matched 3 sample loci to 3 catalog loci; found a paired-end read for 66 (100.0%) of the assembled forward reads; wrote 132 records.
+Sample 'PopA_02': matched 3 sample loci to 3 catalog loci; found a paired-end read for 60 (100.0%) of the assembled forward reads; wrote 120 records.
+
+tsv2bam is done.
diff -r c23695f62bdd -r 56d3555cf5f7 test-data/tsv2bam/PopA_01.bam
Binary file test-data/tsv2bam/PopA_01.bam has changed
diff -r c23695f62bdd -r 56d3555cf5f7 test-data/tsv2bam/PopA_01.matches.bam
Binary file test-data/tsv2bam/PopA_01.matches.bam has changed
diff -r c23695f62bdd -r 56d3555cf5f7 test-data/tsv2bam/PopA_02.bam
Binary file test-data/tsv2bam/PopA_02.bam has changed
diff -r c23695f62bdd -r 56d3555cf5f7 test-data/tsv2bam/PopA_02.matches.bam
Binary file test-data/tsv2bam/PopA_02.matches.bam has changed
diff -r c23695f62bdd -r 56d3555cf5f7 test-data/tsv2bam/tsv2bam.log
--- a/test-data/tsv2bam/tsv2bam.log	Wed Feb 27 09:52:16 2019 -0500
+++ b/test-data/tsv2bam/tsv2bam.log	Thu Jun 20 08:13:18 2019 -0400
@@ -1,14 +1,17 @@
-tsv2bam v2.2, executed 2018-11-27 13:20:44
-tsv2bam -P stacks_inputs -s PopA_01 -s PopA_02 -t 1
+tsv2bam v2.4, executed 2019-06-17 21:22:16 (zlib-1.2.11)
+tsv2bam -P stacks_outputs -M denovo_map/popmap_cstacks.tsv -R demultiplexed/
 Configuration for this run:
-  Stacks directory: 'stacks_inputs/'
+  Stacks directory: 'stacks_outputs/'
+  Population map: 'denovo_map/popmap_cstacks.tsv'
   Num. samples: 2
+  Paired-end reads directory: 'demultiplexed/'
 
+Paired-end reads files found, e.g. 'demultiplexed/PopA_01.2.fq'.
 Loading the catalog...
 Processing sample 'PopA_01'...
 Processing sample 'PopA_02'...
 
-Sample 'PopA_01': matched 3 sample loci to 3 catalog loci; wrote 66 records.
-Sample 'PopA_02': matched 3 sample loci to 3 catalog loci; wrote 60 records.
+Sample 'PopA_01': matched 3 sample loci to 3 catalog loci; found a paired-end read for 66 (100.0%) of the assembled forward reads; wrote 132 records.
+Sample 'PopA_02': matched 3 sample loci to 3 catalog loci; found a paired-end read for 60 (100.0%) of the assembled forward reads; wrote 120 records.
 
 tsv2bam is done.
diff -r c23695f62bdd -r 56d3555cf5f7 test-data/ustacks/PopA_01.alleles.tsv
--- a/test-data/ustacks/PopA_01.alleles.tsv	Wed Feb 27 09:52:16 2019 -0500
+++ b/test-data/ustacks/PopA_01.alleles.tsv	Thu Jun 20 08:13:18 2019 -0400
@@ -1,3 +1,3 @@
-# ustacks version 2.3b; generated on 2019-02-21 19:57:38
+# ustacks version 2.4; generated on 2019-06-18 10:34:45
 1	1	AC	50.00	9
 1	1	CA	50.00	9
diff -r c23695f62bdd -r 56d3555cf5f7 test-data/ustacks/PopA_01.snps.tsv
--- a/test-data/ustacks/PopA_01.snps.tsv	Wed Feb 27 09:52:16 2019 -0500
+++ b/test-data/ustacks/PopA_01.snps.tsv	Thu Jun 20 08:13:18 2019 -0400
@@ -1,4 +1,4 @@
-# ustacks version 2.3b; generated on 2019-02-21 19:57:38
+# ustacks version 2.4; generated on 2019-06-18 10:34:45
 1	1	0	O	24.95	A	-		
 1	1	1	O	24.95	A	-		
 1	1	2	O	24.95	T	-		
@@ -93,191 +93,191 @@
 1	1	91	O	24.95	G	-		
 1	1	92	O	24.95	A	-		
 1	1	93	O	24.95	C	-		
-1	2	0	O	27.73	A	-		
-1	2	1	O	27.73	A	-		
-1	2	2	O	27.73	T	-		
-1	2	3	O	27.73	T	-		
-1	2	4	O	27.73	C	-		
-1	2	5	O	27.73	T	-		
-1	2	6	O	27.73	C	-		
-1	2	7	O	27.73	T	-		
-1	2	8	O	27.73	A	-		
-1	2	9	O	27.73	C	-		
-1	2	10	O	27.73	A	-		
-1	2	11	O	27.73	C	-		
-1	2	12	O	27.73	C	-		
-1	2	13	O	27.73	A	-		
-1	2	14	O	27.73	C	-		
-1	2	15	O	27.73	A	-		
-1	2	16	O	27.73	G	-		
-1	2	17	O	27.73	C	-		
-1	2	18	O	27.73	A	-		
-1	2	19	O	27.73	T	-		
-1	2	20	O	27.73	C	-		
-1	2	21	O	27.73	A	-		
-1	2	22	O	27.73	A	-		
-1	2	23	O	27.73	T	-		
-1	2	24	O	27.73	T	-		
-1	2	25	O	27.73	C	-		
-1	2	26	O	27.73	T	-		
-1	2	27	O	27.73	A	-		
-1	2	28	O	27.73	A	-		
-1	2	29	O	27.73	A	-		
-1	2	30	O	27.73	A	-		
-1	2	31	O	27.73	A	-		
-1	2	32	O	27.73	T	-		
-1	2	33	O	27.73	G	-		
-1	2	34	O	27.73	A	-		
-1	2	35	O	27.73	C	-		
-1	2	36	O	27.73	T	-		
-1	2	37	O	27.73	A	-		
-1	2	38	O	27.73	C	-		
-1	2	39	O	27.73	C	-		
-1	2	40	O	27.73	A	-		
-1	2	41	O	27.73	G	-		
-1	2	42	O	27.73	A	-		
