[med-svn] [bio-tradis] 01/02: New upstream version 1.3.1+dfsg
Andreas Tille
tille at debian.org
Fri Mar 3 22:45:56 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository bio-tradis.
commit 03634387e0df91b4d14eab1526cea4dca4c8bd3b
Author: Andreas Tille <tille at debian.org>
Date: Fri Mar 3 23:44:36 2017 +0100
New upstream version 1.3.1+dfsg
---
.gitignore | 20 +
.travis.yml | 11 +
AUTHORS | 3 +
README.md | 211 +++++++
bin/add_tradis_tags | 20 +
bin/bacteria_tradis | 21 +
bin/check_tradis_tags | 20 +
bin/combine_tradis_plots | 23 +
bin/filter_tradis_tags | 21 +
bin/remove_tradis_tags | 20 +
bin/tradis_comparison.R | 116 ++++
bin/tradis_essentiality.R | 78 +++
bin/tradis_gene_insert_sites | 329 ++++++++++
bin/tradis_merge_plots | 98 +++
bin/tradis_plot | 21 +
dist.ini | 60 ++
install_dependencies.sh | 110 ++++
lib/Bio/Tradis.pm | 31 +
lib/Bio/Tradis/AddTagsToSeq.pm | 203 ++++++
lib/Bio/Tradis/Analysis/Exceptions.pm | 20 +
lib/Bio/Tradis/Analysis/InsertSite.pm | 207 +++++++
lib/Bio/Tradis/CombinePlots.pm | 327 ++++++++++
lib/Bio/Tradis/CommandLine/AddTags.pm | 84 +++
lib/Bio/Tradis/CommandLine/CheckTags.pm | 70 +++
lib/Bio/Tradis/CommandLine/FilterFastqTags.pm | 84 +++
lib/Bio/Tradis/CommandLine/PlotCombine.pm | 101 +++
lib/Bio/Tradis/CommandLine/PlotTradis.pm | 79 +++
lib/Bio/Tradis/CommandLine/RemoveFastqTags.pm | 84 +++
lib/Bio/Tradis/CommandLine/RunMapping.pm | 118 ++++
lib/Bio/Tradis/CommandLine/TradisAnalysis.pm | 271 ++++++++
lib/Bio/Tradis/CommandLine/TradisBam.pm | 99 +++
lib/Bio/Tradis/DetectTags.pm | 54 ++
lib/Bio/Tradis/Exception.pm | 16 +
lib/Bio/Tradis/FilterTags.pm | 162 +++++
lib/Bio/Tradis/Map.pm | 143 +++++
lib/Bio/Tradis/Parser/Bam.pm | 192 ++++++
lib/Bio/Tradis/Parser/Cigar.pm | 71 +++
lib/Bio/Tradis/Parser/Fastq.pm | 101 +++
lib/Bio/Tradis/RemoveTags.pm | 122 ++++
lib/Bio/Tradis/RunTradis.pm | 511 ++++++++++++++++
lib/Bio/Tradis/Samtools.pm | 102 ++++
lib/Bio/Tradis/TradisPlot.pm | 60 ++
.../Tradis_SR_RR_12dark_42r1_rehyb12_index8.xml | 461 ++++++++++++++
recipes/Tradis_adapter_primers.xlsx | Bin 0 -> 49848 bytes
recipes/Transposon10/Chemistry/Chemistry.xml | 413 +++++++++++++
recipes/Transposon10/Exposures/Sony.xml | 7 +
recipes/Transposon10/Exposures/SonyV2.xml | 11 +
recipes/Transposon10/Protocol/1Read1Index.xml | 24 +
recipes/Transposon10/Protocol/1Read2Index.xml | 25 +
recipes/Transposon10/Protocol/2Read1Index.xml | 28 +
recipes/Transposon10/Protocol/2Read2Index.xml | 31 +
recipes/Transposon10/Reads/Reads.xml | 23 +
recipes/Transposon10/Reagents/MaintenanceWash.xml | 25 +
recipes/Transposon10/Reagents/PostRunWash.xml | 25 +
recipes/Transposon10/Reagents/Sequencing.xml | 24 +
recipes/Transposon10/Wash/LineWash.xml | 102 ++++
recipes/Transposon10/Wash/MaintenanceWash.xml | 115 ++++
recipes/Transposon10/Wash/PostRunWash.xml | 180 ++++++
recipes/Transposon10/Wash/PostRunWashOriginal.xml | 115 ++++
recipes/Transposon10/Wash/StandbyWash.xml | 70 +++
recipes/Transposon12/Chemistry/Chemistry.xml | 413 +++++++++++++
recipes/Transposon12/Exposures/Sony.xml | 7 +
recipes/Transposon12/Exposures/SonyV2.xml | 11 +
recipes/Transposon12/Protocol/1Read1Index.xml | 26 +
recipes/Transposon12/Protocol/1Read2Index.xml | 27 +
recipes/Transposon12/Protocol/2Read1Index.xml | 30 +
recipes/Transposon12/Protocol/2Read2Index.xml | 33 +
recipes/Transposon12/Reads/Reads.xml | 23 +
recipes/Transposon12/Reagents/MaintenanceWash.xml | 25 +
recipes/Transposon12/Reagents/PostRunWash.xml | 25 +
recipes/Transposon12/Reagents/Sequencing.xml | 24 +
...30702_ImplementingCarryoverDecontamWash_v3.docx | Bin 0 -> 375530 bytes
recipes/Transposon12/Wash/LineWash.xml | 102 ++++
recipes/Transposon12/Wash/MaintenanceWash.xml | 115 ++++
recipes/Transposon12/Wash/PostRunWash.xml | 180 ++++++
recipes/Transposon12/Wash/PostRunWashOriginal.xml | 115 ++++
recipes/Transposon12/Wash/StandbyWash.xml | 70 +++
software_license | 680 +++++++++++++++++++++
t/Bio/Tradis/AddTagsToSeq.t | 97 +++
t/Bio/Tradis/Analysis/InsertSite.t | 115 ++++
t/Bio/Tradis/CombinePlots.t | 120 ++++
t/Bio/Tradis/CommandLine/TradisAnalysis.t | 92 +++
t/Bio/Tradis/DetectTags.t | 55 ++
t/Bio/Tradis/FilterTags.t | 101 +++
t/Bio/Tradis/Map.t | 77 +++
t/Bio/Tradis/Parser/Bam.t | 105 ++++
t/Bio/Tradis/Parser/Cigar.t | 84 +++
t/Bio/Tradis/Parser/Fastq.t | 52 ++
t/Bio/Tradis/RemoveTags.t | 82 +++
t/Bio/Tradis/RunTradis.t | 261 ++++++++
t/Bio/Tradis/TradisPlot.t | 43 ++
t/data/AddTags/expected_tradis.bam | Bin 0 -> 3098 bytes
t/data/AddTags/expected_tradis.cram | Bin 0 -> 20372 bytes
t/data/AddTags/sample_sm_no_tr.bam | Bin 0 -> 3098 bytes
t/data/AddTags/sample_sm_tr.bam | Bin 0 -> 3062 bytes
t/data/AddTags/sample_sm_tr.cram | Bin 0 -> 20303 bytes
t/data/CombinePlots/comb_expected.stats | 3 +
t/data/CombinePlots/comb_sample.txt | 2 +
t/data/CombinePlots/first.expected.plot | 20 +
t/data/CombinePlots/sample1.sm.plot.gz | Bin 0 -> 63 bytes
t/data/CombinePlots/sample2.sm.plot.gz | Bin 0 -> 63 bytes
t/data/CombinePlots/second.expected.plot | 25 +
.../CombinePlots/tabix_sorted.insert_site_plot.gz | Bin 0 -> 211 bytes
.../tabix_sorted.insert_site_plot.gz.tbi | Bin 0 -> 109 bytes
t/data/CombinePlots/test1.plot | 20 +
t/data/CombinePlots/test2.plot | 20 +
t/data/CombinePlots/test3.plot | 25 +
t/data/CombinePlots/test4.plot | 25 +
t/data/CombinePlots/zip_comb_exp.plot | 100 +++