-1	2	43	O	27.73	G	-		
-1	2	44	O	27.73	A	-		
-1	2	45	O	27.73	G	-		
-1	2	46	O	27.73	A	-		
-1	2	47	O	27.73	C	-		
-1	2	48	O	27.73	A	-		
-1	2	49	O	27.73	A	-		
-1	2	50	O	27.73	C	-		
-1	2	51	O	27.73	T	-		
-1	2	52	O	27.73	C	-		
-1	2	53	O	27.73	C	-		
-1	2	54	O	27.73	G	-		
-1	2	55	O	27.73	C	-		
-1	2	56	O	27.73	A	-		
-1	2	57	O	27.73	G	-		
-1	2	58	O	27.73	T	-		
-1	2	59	O	17.59	T	-		
-1	2	60	O	27.73	A	-		
-1	2	61	O	27.73	A	-		
-1	2	62	O	27.73	A	-		
-1	2	63	O	27.73	C	-		
-1	2	64	O	27.73	A	-		
-1	2	65	O	27.73	C	-		
-1	2	66	O	27.73	T	-		
-1	2	67	O	27.73	C	-		
-1	2	68	O	27.73	T	-		
-1	2	69	O	27.73	G	-		
-1	2	70	O	27.73	A	-		
-1	2	71	O	27.73	C	-		
-1	2	72	O	27.73	T	-		
-1	2	73	O	27.73	G	-		
-1	2	74	O	27.73	C	-		
-1	2	75	O	27.73	C	-		
-1	2	76	O	27.73	A	-		
-1	2	77	O	27.73	C	-		
-1	2	78	O	27.73	G	-		
-1	2	79	O	27.73	C	-		
-1	2	80	O	27.73	C	-		
-1	2	81	O	27.73	A	-		
-1	2	82	O	27.73	G	-		
-1	2	83	O	27.73	C	-		
-1	2	84	O	27.73	T	-		
-1	2	85	O	27.73	A	-		
-1	2	86	O	27.73	C	-		
-1	2	87	O	27.73	C	-		
-1	2	88	O	27.73	T	-		
-1	2	89	O	27.73	C	-		
-1	2	90	O	17.59	T	-		
-1	2	91	O	27.73	A	-		
-1	2	92	O	27.73	G	-		
-1	2	93	O	27.73	A	-		
-1	3	0	O	38.82	A	-		
-1	3	1	O	38.82	A	-		
-1	3	2	O	38.82	T	-		
-1	3	3	O	38.82	T	-		
-1	3	4	O	38.82	C	-		
-1	3	5	O	38.82	G	-		
-1	3	6	O	38.82	G	-		
-1	3	7	O	38.82	C	-		
-1	3	8	O	38.82	T	-		
-1	3	9	O	38.82	T	-		
-1	3	10	O	38.82	G	-		
-1	3	11	O	38.82	C	-		
-1	3	12	O	38.82	A	-		
-1	3	13	O	38.82	A	-		
-1	3	14	O	38.82	C	-		
-1	3	15	O	38.82	G	-		
-1	3	16	O	38.82	C	-		
-1	3	17	O	38.82	A	-		
-1	3	18	O	38.82	A	-		
-1	3	19	O	38.82	G	-		
-1	3	20	O	38.82	T	-		
-1	3	21	O	38.82	G	-		
-1	3	22	O	38.82	A	-		
-1	3	23	O	38.82	C	-		
-1	3	24	O	38.82	G	-		
-1	3	25	O	38.82	A	-		
-1	3	26	O	38.82	T	-		
-1	3	27	O	38.82	T	-		
-1	3	28	O	38.82	C	-		
-1	3	29	O	38.82	C	-		
-1	3	30	O	38.82	C	-		
-1	3	31	O	38.82	A	-		
-1	3	32	O	38.82	C	-		
-1	3	33	O	38.82	G	-		
-1	3	34	O	38.82	G	-		
-1	3	35	O	38.82	A	-		
-1	3	36	O	38.82	C	-		
-1	3	37	O	38.82	A	-		
-1	3	38	O	38.82	T	-		
-1	3	39	O	38.82	A	-		
-1	3	40	O	38.82	A	-		
-1	3	41	O	38.82	C	-		
-1	3	42	O	38.82	T	-		
-1	3	43	O	38.82	G	-		
-1	3	44	O	38.82	A	-		
-1	3	45	O	38.82	T	-		
-1	3	46	O	38.82	C	-		
-1	3	47	O	38.82	T	-		
-1	3	48	O	38.82	A	-		
-1	3	49	O	38.82	A	-		
-1	3	50	O	38.82	G	-		
-1	3	51	O	38.82	T	-		
-1	3	52	O	38.82	A	-		
-1	3	53	O	38.82	A	-		
-1	3	54	O	38.82	C	-		
-1	3	55	O	38.82	T	-		
-1	3	56	O	38.82	T	-		
-1	3	57	O	38.82	C	-		
-1	3	58	O	38.82	C	-		
-1	3	59	O	38.82	A	-		
-1	3	60	O	38.82	A	-		
-1	3	61	O	27.99	A	-		
-1	3	62	O	38.82	T	-		
-1	3	63	O	38.82	C	-		
-1	3	64	O	38.82	T	-		
-1	3	65	O	38.82	G	-		
-1	3	66	O	38.82	G	-		
-1	3	67	O	38.82	G	-		
-1	3	68	O	38.82	A	-		
-1	3	69	O	38.82	A	-		
-1	3	70	O	38.82	T	-		
-1	3	71	O	38.82	G	-		
-1	3	72	O	38.82	G	-		
-1	3	73	O	38.82	G	-		
-1	3	74	O	38.82	A	-		
-1	3	75	O	38.82	T	-		
-1	3	76	O	38.82	T	-		
-1	3	77	O	38.82	T	-		
-1	3	78	O	38.82	C	-		
-1	3	79	O	38.82	A	-		
-1	3	80	O	38.82	T	-		
-1	3	81	O	38.82	A	-		
-1	3	82	O	38.82	A	-		
-1	3	83	O	38.82	T	-		
-1	3	84	O	38.82	T	-		
-1	3	85	O	38.82	A	-		
-1	3	86	O	38.82	A	-		
-1	3	87	O	38.82	G	-		
-1	3	88	O	38.82	G	-		
-1	3	89	O	38.82	A	-		
-1	3	90	O	38.82	C	-		
-1	3	91	O	38.82	T	-		
-1	3	92	O	38.82	A	-		
-1	3	93	O	38.82	T	-		
+1	2	0	O	38.82	A	-		
+1	2	1	O	38.82	A	-		
+1	2	2	O	38.82	T	-		
+1	2	3	O	38.82	T	-		
+1	2	4	O	38.82	C	-		
+1	2	5	O	38.82	G	-		
+1	2	6	O	38.82	G	-		
+1	2	7	O	38.82	C	-		
+1	2	8	O	38.82	T	-		
+1	2	9	O	38.82	T	-		
+1	2	10	O	38.82	G	-		
+1	2	11	O	38.82	C	-		
+1	2	12	O	38.82	A	-		
+1	2	13	O	38.82	A	-		
+1	2	14	O	38.82	C	-		
+1	2	15	O	38.82	G	-		
+1	2	16	O	38.82	C	-		
+1	2	17	O	38.82	A	-		
+1	2	18	O	38.82	A	-		
+1	2	19	O	38.82	G	-		
+1	2	20	O	38.82	T	-		
+1	2	21	O	38.82	G	-		
+1	2	22	O	38.82	A	-		
+1	2	23	O	38.82	C	-		
+1	2	24	O	38.82	G	-		
+1	2	25	O	38.82	A	-		
+1	2	26	O	38.82	T	-		
+1	2	27	O	38.82	T	-		
+1	2	28	O	38.82	C	-		
+1	2	29	O	38.82	C	-		
+1	2	30	O	38.82	C	-		
+1	2	31	O	38.82	A	-		
+1	2	32	O	38.82	C	-		
+1	2	33	O	38.82	G	-		
+1	2	34	O	38.82	G	-		