t/data/CombinePlots/zip_comb_exp.stats | 2 +
t/data/CombinePlots/zip_comb_list.txt | 1 +
t/data/CommandLine/fastq.list | 2 +
t/data/CommandLine/test_1.fastq | 56 ++
t/data/CommandLine/test_2.fastq | 56 ++
t/data/DetectTags/sample_sm_no_tr.bam | Bin 0 -> 3017 bytes
t/data/DetectTags/sample_sm_tr.bam | Bin 0 -> 3062 bytes
t/data/DetectTags/sample_sm_tr.cram | Bin 0 -> 20303 bytes
t/data/FilterTags/expected.1mm.caa.fastq | 40 ++
t/data/FilterTags/expected.caa.fastq | 32 +
t/data/FilterTags/expected.tna.fastq | 12 +
t/data/FilterTags/sample.fastq | 52 ++
t/data/FilterTags/sample.fastq.gz | Bin 0 -> 611 bytes
t/data/InsertSite/2_reads.bam | Bin 0 -> 632 bytes
t/data/InsertSite/small_multi_sequence.bam | Bin 0 -> 12248 bytes
t/data/Map/expected.mapped | 26 +
t/data/Map/smallref.fa | 165 +++++
t/data/Map/test.fastq | 92 +++
t/data/Parsers/test.bam | Bin 0 -> 539 bytes
t/data/Parsers/test.fastq | 8 +
t/data/RemoveTags/expected.rm.1mm.caa.fastq | 40 ++
t/data/RemoveTags/expected.rm.caa.fastq | 40 ++
t/data/RemoveTags/expected.rm.tna.fastq | 12 +
t/data/RemoveTags/sample.caa.fastq | 40 ++
t/data/RemoveTags/sample.tna.fastq | 12 +
t/data/RunTradis/expected.1mm.plot.gz | Bin 0 -> 120 bytes
t/data/RunTradis/expected.plot.gz | Bin 0 -> 119 bytes
t/data/RunTradis/filelist.txt | 2 +
t/data/RunTradis/filtered.fastq | 92 +++
t/data/RunTradis/mapped.sam | 26 +
t/data/RunTradis/notags.fastq | 92 +++
t/data/RunTradis/smallref.fa | 165 +++++
t/data/RunTradis/test.tagged.fastq | 112 ++++
t/data/RunTradis/test.tagged.fastq.gz | Bin 0 -> 1316 bytes
t/data/RunTradis/test2.tagged.fastq | 452 ++++++++++++++
t/data/RunTradis/test2.tagged.fastq.gz | Bin 0 -> 4625 bytes
t/data/TradisPlot/expected.plot.gz | Bin 0 -> 120 bytes
t/data/TradisPlot/sample.fastq | 52 ++
t/data/TradisPlot/test.mapped.bam | Bin 0 -> 1395 bytes
148 files changed, 11284 insertions(+)
diff --git a/.gitignore b/.gitignore
new file mode 100644
index 0000000..d117ab7
--- /dev/null
+++ b/.gitignore
@@ -0,0 +1,20 @@
+blib/
+.build/
+_build/
+cover_db/
+inc/
+Build
+!Build/
+Build.bat
+.last_cover_stats
+Makefile
+Makefile.old
+MANIFEST.bak
+META.yml
+MYMETA.yml
+nytprof.out
+pm_to_blib
+Bio-Tradis-*
+.DS_Store
+*.tar.gz
+*.swp
diff --git a/.travis.yml b/.travis.yml
new file mode 100644
index 0000000..b1893fb
--- /dev/null
+++ b/.travis.yml
@@ -0,0 +1,11 @@
+language: perl
+addons:
+ apt:
+ packages:
+ - zlib1g-dev
+perl:
+ - "5.14"
+sudo: false
+install:
+ - "source ./install_dependencies.sh"
+script: "dzil test"
diff --git a/AUTHORS b/AUTHORS
new file mode 100644
index 0000000..4746756
--- /dev/null
+++ b/AUTHORS
@@ -0,0 +1,3 @@
+Carla Cummins (cc21 at sanger.ac.uk)
+Andrew J. Page (ap13 at sanger.ac.uk)
+Lars Barquist (lars.barquist at uni-wuerzburg.de)
diff --git a/README.md b/README.md
new file mode 100644
index 0000000..6a40e3f
--- /dev/null
+++ b/README.md
@@ -0,0 +1,211 @@
+Bio-Tradis
+==========
+Bio-Tradis contains a set of tools to analyse the output from TraDIS analyses. For command-line usage instructions, please see the tutorial in the file "BioTraDISTutorial.pdf". Note that default parameters are for comparative experiments, and will need to be modified for gene essentiality studies.
+
+For more information on the TraDIS method, see http://bioinformatics.oxfordjournals.org/content/32/7/1109 and http://genome.cshlp.org/content/19/12/2308
+
+[](https://travis-ci.org/sanger-pathogens/Bio-Tradis)
+
+Bio-Tradis provides functionality to:
+* detect TraDIS tags in a BAM file
+* add the tags to the reads
+* filter reads in a FastQ file containing a user defined tag
+* remove tags
+* map to a reference genome
+* create an insertion site plot file
+available as standalone scripts or as perl modules.
+
+Installation
+=======
+
+####HomeBrew/LinuxBrew
+To install the dependancies, the easiest way is through [HomeBrew](http://brew.sh/) (OSX) or [LinuxBrew](http://brew.sh/linuxbrew/) (Linux).
+```
+brew tap homebrew/science
+brew install r smalt samtools cpanm
+sudo cpanm -f Bio::Tradis
+
+R
+source("http://bioconductor.org/biocLite.R")
+biocLite()
+biocLite(c("edgeR","getopt", "MASS"))
+````
+
+####Without Homebrew
+Install [SMALT](https://www.sanger.ac.uk/resources/software/smalt/) version 0.7.6 or greater, [Samtools](http://www.htslib.org/) version 1.3 or greater and [R](https://cran.r-project.org/) version 3.2 or greater. Ensure they are in your PATH.
+
+```
+sudo cpanm -f Bio::Tradis
+R
+source("http://bioconductor.org/biocLite.R")
+biocLite()
+biocLite(c("edgeR","getopt", "MASS"))
+```
+
+####Windows
+Install Linux.
+
+Objects and Methods
+===================
+####Bio::Tradis::DetectTags
+* Required parameters:
+ * `bamfile` - path to/name of file to check
+* Methods:
+ * `tags_present` - returns true if TraDIS tags are detected in `bamfile`
+
+####Bio::Tradis::AddTagsToSeq
+* Required parameters:
+ * `bamfile` - path to/name of file containing reads and tags
+* Optional parameters:
+ * `outfile` - defaults to `file.tr.bam` for an input file named `file.bam`
+* Methods:
+ * `add_tags_to_seq` - add TraDIS tags to reads. For unmapped reads, the tag
+ is added to the start of the read sequence and quality
+ strings. For reads where the flag indicates that it is
+ mapped and reverse complemented, the reverse complemented
+ tags are added to the end of the read strings.