+1	2	35	O	38.82	A	-		
+1	2	36	O	38.82	C	-		
+1	2	37	O	38.82	A	-		
+1	2	38	O	38.82	T	-		
+1	2	39	O	38.82	A	-		
+1	2	40	O	38.82	A	-		
+1	2	41	O	38.82	C	-		
+1	2	42	O	38.82	T	-		
+1	2	43	O	38.82	G	-		
+1	2	44	O	38.82	A	-		
+1	2	45	O	38.82	T	-		
+1	2	46	O	38.82	C	-		
+1	2	47	O	38.82	T	-		
+1	2	48	O	38.82	A	-		
+1	2	49	O	38.82	A	-		
+1	2	50	O	38.82	G	-		
+1	2	51	O	38.82	T	-		
+1	2	52	O	38.82	A	-		
+1	2	53	O	38.82	A	-		
+1	2	54	O	38.82	C	-		
+1	2	55	O	38.82	T	-		
+1	2	56	O	38.82	T	-		
+1	2	57	O	38.82	C	-		
+1	2	58	O	38.82	C	-		
+1	2	59	O	38.82	A	-		
+1	2	60	O	38.82	A	-		
+1	2	61	O	27.99	A	-		
+1	2	62	O	38.82	T	-		
+1	2	63	O	38.82	C	-		
+1	2	64	O	38.82	T	-		
+1	2	65	O	38.82	G	-		
+1	2	66	O	38.82	G	-		
+1	2	67	O	38.82	G	-		
+1	2	68	O	38.82	A	-		
+1	2	69	O	38.82	A	-		
+1	2	70	O	38.82	T	-		
+1	2	71	O	38.82	G	-		
+1	2	72	O	38.82	G	-		
+1	2	73	O	38.82	G	-		
+1	2	74	O	38.82	A	-		
+1	2	75	O	38.82	T	-		
+1	2	76	O	38.82	T	-		
+1	2	77	O	38.82	T	-		
+1	2	78	O	38.82	C	-		
+1	2	79	O	38.82	A	-		
+1	2	80	O	38.82	T	-		
+1	2	81	O	38.82	A	-		
+1	2	82	O	38.82	A	-		
+1	2	83	O	38.82	T	-		
+1	2	84	O	38.82	T	-		
+1	2	85	O	38.82	A	-		
+1	2	86	O	38.82	A	-		
+1	2	87	O	38.82	G	-		
+1	2	88	O	38.82	G	-		
+1	2	89	O	38.82	A	-		
+1	2	90	O	38.82	C	-		
+1	2	91	O	38.82	T	-		
+1	2	92	O	38.82	A	-		
+1	2	93	O	38.82	T	-		
+1	3	0	O	27.73	A	-		
+1	3	1	O	27.73	A	-		
+1	3	2	O	27.73	T	-		
+1	3	3	O	27.73	T	-		
+1	3	4	O	27.73	C	-		
+1	3	5	O	27.73	T	-		
+1	3	6	O	27.73	C	-		
+1	3	7	O	27.73	T	-		
+1	3	8	O	27.73	A	-		
+1	3	9	O	27.73	C	-		
+1	3	10	O	27.73	A	-		
+1	3	11	O	27.73	C	-		
+1	3	12	O	27.73	C	-		
+1	3	13	O	27.73	A	-		
+1	3	14	O	27.73	C	-		
+1	3	15	O	27.73	A	-		
+1	3	16	O	27.73	G	-		
+1	3	17	O	27.73	C	-		
+1	3	18	O	27.73	A	-		
+1	3	19	O	27.73	T	-		
+1	3	20	O	27.73	C	-		
+1	3	21	O	27.73	A	-		
+1	3	22	O	27.73	A	-		
+1	3	23	O	27.73	T	-		
+1	3	24	O	27.73	T	-		
+1	3	25	O	27.73	C	-		
+1	3	26	O	27.73	T	-		
+1	3	27	O	27.73	A	-		
+1	3	28	O	27.73	A	-		
+1	3	29	O	27.73	A	-		
+1	3	30	O	27.73	A	-		
+1	3	31	O	27.73	A	-		
+1	3	32	O	27.73	T	-		
+1	3	33	O	27.73	G	-		
+1	3	34	O	27.73	A	-		
+1	3	35	O	27.73	C	-		
+1	3	36	O	27.73	T	-		
+1	3	37	O	27.73	A	-		
+1	3	38	O	27.73	C	-		
+1	3	39	O	27.73	C	-		
+1	3	40	O	27.73	A	-		
+1	3	41	O	27.73	G	-		
+1	3	42	O	27.73	A	-		
+1	3	43	O	27.73	G	-		
+1	3	44	O	27.73	A	-		
+1	3	45	O	27.73	G	-		
+1	3	46	O	27.73	A	-		
+1	3	47	O	27.73	C	-		
+1	3	48	O	27.73	A	-		
+1	3	49	O	27.73	A	-		
+1	3	50	O	27.73	C	-		
+1	3	51	O	27.73	T	-		
+1	3	52	O	27.73	C	-		
+1	3	53	O	27.73	C	-		
+1	3	54	O	27.73	G	-		
+1	3	55	O	27.73	C	-		
+1	3	56	O	27.73	A	-		
+1	3	57	O	27.73	G	-		
+1	3	58	O	27.73	T	-		
+1	3	59	O	17.59	T	-		
+1	3	60	O	27.73	A	-		
+1	3	61	O	27.73	A	-		
+1	3	62	O	27.73	A	-		
+1	3	63	O	27.73	C	-		
+1	3	64	O	27.73	A	-		
+1	3	65	O	27.73	C	-		
+1	3	66	O	27.73	T	-		
+1	3	67	O	27.73	C	-		
+1	3	68	O	27.73	T	-		
+1	3	69	O	27.73	G	-		
+1	3	70	O	27.73	A	-		
+1	3	71	O	27.73	C	-		
+1	3	72	O	27.73	T	-		
+1	3	73	O	27.73	G	-		
+1	3	74	O	27.73	C	-		
+1	3	75	O	27.73	C	-		
+1	3	76	O	27.73	A	-		
+1	3	77	O	27.73	C	-		
+1	3	78	O	27.73	G	-		
+1	3	79	O	27.73	C	-		
+1	3	80	O	27.73	C	-		
+1	3	81	O	27.73	A	-		
+1	3	82	O	27.73	G	-		
+1	3	83	O	27.73	C	-		
+1	3	84	O	27.73	T	-		
+1	3	85	O	27.73	A	-		
+1	3	86	O	27.73	C	-		
+1	3	87	O	27.73	C	-		
+1	3	88	O	27.73	T	-		
+1	3	89	O	27.73	C	-		
+1	3	90	O	17.59	T	-		
+1	3	91	O	27.73	A	-		
+1	3	92	O	27.73	G	-		
+1	3	93	O	27.73	A	-		
diff -r c23695f62bdd -r 56d3555cf5f7 test-data/ustacks/PopA_01.tags.tsv
--- a/test-data/ustacks/PopA_01.tags.tsv	Wed Feb 27 09:52:16 2019 -0500
+++ b/test-data/ustacks/PopA_01.tags.tsv	Thu Jun 20 08:13:18 2019 -0400
@@ -1,73 +1,73 @@
-# ustacks version 2.3b; generated on 2019-02-21 19:57:38
+# ustacks version 2.4; generated on 2019-06-18 10:34:45
 1	1	consensus			AATTCGTTTGCTGCTTCAGGAATCTCTCGTATAATCTGAGTATGTGCGTACGTACGCTATTTAGATGGATAACCGACGCTGCCAGACGAGAGAC	0	0	0
 1	1	model			OOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOEOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOEOOOOO			