+ This is because many conversion tools (e.g. picard) takes
+ the read orientation into account and will re-reverse the
+ mapped/rev comp reads during conversion, leaving all tags
+ in the correct orientation at the start of the sequences
+ in the resulting FastQ file.
+
+####Bio::Tradis::FilterTags
+* Required parameters:
+ * `fastqfile` - path to/name of file to filter. This may be a gzipped fastq file, in which case a temporary unzipped version is used and removed on completion.
+ * `tag` - TraDIS tag to match
+* Optional parameters:
+ * `mismatch` - number of mismatches to allow when matching the tag. Default = 0
+ * `outfile` - defaults to `file.tag.fastq` for an input file named `file.fastq`
+* Methods:
+ * `filter_tags` - output all reads containing the tag to `outfile`
+
+####Bio::Tradis::RemoveTags
+* Required parameters:
+ * `fastqfile` - path to/name of file to filter.
+ * `tag` - TraDIS tag to remove
+* Optional parameters:
+ * `mismatch` - number of mismatches to allow when removing the tag. Default = 0
+ * `outfile` - defaults to `file.rmtag.fastq` for and input file named `file.fastq`
+* Methods:
+ * `remove_tags` - output all reads with the tags removed from both sequence and
+ quality strings to `outfile`
+
+####Bio::Tradis::Map
+* Required parameters:
+ * `fastqfile` - path to/name of file to map to the reference
+ * `reference` - path to/name of reference genome in fasta format (.fa)
+* Optional parameters:
+ * `refname` - name to assign to the reference index files. Default = ref.index
+ * `outfile` - name to assign the mapped SAM file. Default = mapped.sam
+* Methods:
+ * `index_ref` - create index files of the reference genome. These are required
+ for the mapping step. Only skip this step if index files already
+ exist. -k and -s options for referencing are calculated based
+ on the length of the reads being mapped:
+ * <70 : `-k 13 -s 4`
+ * >70 & <100 : `-k 13 -s 6`
+ * >100 : `-k 20 -s 13`
+ * `do_mapping` - map `fastqfile` to `reference`. Options used for mapping are:
+ `-r -1, -x and -y 0.96`
+
+ For more information on the mapping and indexing options discussed here, see the SMALT manual (ftp://ftp.sanger.ac.uk/pub4/resources/software/smalt/smalt-manual-0.7.4.pdf)
+
+####Bio::Tradis::TradisPlot
+* Required parameters:
+ * `mappedfile` - mapped and sorted BAM file
+* Optional parameters:
+ * `outfile` - base name to assign to the resulting insertion site plot. Default = tradis.plot
+ * `mapping_score` - cutoff value for mapping score. Default = 30
+* Methods:
+ * `plot` - create insertion site plots for reads in `mappedfile`. This file will be readable by the Artemis genome browser (http://www.sanger.ac.uk/resources/software/artemis/)
+
+####Bio::Tradis::RunTradis
+* Required parameters:
+ * `fastqfile` - file containing a list of fastqs (gzipped or raw) to run the
+ complete analysis on. This includes all (including
+ intermediary format conversion and sorting) steps starting from
+ filtering and, finally, producing an insertion site plot and a
+ statistical summary of the analysis.
+ * `tag` - TraDIS tag to filter for and then remove
+ * `reference` - path to/name of reference genome in fasta format (.fa)
+* Optional parameters:
+ * `mismatch` - number of mismatches to allow when filtering/removing the tag. Default = 0
+ * `tagdirection` - direction of the tag, 5' or 3'. Default = 3
+ * `mapping_score` - cutoff value for mapping score. Default = 30
+* Methods:
+ * `run_tradis` - run complete analysis
+
+Examples
+========
+Check whether `file.bam` contains TraDIS tag fields and, if so, adds the tags
+to the reads' sequence and quality strings.
+
+```Perl
+my $detector = Bio::Tradis::DetectTags(bamfile => 'file.bam');
+if($detector->tags_present){
+ Bio::Tradis::AddTagsToSeq(bamfile => 'file.bam', outfile => 'tradis.bam')->add_tags_to_seq;
+}
+```
+Filter a FastQ file with TraDIS tags attached for those matching the given tag.
+Then, remove the same tag from the start of all sequences in preparation for mapping.
+
+```Perl
+Bio::Tradis::FilterTags(
+ fastqfile => 'tradis.fastq',
+ tag => 'TAAGAGTGAC',
+ outfile => 'filtered.fastq'
+)->filter_tags;
+Bio::Tradis::RemoveTags(
+ fastqfile => 'filtered.fastq',
+ tag => 'TAAGAGTGAC',
+ outfile => 'notags.fastq'
+)->remove_tags;
+```
+Create mapping object, index the given reference file and then map the
+fastq file to the reference. This will produce index files for the reference and a mapped SAM file named `tradis_mapped.sam`.
+
+```Perl
+my $mapping = Bio::Tradis::Map(
+ fastqfile => 'notags.fastq',
+ reference => 'path/to/reference.fa',
+ outfile => 'tradis_mapped.sam'
+);
+$mapping->index_ref;
+$mapping->do_mapping;
+```
+Generate insertion site plot for only reads with a mapping score >= 50
+
+```Perl
+Bio::Tradis::TradisPlot(mappedfile => 'mapped.bam', mapping_score => 50)->plot;
+```
+Run complete analysis on fastq files listed in `file.list`. This includes filtering and removing the tags allowing one mismatch to the given tag, mapping, BAM sorting and creation of an insertion site plot and stats file for each file listed in `file.list`.
+
+```Perl
+Bio::Tradis::RunTradis(
+ fastqfile => 'file.list',
+ tag => 'GTTGAGGCCA',
+ reference => 'path/to/reference.fa',
+ mismatch => 1
+)->run_tradis;
+```
+Scripts
+=======
+Executable scripts to carry out most of the listed functions are available in the `bin`:
+
+* `check_tradis_tags` - Prints 1 if tags are present, prints 0 if not.
+* `add_tradis_tags` - Generates a BAM file with tags added to read strings.
+* `filter_tradis_tags` - Create a fastq file containing reads that match the supplied tag
+* `remove_tradis_tags` - Creates a fastq file containing reads with the supplied tag removed from the sequences
+* `tradis_plot` - Creates an gzipped insertion site plot
+* `bacteria_tradis` - Runs complete analysis, starting with a fastq file and produces mapped BAM files and plot files for each file in the given file list and a statistical summary of all files. Note that the -f option expects a text file containing a list of fastq files, one per line.
+
+A help menu for each script can be accessed by running the script with no parameters
+
+Analysis Scripts
+================
+Three scripts are provided to perform basic analysis of TraDIS results in `bin`:
+
+* `tradis_gene_insert_sites` - Takes genome annotation in embl format along with plot files produced by bacteria_tradis and generates tab-delimited files containing gene-wise annotations of insert sites and read counts.
+* `tradis_essentiality.R` - Takes a single tab-delimited file from tradis_gene_insert_sites to produce calls of gene essentiality. Also produces a number of diagnostic plots.