-1	1	primary	0	lane1_fakedata7_9 1:N:0:/1	AATTCGTTTGCTGCTTCAGGAATCTCTCGTATAATCTGAGTATGTGCGTACGTACGCTATTTAGATGGATAACCGACGCTGCCAGACGCGAGAC			
-1	1	primary	0	lane1_fakedata7_10 1:N:0:/1	AATTCGTTTGCTGCTTCAGGAATCTCTCGTATAATCTGAGTATGTGCGTACGTACGCTATTTAGATGGATAACCGACGCTGCCAGACGCGAGAC			
-1	1	primary	0	lane1_fakedata7_11 1:N:0:/1	AATTCGTTTGCTGCTTCAGGAATCTCTCGTATAATCTGAGTATGTGCGTACGTACGCTATTTAGATGGATAACCGACGCTGCCAGACGCGAGAC			
-1	1	primary	0	lane1_fakedata7_12 1:N:0:/1	AATTCGTTTGCTGCTTCAGGAATCTCTCGTATAATCTGAGTATGTGCGTACGTACGCTATTTAGATGGATAACCGACGCTGCCAGACGCGAGAC			
-1	1	primary	0	lane1_fakedata7_13 1:N:0:/1	AATTCGTTTGCTGCTTCAGGAATCTCTCGTATAATCTGAGTATGTGCGTACGTACGCTATTTAGATGGATAACCGACGCTGCCAGACGCGAGAC			
-1	1	primary	0	lane1_fakedata7_14 1:N:0:/1	AATTCGTTTGCTGCTTCAGGAATCTCTCGTATAATCTGAGTATGTGCGTACGTACGCTATTTAGATGGATAACCGACGCTGCCAGACGCGAGAC			
-1	1	primary	0	lane1_fakedata7_15 1:N:0:/1	AATTCGTTTGCTGCTTCAGGAATCTCTCGTATAATCTGAGTATGTGCGTACGTACGCTATTTAGATGGATAACCGACGCTGCCAGACGCGAGAC			
-1	1	primary	0	lane1_fakedata7_16 1:N:0:/1	AATTCGTTTGCTGCTTCAGGAATCTCTCGTATAATCTGAGTATGTGCGTACGTACGCTATTTAGATGGATAACCGACGCTGCCAGACGCGAGAC			
-1	1	primary	0	lane1_fakedata7_17 1:N:0:/1	AATTCGTTTGCTGCTTCAGGAATCTCTCGTATAATCTGAGTATGTGCGTACGTACGCTATTTAGATGGATAACCGACGCTGCCAGACGCGAGAC			
-1	1	primary	1	lane1_fakedata7_0 1:N:0:/1	AATTCGTTTGCTGCTTCAGGAATCTCTCGTATACTCTGAGTATGTGCGTACGTACGCTATTTAGATGGATAACCGACGCTGCCAGACGAGAGAC			
-1	1	primary	1	lane1_fakedata7_1 1:N:0:/1	AATTCGTTTGCTGCTTCAGGAATCTCTCGTATACTCTGAGTATGTGCGTACGTACGCTATTTAGATGGATAACCGACGCTGCCAGACGAGAGAC			
-1	1	primary	1	lane1_fakedata7_2 1:N:0:/1	AATTCGTTTGCTGCTTCAGGAATCTCTCGTATACTCTGAGTATGTGCGTACGTACGCTATTTAGATGGATAACCGACGCTGCCAGACGAGAGAC			
-1	1	primary	1	lane1_fakedata7_3 1:N:0:/1	AATTCGTTTGCTGCTTCAGGAATCTCTCGTATACTCTGAGTATGTGCGTACGTACGCTATTTAGATGGATAACCGACGCTGCCAGACGAGAGAC			
-1	1	primary	1	lane1_fakedata7_4 1:N:0:/1	AATTCGTTTGCTGCTTCAGGAATCTCTCGTATACTCTGAGTATGTGCGTACGTACGCTATTTAGATGGATAACCGACGCTGCCAGACGAGAGAC			
-1	1	primary	1	lane1_fakedata7_5 1:N:0:/1	AATTCGTTTGCTGCTTCAGGAATCTCTCGTATACTCTGAGTATGTGCGTACGTACGCTATTTAGATGGATAACCGACGCTGCCAGACGAGAGAC			
-1	1	primary	1	lane1_fakedata7_6 1:N:0:/1	AATTCGTTTGCTGCTTCAGGAATCTCTCGTATACTCTGAGTATGTGCGTACGTACGCTATTTAGATGGATAACCGACGCTGCCAGACGAGAGAC			
-1	1	primary	1	lane1_fakedata7_7 1:N:0:/1	AATTCGTTTGCTGCTTCAGGAATCTCTCGTATACTCTGAGTATGTGCGTACGTACGCTATTTAGATGGATAACCGACGCTGCCAGACGAGAGAC			
-1	1	primary	1	lane1_fakedata7_8 1:N:0:/1	AATTCGTTTGCTGCTTCAGGAATCTCTCGTATACTCTGAGTATGTGCGTACGTACGCTATTTAGATGGATAACCGACGCTGCCAGACGAGAGAC			
-1	2	consensus			AATTCTCTACACCACAGCATCAATTCTAAAAATGACTACCAGAGAGACAACTCCGCAGTTAAACACTCTGACTGCCACGCCAGCTACCTCTAGA	0	0	0
+1	1	primary	0	lane1_fakedata7_0 1:N:0:/1	AATTCGTTTGCTGCTTCAGGAATCTCTCGTATACTCTGAGTATGTGCGTACGTACGCTATTTAGATGGATAACCGACGCTGCCAGACGAGAGAC			
+1	1	primary	0	lane1_fakedata7_1 1:N:0:/1	AATTCGTTTGCTGCTTCAGGAATCTCTCGTATACTCTGAGTATGTGCGTACGTACGCTATTTAGATGGATAACCGACGCTGCCAGACGAGAGAC			
+1	1	primary	0	lane1_fakedata7_2 1:N:0:/1	AATTCGTTTGCTGCTTCAGGAATCTCTCGTATACTCTGAGTATGTGCGTACGTACGCTATTTAGATGGATAACCGACGCTGCCAGACGAGAGAC			
+1	1	primary	0	lane1_fakedata7_3 1:N:0:/1	AATTCGTTTGCTGCTTCAGGAATCTCTCGTATACTCTGAGTATGTGCGTACGTACGCTATTTAGATGGATAACCGACGCTGCCAGACGAGAGAC			
+1	1	primary	0	lane1_fakedata7_4 1:N:0:/1	AATTCGTTTGCTGCTTCAGGAATCTCTCGTATACTCTGAGTATGTGCGTACGTACGCTATTTAGATGGATAACCGACGCTGCCAGACGAGAGAC			
+1	1	primary	0	lane1_fakedata7_5 1:N:0:/1	AATTCGTTTGCTGCTTCAGGAATCTCTCGTATACTCTGAGTATGTGCGTACGTACGCTATTTAGATGGATAACCGACGCTGCCAGACGAGAGAC			
+1	1	primary	0	lane1_fakedata7_6 1:N:0:/1	AATTCGTTTGCTGCTTCAGGAATCTCTCGTATACTCTGAGTATGTGCGTACGTACGCTATTTAGATGGATAACCGACGCTGCCAGACGAGAGAC			
+1	1	primary	0	lane1_fakedata7_7 1:N:0:/1	AATTCGTTTGCTGCTTCAGGAATCTCTCGTATACTCTGAGTATGTGCGTACGTACGCTATTTAGATGGATAACCGACGCTGCCAGACGAGAGAC			
+1	1	primary	0	lane1_fakedata7_8 1:N:0:/1	AATTCGTTTGCTGCTTCAGGAATCTCTCGTATACTCTGAGTATGTGCGTACGTACGCTATTTAGATGGATAACCGACGCTGCCAGACGAGAGAC			