+* `tradis_comparison.R` - Takes tab files to compare two growth conditions using edgeR. This analysis requires experimental replicates.
diff --git a/bin/add_tradis_tags b/bin/add_tradis_tags
new file mode 100755
index 0000000..f4cf68f
--- /dev/null
+++ b/bin/add_tradis_tags
@@ -0,0 +1,20 @@
+#!/usr/bin/env perl
+
+package Bio::Tradis::Bin::DetectTags;
+
+# ABSTRACT: check if tr tag is present
+# PODNAME: check_tags
+
+=head1 SYNOPSIS
+
+Checks the presence of tr/tq tags in a given BAM file
+
+=cut
+
+BEGIN { unshift( @INC, '../lib' ) }
+BEGIN { unshift( @INC, './lib' ) }
+BEGIN { unshift( @INC, '/software/pathogen/internal/prod/lib/' ) }
+
+use Bio::Tradis::CommandLine::AddTags;
+
+Bio::Tradis::CommandLine::AddTags->new(args => \@ARGV, script_name => $0)->run;
diff --git a/bin/bacteria_tradis b/bin/bacteria_tradis
new file mode 100755
index 0000000..5680dcc
--- /dev/null
+++ b/bin/bacteria_tradis
@@ -0,0 +1,21 @@
+#!/usr/bin/env perl
+
+package Bio::Tradis::Bin::RunTradis;
+
+# ABSTRACT: Perform full tradis analysis
+# PODNAME: run_tradis
+
+=head1 SYNOPSIS
+
+Take a fastq, reference and a tag and generates insertion
+site plots for use in Artemis
+
+=cut
+
+BEGIN { unshift( @INC, '../lib' ) }
+BEGIN { unshift( @INC, './lib' ) }
+BEGIN { unshift( @INC, '/software/pathogen/internal/prod/lib/' ) }
+
+use Bio::Tradis::CommandLine::TradisAnalysis;
+
+Bio::Tradis::CommandLine::TradisAnalysis->new(args => \@ARGV, script_name => $0)->run;
diff --git a/bin/check_tradis_tags b/bin/check_tradis_tags
new file mode 100755
index 0000000..ac1007c
--- /dev/null
+++ b/bin/check_tradis_tags
@@ -0,0 +1,20 @@
+#!/usr/bin/env perl
+
+package Bio::Tradis::Bin::DetectTags;
+
+# ABSTRACT: check if tr tag is present
+# PODNAME: check_tags
+
+=head1 SYNOPSIS
+
+Checks the presence of tr/tq tags in a given BAM file
+
+=cut
+
+BEGIN { unshift( @INC, '../lib' ) }
+BEGIN { unshift( @INC, './lib' ) }
+BEGIN { unshift( @INC, '/software/pathogen/internal/prod/lib/' ) }
+
+use Bio::Tradis::CommandLine::CheckTags;
+
+Bio::Tradis::CommandLine::CheckTags->new(args => \@ARGV, script_name => $0)->run;
diff --git a/bin/combine_tradis_plots b/bin/combine_tradis_plots
new file mode 100755
index 0000000..9d90d2c
--- /dev/null
+++ b/bin/combine_tradis_plots
@@ -0,0 +1,23 @@
+#!/usr/bin/env perl
+
+package Bio::Tradis::Bin::CombineTradisPlots;
+
+# ABSTRACT: Combine multiple plotfiles and generate updated statistics for the combined files
+
+# PODNAME: combine_tradis_plot
+
+=head1 SYNOPSIS
+
+Takes a tab-delimited file with an ID as the first column followed by
+a list of plotfiles to combine per row. The ID will be used to name the new
+plotfile and as an identifier in the stats file, so ensure these are unique.
+
+=cut
+
+BEGIN { unshift( @INC, '../lib' ) }
+BEGIN { unshift( @INC, './lib' ) }
+BEGIN { unshift( @INC, '/software/pathogen/internal/prod/lib/' ) }
+
+use Bio::Tradis::CommandLine::PlotCombine;
+
+Bio::Tradis::CommandLine::PlotCombine->new(args => \@ARGV, script_name => $0)->run;
diff --git a/bin/filter_tradis_tags b/bin/filter_tradis_tags
new file mode 100755
index 0000000..01ae6a2
--- /dev/null
+++ b/bin/filter_tradis_tags
@@ -0,0 +1,21 @@
+#!/usr/bin/env perl
+
+package Bio::Tradis::Bin::FilterTags;
+
+# ABSTRACT: filter tags at start of fastq sequences
+# PODNAME: filter_tags
+
+=head1 SYNOPSIS
+
+Checks tags at the start of the fastq sequence and returns a file containing those that
+match the tag provided
+
+=cut
+
+BEGIN { unshift( @INC, '../lib' ) }
+BEGIN { unshift( @INC, './lib' ) }
+BEGIN { unshift( @INC, '/software/pathogen/internal/prod/lib/' ) }
+
+use Bio::Tradis::CommandLine::FilterFastqTags;
+
+Bio::Tradis::CommandLine::FilterFastqTags->new(args => \@ARGV, script_name => $0)->run;
diff --git a/bin/remove_tradis_tags b/bin/remove_tradis_tags
new file mode 100755
index 0000000..0d54139
--- /dev/null
+++ b/bin/remove_tradis_tags
@@ -0,0 +1,20 @@
+#!/usr/bin/env perl
+
+package Bio::Tradis::Bin::RemoveTags;
+
+# ABSTRACT: remove user specified tags from start of fastq sequences
+# PODNAME: remove_tags
+
+=head1 SYNOPSIS
+
+Removes tags from the sequence and quality strings based on user input
+
+=cut
+
+BEGIN { unshift( @INC, '../lib' ) }
+BEGIN { unshift( @INC, './lib' ) }
+BEGIN { unshift( @INC, '/software/pathogen/internal/prod/lib/' ) }
+
+use Bio::Tradis::CommandLine::RemoveFastqTags;
+
+Bio::Tradis::CommandLine::RemoveFastqTags->new(args => \@ARGV, script_name => $0)->run;
diff --git a/bin/tradis_comparison.R b/bin/tradis_comparison.R
new file mode 100755
index 0000000..c3f5164
--- /dev/null
+++ b/bin/tradis_comparison.R
@@ -0,0 +1,116 @@
+#!/usr/bin/env Rscript
+
+# PODNAME: tradis_comparison.R
+# ABSTRACT: tradis_comparison.R
+
+library("edgeR")
+library("getopt")
+
+options(width=80)
+
+opt = getopt(matrix( c('help', 'h', 0, "logical",
+ 'verbose', 'v', 0, "integer",
+ 'controls', 'c', 1, "character",
+ 'conditions', 'm', 1, "character",
+ 'output', 'o', 1, "character",
+ 'plot', 'p', 1, "character",
+ 'filter', 'f', 0, "logical",
+ 'mincount', 't', 1, "integer"
+), ncol=4, byrow=TRUE ) );
+
+if(! is.null(opt$help) || is.null(opt$controls ) || is.null(opt$conditions ) )
+{
+ cat(paste("Usage: tradis_comparison.R [-h] [-f] [-t read cutoff] [-o outputfile.csv] [-p outputplot.pdf] --controls controls.txt --conditions conditions.txt\n\n"));
+ writeLines(c(strwrap("Compares two experimental conditions using the method of Dembek et al. mBio 2015. Read counts per gene are compared using edgeR. This analysis requires experimental replicates."),
+ "\n\nRequired Arguments:\n",
+ strwrap("--controls : 'control' libraries, generally growth in a permissive condition"),
+ strwrap("--conditions : libraries exposed to the experimental condition being compared"),
+ "\nOptional Arguments:\n",
+ strwrap("-o : output filename"),
+ strwrap("-p : output filename for diagnostic plots"),
+ strwrap("-f : enable filtering on minimum read counts"),
+ strwrap("-t : if --filter is enabled, sets minimum read count necessary in one condition for a gene to be included in the comparison."),"\n"))
+ q(status=1);
+}
+
+if( is.null(opt$filter)) {opt$filter=FALSE}
+if( is.null(opt$mincount)) {opt$mincount = 0}
+
+# parse contols and conditions files to lists
+control_files <- scan(opt$controls, what="", sep="\n")
+condition_files <- scan(opt$conditions, what="", sep="\n")
+
+if(length(control_files) < 2 || length(condition_files) < 2){
+ print("2 or more controls/conditions must be provided")
+}
+if(length(control_files) != length(condition_files)){
+ print("Unequal number of conditions and controls provided")
+}
+
+control_list = list()
+for(i in 1:length(control_files)){
+ control_list[[i]] <- read.table(control_files[i], sep="\t",header=TRUE, quote="\"", stringsAsFactors=F)
+}
+condition_list = list()
+for(i in 1:length(condition_files)){
+ condition_list[[i]] <- read.table(condition_files[i], sep="\t",header=TRUE, quote="\"", stringsAsFactors=F)
+}
+
+# set default output filename
+if ( is.null(opt$output ) ) { opt$output = paste(opt$condition1,opt$control1, ".output.csv",sep = "")}
+
+#only look at genes with counts > 0 (or input alternative) in some condition
+all_list <- c(control_list, condition_list)
+
+# make list of rows where read count > 0 (or input alternative) in all controls and conditions
+read_counts = do.call(cbind, lapply(all_list, function(x){ x$read_count }))
+
+#old case for only 0.
+if(! opt$filter){
+ zeros = apply( apply(read_counts, 1, ">", 0), 2, any )
+} else {
+ zeros_cont = apply( apply(read_counts[,1:length(control_files)], 1, ">", opt$mincount), 2, all )
+ zeros_cond = apply( apply(read_counts[,(length(control_files) + 1):(length(control_files) + length(condition_files))], 1, ">", opt$mincount), 2, all )
+ zeros = (zeros_cont | zeros_cond)
+}
+
+
+# remove these rows
+noness_list = lapply(all_list, function(x){ x[zeros,] } )
+
+#build count matrix
+count_mat <- do.call(cbind, lapply(noness_list, function(x){x[,7]}))
+conds = c()
+for(i in 1:length(control_files)){
+ conds <- c(conds, "ctrl")
+}
+for(i in 1:length(condition_files)){
+ conds <- c(conds, "cond")
+}
+conds <- as.factor(conds)
+
+
+if( is.null(opt$plot) ){ opt$plot = paste(opt$condition1,opt$control1,".output.pdf",sep = "") }
+pdf( opt$plot )
+
+#edgeR
+d <- DGEList(counts = count_mat, group=conds)
+plotMDS.DGEList(d, labels=conds)
+d <- calcNormFactors(d)
+d <- estimateCommonDisp(d)
+d <- estimateTagwiseDisp(d)
+de.tgw <- exactTest(d,pair=c("ctrl","cond"))
+
+ctrl1_noness <- noness_list[[1]]
+diff <- cbind(ctrl1_noness[,1:2],ctrl1_noness[,11],de.tgw$table,q.value=p.adjust(de.tgw$table$PValue,"BH"))
+
+
+#volcano plot
+plot(diff$logFC, -log(diff$q.value, base=2), xlim=range(c(-6,6)),xlab="Log2 Fold-Change, cond - Ctrl",ylab="-Log2 Q-value", cex = .5, pch=20)
+abline(h=-log(0.01), col="red")
+abline(v=-2, col="red")
+abline(v=2, col="red")
+
+
+#write results
+write.table(diff,file=opt$output,append=FALSE, quote=TRUE, sep=",", row.names=FALSE, col.names=c("locus_tag","gene_name","function","logFC","logCPM","PValue","q.value"))
diff --git a/bin/tradis_essentiality.R b/bin/tradis_essentiality.R
new file mode 100755
index 0000000..6626e82
--- /dev/null
+++ b/bin/tradis_essentiality.R
@@ -0,0 +1,78 @@
+#!/usr/bin/env Rscript
+
+# PODNAME: tradis_essentiality.R
+# ABSTRACT: tradis_essentiality.R
+
+library("MASS")
+options(warn=-1)
+options(width=80)
+
+args <- commandArgs(trailingOnly = TRUE)
+input = args[1]
+
+if( is.na(input) ){
+ cat(paste("Usage: tradis_essentiality.R data.tab\n\n"))
+ cat(strwrap("Produces calls of gene essentiality using an adaptation of the method described in Langridge et al. Genome Research 2009 and Barquist et al. NAR 2013. A loess curve is fit to the distribution of insertion indices, and used to identify the minima between the 'essential' and 'non-essential' distributions. These distributions are then used to fit gamma distributions, which are then used to calculate log-odds ratios, which are used to determine an insertion-index threshold for [...]
+ q(status=1)
+}
+
+STM_baseline <- read.table(input, sep="\t",header=TRUE,stringsAsFactors=F, quote="\"")
+
+ii <- STM_baseline$ins_index
+
+#identify second maxima
+h <- hist(ii, breaks=100,plot=FALSE)
+maxindex <- which.max(h$density[3:length(h$density)])
+maxval <- h$mids[maxindex+2]
+
+# print pdf of loess curve and later on, histogram
+pdf(paste(input, "QC_and_changepoint_plots", "pdf", sep = "."))
+
+#find inter-mode minima with loess
+nG <- length(STM_baseline$read_count)
+r <- floor(maxval *1000)
+I = ii < r / 1000
+h1 = hist(ii[I],breaks=(0:r/1000))
+lo <- loess(h1$density ~ c(1:length(h1$density))) #loess smothing over density
+plot(h1$density, main="Density")
+lines(predict(lo),col='red',lwd=2)
+m = h1$mids[which.min(predict(lo))]
+I1 = ((ii < m)&(ii >= 0))
+
+h = hist(ii, breaks=100,plot=FALSE)
+I2 = ((ii >= m)&(ii < h$mids[max(which(h$counts>5))]))
+f1 = (sum(I1) + sum(ii == 0))/nG
+f2 = (sum(I2))/nG
+
+d1 = fitdistr(ii[I1], "exponential")
+d2 = fitdistr(ii[I2], "gamma") #fit curves
+
+# print pdf of histogram
+#pdf("Loess_and_changepoint_estimation.pdf")
+
+#plots
+hist(ii,breaks=200, xlim=c(0,0.1), freq=FALSE,xlab="Insertion index", main="Gamma fits")
+lines(0:50/500, f1*dgamma(0:50/500, 1, d1$estimate[1])) # was [2]
+lines(0:50/500, f2*dgamma(0:50/500, d2$estimate[1], d2$estimate[2]))
+# print changepoint
+
+#calculate log-odds ratios to choose thresholds
+lower <- max(which(log((pgamma(1:500/10000, d2$e[1],d2$e[2])*(1-pgamma(1:500/10000, 1,d1$e[1], lower.tail=FALSE)))/(pgamma(1:500/10000, 1,d1$e[1], lower.tail=FALSE)*(1-pgamma(1:500/10000, d2$e[1],d2$e[2]))) , base=2) < -2))
+upper <- min(which(log((pgamma(1:500/10000, d2$e[1],d2$e[2])*(1-pgamma(1:500/10000, 1,d1$e[1], lower.tail=FALSE)))/(pgamma(1:500/10000, 1,d1$e[1], lower.tail=FALSE)*(1-pgamma(1:500/10000, d2$e[1],d2$e[2]))) , base=2) > 2))
+
+essen <- lower/10000
+ambig <- upper/10000
+
+lines(c(lower/10000, lower/10000), c(0,20), col="red")
+lines(c(upper/10000, upper/10000), c(0,20), col="red")
+
+mtext(paste(essen, ":", "Essential changepoint"), side=3, adj=1, padj=2)
+mtext(paste(ambig, ":", "Ambiguous changepoint"), side=3, adj=1, padj=3.75)
+dev.off()
+
+
+write.csv(STM_baseline, file=paste(input, "all", "csv", sep="."), row.names = FALSE, col.names= TRUE, quote=FALSE)
+write.csv(STM_baseline[STM_baseline$ins_index < essen,], file=paste(input, "essen", "csv", sep="."), row.names = FALSE, col.names= TRUE, quote=FALSE)
+write.csv(STM_baseline[STM_baseline$ins_index >= essen & STM_baseline$ins_index < ambig,], file=paste(input, "ambig", "csv", sep="."), row.names = FALSE, col.names= TRUE, quote=FALSE)
+
+
diff --git a/bin/tradis_gene_insert_sites b/bin/tradis_gene_insert_sites
new file mode 100755
index 0000000..29446c5
--- /dev/null
+++ b/bin/tradis_gene_insert_sites
@@ -0,0 +1,329 @@
+#!/usr/bin/env perl
+
+package Bio::Tradis::Bin::GeneInsertSites;
+
+# ABSTRACT: Generate insertion site details from TraDIS pipeline plots
+
+# PODNAME: tradis_gene_insert_sites
+
+=head1 NAME
+
+tradis_gene_insert_sites.pl
+
+=head1 SYNOPSIS
+
+=head1 DESCRIPTION
+
+This script is for TRADIS analysis. It takes in a plot file created by the TRADIS pathogen informatics pipeline, and an embl file of
+annotation.