+1	1	primary	1	lane1_fakedata7_9 1:N:0:/1	AATTCGTTTGCTGCTTCAGGAATCTCTCGTATAATCTGAGTATGTGCGTACGTACGCTATTTAGATGGATAACCGACGCTGCCAGACGCGAGAC			
+1	1	primary	1	lane1_fakedata7_10 1:N:0:/1	AATTCGTTTGCTGCTTCAGGAATCTCTCGTATAATCTGAGTATGTGCGTACGTACGCTATTTAGATGGATAACCGACGCTGCCAGACGCGAGAC			
+1	1	primary	1	lane1_fakedata7_11 1:N:0:/1	AATTCGTTTGCTGCTTCAGGAATCTCTCGTATAATCTGAGTATGTGCGTACGTACGCTATTTAGATGGATAACCGACGCTGCCAGACGCGAGAC			
+1	1	primary	1	lane1_fakedata7_12 1:N:0:/1	AATTCGTTTGCTGCTTCAGGAATCTCTCGTATAATCTGAGTATGTGCGTACGTACGCTATTTAGATGGATAACCGACGCTGCCAGACGCGAGAC			
+1	1	primary	1	lane1_fakedata7_13 1:N:0:/1	AATTCGTTTGCTGCTTCAGGAATCTCTCGTATAATCTGAGTATGTGCGTACGTACGCTATTTAGATGGATAACCGACGCTGCCAGACGCGAGAC			
+1	1	primary	1	lane1_fakedata7_14 1:N:0:/1	AATTCGTTTGCTGCTTCAGGAATCTCTCGTATAATCTGAGTATGTGCGTACGTACGCTATTTAGATGGATAACCGACGCTGCCAGACGCGAGAC			
+1	1	primary	1	lane1_fakedata7_15 1:N:0:/1	AATTCGTTTGCTGCTTCAGGAATCTCTCGTATAATCTGAGTATGTGCGTACGTACGCTATTTAGATGGATAACCGACGCTGCCAGACGCGAGAC			
+1	1	primary	1	lane1_fakedata7_16 1:N:0:/1	AATTCGTTTGCTGCTTCAGGAATCTCTCGTATAATCTGAGTATGTGCGTACGTACGCTATTTAGATGGATAACCGACGCTGCCAGACGCGAGAC			
+1	1	primary	1	lane1_fakedata7_17 1:N:0:/1	AATTCGTTTGCTGCTTCAGGAATCTCTCGTATAATCTGAGTATGTGCGTACGTACGCTATTTAGATGGATAACCGACGCTGCCAGACGCGAGAC			
+1	2	consensus			AATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT	0	0	0
 1	2	model			OOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOO			
-1	2	primary	0	lane1_fakedata2_0 1:N:0:/1	AATTCTCTACACCACAGCATCAATTCTAAAAATGACTACCAGAGAGACAACTCCGCAGTTAAACACTCTGACTGCCACGCCAGCTACCTCTAGA			
-1	2	primary	0	lane1_fakedata2_1 1:N:0:/1	AATTCTCTACACCACAGCATCAATTCTAAAAATGACTACCAGAGAGACAACTCCGCAGTTAAACACTCTGACTGCCACGCCAGCTACCTCTAGA			
-1	2	primary	0	lane1_fakedata2_2 1:N:0:/1	AATTCTCTACACCACAGCATCAATTCTAAAAATGACTACCAGAGAGACAACTCCGCAGTTAAACACTCTGACTGCCACGCCAGCTACCTCTAGA			
-1	2	primary	0	lane1_fakedata2_3 1:N:0:/1	AATTCTCTACACCACAGCATCAATTCTAAAAATGACTACCAGAGAGACAACTCCGCAGTTAAACACTCTGACTGCCACGCCAGCTACCTCTAGA			
-1	2	primary	0	lane1_fakedata2_4 1:N:0:/1	AATTCTCTACACCACAGCATCAATTCTAAAAATGACTACCAGAGAGACAACTCCGCAGTTAAACACTCTGACTGCCACGCCAGCTACCTCTAGA			
-1	2	primary	0	lane1_fakedata2_6 1:N:0:/1	AATTCTCTACACCACAGCATCAATTCTAAAAATGACTACCAGAGAGACAACTCCGCAGTTAAACACTCTGACTGCCACGCCAGCTACCTCTAGA			
-1	2	primary	0	lane1_fakedata2_7 1:N:0:/1	AATTCTCTACACCACAGCATCAATTCTAAAAATGACTACCAGAGAGACAACTCCGCAGTTAAACACTCTGACTGCCACGCCAGCTACCTCTAGA			
-1	2	primary	0	lane1_fakedata2_8 1:N:0:/1	AATTCTCTACACCACAGCATCAATTCTAAAAATGACTACCAGAGAGACAACTCCGCAGTTAAACACTCTGACTGCCACGCCAGCTACCTCTAGA			
-1	2	primary	0	lane1_fakedata2_9 1:N:0:/1	AATTCTCTACACCACAGCATCAATTCTAAAAATGACTACCAGAGAGACAACTCCGCAGTTAAACACTCTGACTGCCACGCCAGCTACCTCTAGA			
-1	2	primary	0	lane1_fakedata2_10 1:N:0:/1	AATTCTCTACACCACAGCATCAATTCTAAAAATGACTACCAGAGAGACAACTCCGCAGTTAAACACTCTGACTGCCACGCCAGCTACCTCTAGA			
-1	2	primary	0	lane1_fakedata2_11 1:N:0:/1	AATTCTCTACACCACAGCATCAATTCTAAAAATGACTACCAGAGAGACAACTCCGCAGTTAAACACTCTGACTGCCACGCCAGCTACCTCTAGA			
-1	2	primary	0	lane1_fakedata2_12 1:N:0:/1	AATTCTCTACACCACAGCATCAATTCTAAAAATGACTACCAGAGAGACAACTCCGCAGTTAAACACTCTGACTGCCACGCCAGCTACCTCTAGA			
-1	2	primary	0	lane1_fakedata2_13 1:N:0:/1	AATTCTCTACACCACAGCATCAATTCTAAAAATGACTACCAGAGAGACAACTCCGCAGTTAAACACTCTGACTGCCACGCCAGCTACCTCTAGA			
-1	2	primary	0	lane1_fakedata2_14 1:N:0:/1	AATTCTCTACACCACAGCATCAATTCTAAAAATGACTACCAGAGAGACAACTCCGCAGTTAAACACTCTGACTGCCACGCCAGCTACCTCTAGA			
-1	2	primary	0	lane1_fakedata2_15 1:N:0:/1	AATTCTCTACACCACAGCATCAATTCTAAAAATGACTACCAGAGAGACAACTCCGCAGTTAAACACTCTGACTGCCACGCCAGCTACCTCTAGA			
-1	2	primary	0	lane1_fakedata2_16 1:N:0:/1	AATTCTCTACACCACAGCATCAATTCTAAAAATGACTACCAGAGAGACAACTCCGCAGTTAAACACTCTGACTGCCACGCCAGCTACCTCTAGA			
-1	2	primary	0	lane1_fakedata2_18 1:N:0:/1	AATTCTCTACACCACAGCATCAATTCTAAAAATGACTACCAGAGAGACAACTCCGCAGTTAAACACTCTGACTGCCACGCCAGCTACCTCTAGA			
-1	2	primary	0	lane1_fakedata2_19 1:N:0:/1	AATTCTCTACACCACAGCATCAATTCTAAAAATGACTACCAGAGAGACAACTCCGCAGTTAAACACTCTGACTGCCACGCCAGCTACCTCTAGA			