+It then outputs a tab delimited file with the insert site details. This is then used as input to an R script to calculate essentialit
+y.
+
+=head1 CONTACT
+
+path-help at sanger.ac.uk
+Original author: Lars Barquist
+
+=head1 METHODS
+
+=cut
+
+use strict;
+use warnings;
+no warnings 'uninitialized';
+use Bio::SeqIO;
+use Getopt::Long;
+use Text::CSV;
+use File::Basename;
+use Data::Dumper;
+
+my ($help,$output_suffix,$trim5,$trim3,$joined_output);
+
+GetOptions(
+ 'o|output_suffix=s' => \$output_suffix,
+ 'trim5=f' => \$trim5,
+ 'trim3=f' => \$trim3,
+ 'j|joined_output' => \$joined_output,
+ 'h|help' => \$help,
+);
+
+my $usage = qq[
+Take in a plot file(s) and an embl file and produce a tab delimited file with insert site details to use as input to an R script to t
+est for essentiality.
+
+Usage: tradis_gene_insert_sites
+ -o|output_suffix <suffix to add to output files (optional, default = tradis_gene_insert_sites.csv)>
+ -trim5 <trim insertion sites from 5' end of gene (optional, default = 0)>
+ -trim3 <trim insertion sites from 3' end of gene (optional, default = 0)>
+ -j|joined_output <output a single file with all info. default = one file per input file>
+ -h|help <display this message>
+
+tradis_gene_insert_sites my_annotation.embl my_insert_site_plot.gz
+
+tradis_gene_insert_sites my_annotation.embl my_insert_site_plot
+
+# multiple plot files
+tradis_gene_insert_sites my_annotation.embl plot1.gz plot2.gz plot3.gz plot4.gz
+
+# specifiy an output suffix
+# this will result in a file named my_insert_site_plot1.my_output.csv
+tradis_gene_insert_sites -o my_output.csv my_annotation.embl my_insert_site_plot1
+
+# Trim insertion sites from start or end of gene
+tradis_gene_insert_sites my_annotation.embl -trim5 0.1 -trim3 0.1 my_annotation.embl my_insert_site_plot.gz
+
+The trim parameter is the fraction of the gene length trimmed.
+
+# place all info into a single file
+tradis_gene_insert_sites -o output_suffix.csv -j my_annotation.embl plot1.gz plot2.gz plot3.gz
+
+Resulting file: joined_output.output_suffix.csv
+
+];
+
+
+$output_suffix ||= "tradis_gene_insert_sites.csv";
+$trim5 ||= 0;
+$trim3 ||= 0;
+
+( !$help
+ && scalar( @ARGV ) >= 2
+ && $trim5 >= 0 && $trim5 < 1
+ && $trim3 >= 0 && $trim3 < 1 ) or die $usage;
+
+my $embl_file = shift @ARGV;
+my $cds_coordinates = cds_locations($embl_file);
+my $annotation_file = Bio::SeqIO->new(-file => $embl_file, -format => 'EMBL') or die "Error: Couldnt open the annotation file\n";
+
+
+my @out_list = create_output_files( \@ARGV, $joined_output, $output_suffix );
+my @ins_list = prepare_inputs( \@ARGV, $joined_output );
+
+my $loop_index = 0;
+for my $insert_sites ( @ins_list ){
+ my $output_filename = $out_list[$loop_index];
+ open(my $out_fh, "+>", $output_filename) or die "Couldnt open output file\n";
+ my $csv = Text::CSV->new ( { binary => 1, sep_char => "\t" } ) or die "";
+ $csv->eol("\n");
+ $csv->print($out_fh, output_header());
+
+ while (my $sequence_annotation = $annotation_file->next_seq())
+ {
+ for my $feature ($sequence_annotation->get_SeqFeatures())
+ {
+ next if($feature->primary_tag eq 'gene' && ( is_gene_within_cds($cds_coordinates, $feature) == 1) );
+
+ next if !($feature->primary_tag eq 'CDS' || $feature->primary_tag eq 'polypeptide' || $feature->primary_tag eq 'gene');
+ my $feature_id = get_feature_id($feature);
+ my $gene_name = get_gene_name($feature);
+ my $product_value = get_product_value($feature);
+ my $rna_value = get_rna_value($feature);
+
+ # Trim insertion sites from start or end of gene
+ # Number of bases trimmed are -trim5 or -trim3 parameters multiplied by gene length.
+ my ($read_start,$read_end);
+ if($feature->strand == 1){
+ $read_start = $feature->start + int($trim5 * ($feature->end - $feature->start + 1));
+ $read_end = $feature->end - int($trim3 * ($feature->end - $feature->start + 1));
+ }else {
+ $read_start = $feature->start + int($trim3 * ($feature->end - $feature->start + 1));
+ $read_end = $feature->end - int($trim5 * ($feature->end - $feature->start + 1));
+ }
+
+ my $count = 0;
+ my $inserts = 0;
+ for(my $j=$read_start;$j < $read_end; $j++){
+ $count += $insert_sites->[$j];
+ $inserts += 1 if $insert_sites->[$j] > 0;
+ }
+ my $ins_index = $inserts / ($read_end - $read_start + 1);
+
+ my $row = [$feature_id,$gene_name,$rna_value,$feature->start,$feature->end,$feature->strand,$count,$ins_index, ($feature->end - $
+ feature->start + 1),$inserts,$product_value];
+ $csv->print($out_fh, $row);
+ }
+ }
+ close($out_fh);
+ $loop_index++;
+}
+
+sub prepare_inputs {
+ my ( $files, $joined_output ) = @_;
+
+ if( $joined_output ){
+ my $insert_sites;
+ for my $f ( @{ $files } ) {
+ $insert_sites = read_in_plot_file( $f, $insert_sites );
+ }
+ return ($insert_sites);
+ }
+ else {
+ my @ins_list;
+ for my $f ( @{ $files } ){
+ push( @ins_list, read_in_plot_file( $f, [] ) );
+ }
+ return @ins_list;
+ }
+}
+
+sub create_output_files {
+ my ( $files, $joined_output, $output_suffix ) = @_;
+
+ return ("joined_output.$output_suffix") if ( $joined_output );
+
+ my @outfiles;
+ for my $f ( @{ $files } ){
+ my $basename = fileparse( $f, '.gz' );
+ $basename =~ s/\.insert_site_plot//;
+ push( @outfiles, "$basename.$output_suffix" );
+ }
+ return @outfiles;
+}
+
+sub is_gene_within_cds
+{
+ my($cds_coordinates, $gene_feature) = @_;
+ for my $current_coords(@{$cds_coordinates})
+ {
+ next if( $current_coords->[0] > $gene_feature->start);
+ next if( $current_coords->[1] < $gene_feature->end);
+ return 1;
+ }
+
+ return 0;
+}
+
+sub cds_locations
+{
+ my($embl_file) = @_;
+ my @cds_coordinates;
+
+ my $annotation_file = Bio::SeqIO->new(-file => $embl_file, -format => 'EMBL') or die "Error: Couldnt open the annotation file\n";
+ while (my $sequence_annotation = $annotation_file->next_seq())
+ {
+ for my $feature ($sequence_annotation->get_SeqFeatures())
+ {
+ next if !($feature->primary_tag eq 'CDS');
+ push(@cds_coordinates, [$feature->start,$feature->end]);
+ }
+ }
+ return \@cds_coordinates;
+}
+
+
+sub get_feature_id
+{
+ my($feature) = @_;
+ my $feature_id = int(rand(10000));
+ my @junk;
+ if($feature->has_tag('locus_tag'))
+ {
+ ($feature_id, @junk) = $feature->get_tag_values('locus_tag');
+ }
+ elsif($feature->has_tag('ID'))
+ {
+ ($feature_id, @junk) = $feature->get_tag_values('ID');
+ }
+ elsif($feature->has_tag('systematic_id'))
+ {
+ ($feature_id, @junk) = $feature->get_tag_values('systematic_id');
+ }
+ else
+ {
+ $feature_id = join("_",($feature->seq_id(), $feature->strand, $feature->start, $feature->end ));
+ }
+ $feature_id =~ s/^"|"$//g;
+ return $feature_id ;
+}
+
+sub get_gene_name
+{
+ my($feature) = @_;
+ my $gene_name;
+ my @junk;
+ if($feature->has_tag('gene'))
+ {
+ ($gene_name, @junk) = $feature->get_tag_values('gene');
+ }
+ else
+ {
+ $gene_name = get_feature_id($feature);
+ }
+ $gene_name =~ s/\W//g;
+ return $gene_name;
+}
+
+sub get_product_value
+{
+ my($feature) = @_;
+ my $product = "";
+ my @junk;
+ if($feature->has_tag('product'))
+ {
+ ($product, @junk) = $feature->get_tag_values('product');
+ }
+ my $pseudo_gene = get_pseudo_gene_value($feature);
+ if(defined($pseudo_gene))
+ {
+ return $pseudo_gene;
+ }
+
+ return $product;
+}
+
+sub read_in_plot_file
+{
+ my($plot_filename,$read_ar) = @_;
+
+ my $fh;
+
+ if($plot_filename =~ m/gz$/)
+ {
+ open($fh, "-|",'gunzip -c '.$plot_filename) or die "Couldnt open plot file\n";
+ }
+ else
+ {
+ open($fh, $plot_filename) or die "Couldnt open plot file\n";
+ }
+ my $i = 0;
+ while(<$fh>)
+ {
+ chomp;
+ my @inserts_per_base = split /\s/, $_;
+ my $combined_insert_for_base = $inserts_per_base[0] + $inserts_per_base[1];
+ if(defined($read_ar->[$i]))
+ {
+ $read_ar->[$i] += $combined_insert_for_base;
+ }
+ else
+ {
+ push(@{$read_ar}, $combined_insert_for_base);
+ }
+ $i++;
+ }
+ close($fh);
+ return $read_ar;
+}
+
+sub get_rna_value
+{
+ my($feature) = @_;
+
+ return 1 if($feature->has_tag('ncRNA'));
+ return 0;
+}
+
+sub get_pseudo_gene_value
+{
+ my($feature) = @_;
+ if($feature->has_tag('pseudo'))
+ {
+ return "pseudogene";
+ }
+ return undef;
+}
+
+sub output_header
+{
+ ['locus_tag','gene_name','ncrna','start','end','strand','read_count','ins_index','gene_length','ins_count','fcn'];
+}
diff --git a/bin/tradis_merge_plots b/bin/tradis_merge_plots
new file mode 100755
index 0000000..05c1109
--- /dev/null
+++ b/bin/tradis_merge_plots
@@ -0,0 +1,98 @@
+#!/usr/bin/env perl
+
+package Bio::Tradis::Bin::MergePlots;
+
+# ABSTRACT:
+
+# PODNAME: tradis_merge_plots
+
+=head1 NAME
+
+tradis_merge_plots
+
+=head1 SYNOPSIS
+
+tradis_merge_plots - Given a study name or ID, group by sample and tag, and generate tab files for input to R.
+
+=head1 DESCRIPTION
+
+Given a study name or ID, group by sample and tag, and generate tab files for input to R.
+
+=head1 CONTACT
+
+path-help at sanger.ac.uk
+
+=head1 METHODS
+
+=cut
+
+package TraDISMergePlots::Main;
+
+use Moose;
+use Getopt::Long;
+use File::Basename;
+my ( $study, $help );
+
+GetOptions(
+ 'h|help' => \$help,
+);
+
+
+( defined($ARGV[0]) && !$help ) or die <<USAGE;
+Usage: tradis_merge_plots [options]
+Given a study name or ID, group by sample and tag, and generate tab files for input to R.