-1	2	secondary		lane1_fakedata2_5 1:N:0:/1	AATTCTCTACACCACAGCATCAATTCTAAAAATGACTACCAGAGAGACAACTCCGCAGTAAAACACTCTGACTGCCACGCCAGCTACCTCTAGA			
-1	2	secondary		lane1_fakedata2_17 1:N:0:/1	AATTCTCTACACCACAGCATCAATTCTAAAAATGACTACCAGAGAGACAACTCCGCAGTTAAACACTCTGACTGCCACGCCAGCTACCTCCAGA			
-1	3	consensus			AATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT	0	0	0
+1	2	primary	0	lane1_fakedata0_0 1:N:0:/1	AATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT			
+1	2	primary	0	lane1_fakedata0_1 1:N:0:/1	AATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT			
+1	2	primary	0	lane1_fakedata0_2 1:N:0:/1	AATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT			
+1	2	primary	0	lane1_fakedata0_3 1:N:0:/1	AATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT			
+1	2	primary	0	lane1_fakedata0_4 1:N:0:/1	AATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT			
+1	2	primary	0	lane1_fakedata0_5 1:N:0:/1	AATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT			
+1	2	primary	0	lane1_fakedata0_6 1:N:0:/1	AATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT			
+1	2	primary	0	lane1_fakedata0_7 1:N:0:/1	AATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT			
+1	2	primary	0	lane1_fakedata0_8 1:N:0:/1	AATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT			
+1	2	primary	0	lane1_fakedata0_9 1:N:0:/1	AATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT			
+1	2	primary	0	lane1_fakedata0_10 1:N:0:/1	AATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT			
+1	2	primary	0	lane1_fakedata0_11 1:N:0:/1	AATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT			
+1	2	primary	0	lane1_fakedata0_12 1:N:0:/1	AATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT			
+1	2	primary	0	lane1_fakedata0_13 1:N:0:/1	AATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT			
+1	2	primary	0	lane1_fakedata0_14 1:N:0:/1	AATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT			
+1	2	primary	0	lane1_fakedata0_16 1:N:0:/1	AATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT			
+1	2	primary	0	lane1_fakedata0_17 1:N:0:/1	AATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT			
+1	2	primary	0	lane1_fakedata0_18 1:N:0:/1	AATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT			
+1	2	primary	0	lane1_fakedata0_19 1:N:0:/1	AATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT			
+1	2	primary	0	lane1_fakedata0_20 1:N:0:/1	AATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT			
+1	2	primary	0	lane1_fakedata0_21 1:N:0:/1	AATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT			
+1	2	primary	0	lane1_fakedata0_22 1:N:0:/1	AATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT			
+1	2	primary	0	lane1_fakedata0_23 1:N:0:/1	AATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT			
+1	2	primary	0	lane1_fakedata0_24 1:N:0:/1	AATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT			
+1	2	primary	0	lane1_fakedata0_25 1:N:0:/1	AATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT			
+1	2	primary	0	lane1_fakedata0_26 1:N:0:/1	AATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT			
+1	2	primary	0	lane1_fakedata0_27 1:N:0:/1	AATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT			
+1	2	secondary		lane1_fakedata0_15 1:N:0:/1	AATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAGTCTGGGAATGGGATTTCATAATTAAGGACTAT			
+1	3	consensus			AATTCTCTACACCACAGCATCAATTCTAAAAATGACTACCAGAGAGACAACTCCGCAGTTAAACACTCTGACTGCCACGCCAGCTACCTCTAGA	0	0	0
 1	3	model			OOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOO			
-1	3	primary	0	lane1_fakedata0_0 1:N:0:/1	AATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT			
-1	3	primary	0	lane1_fakedata0_1 1:N:0:/1	AATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT			
-1	3	primary	0	lane1_fakedata0_2 1:N:0:/1	AATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT			
-1	3	primary	0	lane1_fakedata0_3 1:N:0:/1	AATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT			
-1	3	primary	0	lane1_fakedata0_4 1:N:0:/1	AATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT			
-1	3	primary	0	lane1_fakedata0_5 1:N:0:/1	AATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT			
-1	3	primary	0	lane1_fakedata0_6 1:N:0:/1	AATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT			
-1	3	primary	0	lane1_fakedata0_7 1:N:0:/1	AATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT			
-1	3	primary	0	lane1_fakedata0_8 1:N:0:/1	AATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT			
-1	3	primary	0	lane1_fakedata0_9 1:N:0:/1	AATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT			
-1	3	primary	0	lane1_fakedata0_10 1:N:0:/1	AATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT			
-1	3	primary	0	lane1_fakedata0_11 1:N:0:/1	AATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT			
-1	3	primary	0	lane1_fakedata0_12 1:N:0:/1	AATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT			
-1	3	primary	0	lane1_fakedata0_13 1:N:0:/1	AATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT			
-1	3	primary	0	lane1_fakedata0_14 1:N:0:/1	AATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT			
-1	3	primary	0	lane1_fakedata0_16 1:N:0:/1	AATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT			
-1	3	primary	0	lane1_fakedata0_17 1:N:0:/1	AATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT			
-1	3	primary	0	lane1_fakedata0_18 1:N:0:/1	AATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT			
-1	3	primary	0	lane1_fakedata0_19 1:N:0:/1	AATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT			
-1	3	primary	0	lane1_fakedata0_20 1:N:0:/1	AATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT			
-1	3	primary	0	lane1_fakedata0_21 1:N:0:/1	AATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT			
-1	3	primary	0	lane1_fakedata0_22 1:N:0:/1	AATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT			
-1	3	primary	0	lane1_fakedata0_23 1:N:0:/1	AATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT			
-1	3	primary	0	lane1_fakedata0_24 1:N:0:/1	AATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT			
-1	3	primary	0	lane1_fakedata0_25 1:N:0:/1	AATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT			
-1	3	primary	0	lane1_fakedata0_26 1:N:0:/1	AATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT			
-1	3	primary	0	lane1_fakedata0_27 1:N:0:/1	AATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT			
-1	3	secondary		lane1_fakedata0_15 1:N:0:/1	AATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAGTCTGGGAATGGGATTTCATAATTAAGGACTAT			
+1	3	primary	0	lane1_fakedata2_0 1:N:0:/1	AATTCTCTACACCACAGCATCAATTCTAAAAATGACTACCAGAGAGACAACTCCGCAGTTAAACACTCTGACTGCCACGCCAGCTACCTCTAGA			
+1	3	primary	0	lane1_fakedata2_1 1:N:0:/1	AATTCTCTACACCACAGCATCAATTCTAAAAATGACTACCAGAGAGACAACTCCGCAGTTAAACACTCTGACTGCCACGCCAGCTACCTCTAGA			
+1	3	primary	0	lane1_fakedata2_2 1:N:0:/1	AATTCTCTACACCACAGCATCAATTCTAAAAATGACTACCAGAGAGACAACTCCGCAGTTAAACACTCTGACTGCCACGCCAGCTACCTCTAGA			
+1	3	primary	0	lane1_fakedata2_3 1:N:0:/1	AATTCTCTACACCACAGCATCAATTCTAAAAATGACTACCAGAGAGACAACTCCGCAGTTAAACACTCTGACTGCCACGCCAGCTACCTCTAGA			
+1	3	primary	0	lane1_fakedata2_4 1:N:0:/1	AATTCTCTACACCACAGCATCAATTCTAAAAATGACTACCAGAGAGACAACTCCGCAGTTAAACACTCTGACTGCCACGCCAGCTACCTCTAGA			
+1	3	primary	0	lane1_fakedata2_6 1:N:0:/1	AATTCTCTACACCACAGCATCAATTCTAAAAATGACTACCAGAGAGACAACTCCGCAGTTAAACACTCTGACTGCCACGCCAGCTACCTCTAGA			
+1	3	primary	0	lane1_fakedata2_7 1:N:0:/1	AATTCTCTACACCACAGCATCAATTCTAAAAATGACTACCAGAGAGACAACTCCGCAGTTAAACACTCTGACTGCCACGCCAGCTACCTCTAGA			
+1	3	primary	0	lane1_fakedata2_8 1:N:0:/1	AATTCTCTACACCACAGCATCAATTCTAAAAATGACTACCAGAGAGACAACTCCGCAGTTAAACACTCTGACTGCCACGCCAGCTACCTCTAGA			
+1	3	primary	0	lane1_fakedata2_9 1:N:0:/1	AATTCTCTACACCACAGCATCAATTCTAAAAATGACTACCAGAGAGACAACTCCGCAGTTAAACACTCTGACTGCCACGCCAGCTACCTCTAGA			
+1	3	primary	0	lane1_fakedata2_10 1:N:0:/1	AATTCTCTACACCACAGCATCAATTCTAAAAATGACTACCAGAGAGACAACTCCGCAGTTAAACACTCTGACTGCCACGCCAGCTACCTCTAGA			
+1	3	primary	0	lane1_fakedata2_11 1:N:0:/1	AATTCTCTACACCACAGCATCAATTCTAAAAATGACTACCAGAGAGACAACTCCGCAGTTAAACACTCTGACTGCCACGCCAGCTACCTCTAGA			