+
+# run over sequencescape study 1234
+tradis_merge_plots 1234
+
+# Provide a name instead of a study ID
+tradis_merge_plots "My Study"
+
+# This help message
+tradis_merge_plots -h
+
+USAGE
+$study = $ARGV[0];
+
+
+open(my $coverage_plots_fh, '-|', 'tradisfind -t study -i "'.$study.'" -d');
+
+my %coverage_plots;
+while(<$coverage_plots_fh>)
+{
+ my $line = $_;
+ chomp($line);
+ my @full_details = split("\t", $line);
+ my @file_path_details = split('/', $full_details[0]);
+ my @lane_details = split('#',$file_path_details[14]);
+ $full_details[1] =~ s!\.gff!.embl!i;
+
+ # library name, path to annotation, tag number => path
+ if(! defined($coverage_plots{$file_path_details[13]}{$full_details[1]}{$lane_details[1]}) )
+ {
+ my @plots;
+ push(@plots, $full_details[0]);
+ $coverage_plots{$file_path_details[13]}{$full_details[1]}{$lane_details[1]} = \@plots;
+ }
+ else
+ {
+ push(@{$coverage_plots{$file_path_details[13]}{$full_details[1]}{$lane_details[1]}},$full_details[0]);
+ }
+}
+
+for my $library_name (keys %coverage_plots)
+{
+ for my $path_to_annotation (keys %{$coverage_plots{$library_name}})
+ {
+ my $annotation_name = fileparse( $path_to_annotation );
+ for my $tag (keys %{$coverage_plots{$library_name}{$path_to_annotation}})
+ {
+ my $joined_plots = join(' ', @{$coverage_plots{$library_name}{$path_to_annotation}{$tag}});
+
+ my $outputfilename = join("_",($library_name, $tag,$annotation_name));
+ my $cmd = join(" ", ("tradis_gene_insert_sites", '-o', $outputfilename.'.csv', $path_to_annotation, $joined_plots ));
+ `bsub -M1000 -R 'select[mem>1000] rusage[mem=1000]' '$cmd'`;
+ print "Output from bsub will be in: ".$outputfilename.'.csv'."\n";
+ }
+ }
+}
diff --git a/bin/tradis_plot b/bin/tradis_plot
new file mode 100755
index 0000000..ce00c9e
--- /dev/null
+++ b/bin/tradis_plot
@@ -0,0 +1,21 @@
+#!/usr/bin/env perl
+
+package Bio::Tradis::Bin::TradisPlot;
+
+# ABSTRACT: Generate plots as part of a tradis analysis
+# PODNAME: tradis_plot
+
+=head1 SYNOPSIS
+
+Generate insertion plots for Artemis from a mapped fastq file and
+a reference in GFF format
+
+=cut
+
+BEGIN { unshift( @INC, '../lib' ) }
+BEGIN { unshift( @INC, './lib' ) }
+BEGIN { unshift( @INC, '/software/pathogen/internal/prod/lib/' ) }
+
+use Bio::Tradis::CommandLine::PlotTradis;
+
+Bio::Tradis::CommandLine::PlotTradis->new(args => \@ARGV, script_name => $0)->run;
diff --git a/dist.ini b/dist.ini
new file mode 100644
index 0000000..623def7
--- /dev/null
+++ b/dist.ini
@@ -0,0 +1,60 @@
+name = Bio-Tradis
+author = Carla Cummins <path-help at sanger.ac.uk>
+license = GPL_3
+copyright_holder = Wellcome Trust Sanger Institute
+copyright_year = 2013
+version = 1.3.1
+
+[MetaResources]
+homepage = http://www.sanger.ac.uk/
+repository.web = https://github.com/sanger-pathogens/Bio-Tradis
+repository.url = https://github.com/sanger-pathogens/Bio-Tradis.git
+repository.type = git
+
+[RequiresExternal]
+requires = awk
+requires = samtools
+requires = gunzip
+requires = gzip
+requires = smalt
+requires = tabix
+
+[@Git]
+[@Starter]
+[RunExtraTests]
+[AutoPrereqs]
+
+[FileFinder::ByName / BinNotR]
+dir = bin
+skip = .*\.R$
+
+[PodWeaver]
+finder = :InstallModules
+finder = BinNotR
+
+[PkgVersion]
+
+[Encoding]
+filename = t/data/AddTags/expected_tradis.bam
+filename = t/data/AddTags/sample_sm_tr.bam
+filename = t/data/AddTags/sample_sm_no_tr.bam
+filename = t/data/CombinePlots/sample1.sm.plot.gz
+filename = t/data/CombinePlots/sample2.sm.plot.gz
+filename = t/data/DetectTags/sample_sm_tr.bam
+filename = t/data/DetectTags/sample_sm_no_tr.bam
+filename = t/data/FilterTags/sample.fastq.gz
+filename = t/data/InsertSite/small_multi_sequence.bam
+filename = t/data/Parsers/test.bam
+filename = t/data/RunTradis/expected.1mm.plot.gz
+filename = t/data/RunTradis/expected.plot.gz
+filename = t/data/RunTradis/test.tagged.fastq.gz
+filename = t/data/RunTradis/test2.tagged.fastq.gz
+filename = t/data/TradisPlot/expected.plot.gz
+filename = t/data/TradisPlot/test.mapped.bam
+filename = t/data/AddTags/expected_tradis.cram
+filename = t/data/DetectTags/sample_sm_tr.cram
+filename = t/data/AddTags/sample_sm_tr.cram
+filename = t/data/CombinePlots/tabix_sorted.insert_site_plot.gz.tbi
+filename = t/data/CombinePlots/tabix_sorted.insert_site_plot.gz
+filename = t/data/InsertSite/2_reads.bam
+encoding = bytes
diff --git a/install_dependencies.sh b/install_dependencies.sh
new file mode 100755
index 0000000..9a2d133
--- /dev/null
+++ b/install_dependencies.sh
@@ -0,0 +1,110 @@
+#!/bin/bash
+
+set -x
+set -e
+
+start_dir=$(pwd)
+
+SMALT_VERSION="0.7.6"
+TABIX_VERSION="master"
+SAMTOOLS_VERSION="1.3"
+
+SMALT_DOWNLOAD_URL="http://downloads.sourceforge.net/project/smalt/smalt-${SMALT_VERSION}-bin.tar.gz"
+TABIX_DOWNLOAD_URL="https://github.com/samtools/tabix/archive/${TABIX_VERSION}.tar.gz"
+SAMTOOLS_DOWNLOAD_URL="https://github.com/samtools/samtools/releases/download/${SAMTOOLS_VERSION}/samtools-${SAMTOOLS_VERSION}.tar.bz2"
+
+# Make an install location
+if [ ! -d 'build' ]; then
+ mkdir build
+fi
+cd build
+build_dir=$(pwd)
+
+# DOWNLOAD ALL THE THINGS
+download () {
+ url=$1
+ download_location=$2
+
+ if [ -e $download_location ]; then
+ echo "Skipping download of $url, $download_location already exists"
+ else
+ echo "Downloading $url to $download_location"
+ wget $url -O $download_location
+ fi
+}
+
+download $SMALT_DOWNLOAD_URL "smalt-${SMALT_VERSION}.tgz"
+download $TABIX_DOWNLOAD_URL "tabix-${TABIX_VERSION}.tgz"
+download $SAMTOOLS_DOWNLOAD_URL "samtools-${SAMTOOLS_VERSION}.tbz"
+
+# Update dependencies
+if [ "$TRAVIS" = 'true' ]; then
+ echo "Using Travis's apt plugin"
+else
+ sudo apt-get update -q
+ sudo apt-get install -y -q zlib1g-dev
+fi
+
+# Build all the things
+## smalt
+cd $build_dir
+smalt_dir=$(pwd)/"smalt-${SMALT_VERSION}-bin"
+if [ ! -d $smalt_dir ]; then
+ tar xzfv smalt-${SMALT_VERSION}.tgz
+fi
+cd $smalt_dir
+if [ ! -e "$smalt_dir/smalt" ]; then
+ ln "$smalt_dir/smalt_x86_64" "$smalt_dir/smalt"
+fi
+
+## tabix
+cd $build_dir
+tabix_dir=$(pwd)/"tabix-$TABIX_VERSION"
+if [ ! -d $tabix_dir ]; then
+ tar xzfv "${build_dir}/tabix-${TABIX_VERSION}.tgz"
+fi
+cd $tabix_dir
+if [ -e ${tabix_dir}/tabix ]; then
+ echo "Already built tabix"
+else
+ echo "Building tabix"
+ make
+fi
+
+## samtools
+cd $build_dir
+samtools_dir=$(pwd)/"samtools-$SAMTOOLS_VERSION"
+if [ ! -d $samtools_dir ]; then
+ tar xjfv "${build_dir}/samtools-${SAMTOOLS_VERSION}.tbz"
+fi
+cd $samtools_dir
+if [ -e ${samtools_dir}/samtools ]; then
+ echo "Already built samtools"
+else
+ echo "Building samtools"
+ sed -i 's/^\(DFLAGS=.\+\)-D_CURSES_LIB=1/\1-D_CURSES_LIB=0/' Makefile
+ sed -i 's/^\(LIBCURSES=\)/#\1/' Makefile
+ make prefix=${samtools_dir} install
+fi
+
+# Setup environment variables
+update_path () {
+ new_dir=$1
+ if [[ ! "$PATH" =~ (^|:)"${new_dir}"(:|$) ]]; then
+ export PATH=${new_dir}:${PATH}
+ fi
+}
+
+update_path ${smalt_