+1	3	primary	0	lane1_fakedata2_12 1:N:0:/1	AATTCTCTACACCACAGCATCAATTCTAAAAATGACTACCAGAGAGACAACTCCGCAGTTAAACACTCTGACTGCCACGCCAGCTACCTCTAGA			
+1	3	primary	0	lane1_fakedata2_13 1:N:0:/1	AATTCTCTACACCACAGCATCAATTCTAAAAATGACTACCAGAGAGACAACTCCGCAGTTAAACACTCTGACTGCCACGCCAGCTACCTCTAGA			
+1	3	primary	0	lane1_fakedata2_14 1:N:0:/1	AATTCTCTACACCACAGCATCAATTCTAAAAATGACTACCAGAGAGACAACTCCGCAGTTAAACACTCTGACTGCCACGCCAGCTACCTCTAGA			
+1	3	primary	0	lane1_fakedata2_15 1:N:0:/1	AATTCTCTACACCACAGCATCAATTCTAAAAATGACTACCAGAGAGACAACTCCGCAGTTAAACACTCTGACTGCCACGCCAGCTACCTCTAGA			
+1	3	primary	0	lane1_fakedata2_16 1:N:0:/1	AATTCTCTACACCACAGCATCAATTCTAAAAATGACTACCAGAGAGACAACTCCGCAGTTAAACACTCTGACTGCCACGCCAGCTACCTCTAGA			
+1	3	primary	0	lane1_fakedata2_18 1:N:0:/1	AATTCTCTACACCACAGCATCAATTCTAAAAATGACTACCAGAGAGACAACTCCGCAGTTAAACACTCTGACTGCCACGCCAGCTACCTCTAGA			
+1	3	primary	0	lane1_fakedata2_19 1:N:0:/1	AATTCTCTACACCACAGCATCAATTCTAAAAATGACTACCAGAGAGACAACTCCGCAGTTAAACACTCTGACTGCCACGCCAGCTACCTCTAGA			
+1	3	secondary		lane1_fakedata2_5 1:N:0:/1	AATTCTCTACACCACAGCATCAATTCTAAAAATGACTACCAGAGAGACAACTCCGCAGTAAAACACTCTGACTGCCACGCCAGCTACCTCTAGA			
+1	3	secondary		lane1_fakedata2_17 1:N:0:/1	AATTCTCTACACCACAGCATCAATTCTAAAAATGACTACCAGAGAGACAACTCCGCAGTTAAACACTCTGACTGCCACGCCAGCTACCTCCAGA			
diff -r c23695f62bdd -r 56d3555cf5f7 test-data/ustacks/PopA_02.alleles.tsv
--- a/test-data/ustacks/PopA_02.alleles.tsv	Wed Feb 27 09:52:16 2019 -0500
+++ b/test-data/ustacks/PopA_02.alleles.tsv	Thu Jun 20 08:13:18 2019 -0400
@@ -1,3 +1,3 @@
-# ustacks version 2.3b; generated on 2019-02-21 19:57:38
+# ustacks version 2.4; generated on 2019-06-18 10:34:45
 2	1	AC	50.00	6
 2	1	CA	50.00	6
diff -r c23695f62bdd -r 56d3555cf5f7 test-data/ustacks/PopA_02.snps.tsv
--- a/test-data/ustacks/PopA_02.snps.tsv	Wed Feb 27 09:52:16 2019 -0500
+++ b/test-data/ustacks/PopA_02.snps.tsv	Thu Jun 20 08:13:18 2019 -0400
@@ -1,4 +1,4 @@
-# ustacks version 2.3b; generated on 2019-02-21 19:57:38
+# ustacks version 2.4; generated on 2019-06-18 10:34:45
 2	1	0	O	16.64	A	-		
 2	1	1	O	16.64	A	-		
 2	1	2	O	16.64	T	-		
diff -r c23695f62bdd -r 56d3555cf5f7 test-data/ustacks/PopA_02.tags.tsv
--- a/test-data/ustacks/PopA_02.tags.tsv	Wed Feb 27 09:52:16 2019 -0500
+++ b/test-data/ustacks/PopA_02.tags.tsv	Thu Jun 20 08:13:18 2019 -0400
@@ -1,4 +1,4 @@
-# ustacks version 2.3b; generated on 2019-02-21 19:57:38
+# ustacks version 2.4; generated on 2019-06-18 10:34:45
 2	1	consensus			AATTCGTTTGCTGCTTCAGGAATCTCTCGTATAATCTGAGTATGTGCGTACGTACGCTATTTAGATGGATAACCGACGCTGCCAGACGAGAGAC	0	0	0
 2	1	model			OOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOEOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOEOOOOO			
 2	1	primary	0	lane1_fakedata7_7 1:N:0:/1	AATTCGTTTGCTGCTTCAGGAATCTCTCGTATACTCTGAGTATGTGCGTACGTACGCTATTTAGATGGATAACCGACGCTGCCAGACGAGAGAC			
@@ -11,8 +11,8 @@
 2	1	primary	1	lane1_fakedata7_3 1:N:0:/1	AATTCGTTTGCTGCTTCAGGAATCTCTCGTATAATCTGAGTATGTGCGTACGTACGCTATTTAGATGGATAACCGACGCTGCCAGACGCGAGAC			
 2	1	primary	1	lane1_fakedata7_4 1:N:0:/1	AATTCGTTTGCTGCTTCAGGAATCTCTCGTATAATCTGAGTATGTGCGTACGTACGCTATTTAGATGGATAACCGACGCTGCCAGACGCGAGAC			
 2	1	primary	1	lane1_fakedata7_5 1:N:0:/1	AATTCGTTTGCTGCTTCAGGAATCTCTCGTATAATCTGAGTATGTGCGTACGTACGCTATTTAGATGGATAACCGACGCTGCCAGACGCGAGAC			
+2	1	secondary		lane1_fakedata7_6 1:N:0:/1	AATTCGTTTGCTGCTTCAGGAACCTCTCGTATACTCTGAGTATGTGCGTACGTACGCTATTTAGATGGATAACCGACGCTGCCAGACGAGAGAC			
 2	1	secondary		lane1_fakedata7_10 1:N:0:/1	AATTCGTTTGCTGCTTCAGGAATCTTTCGTATACTCTGAGTATGTGCGTACGTACGCTATTTAGATGGATAACCGACGCTGCCAGACGAGAGAC			
-2	1	secondary		lane1_fakedata7_6 1:N:0:/1	AATTCGTTTGCTGCTTCAGGAACCTCTCGTATACTCTGAGTATGTGCGTACGTACGCTATTTAGATGGATAACCGACGCTGCCAGACGAGAGAC			
 2	2	consensus			AATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT	0	0	0
 2	2	model			OOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOO			
 2	2	primary	0	lane1_fakedata0_0 1:N:0:/1	AATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT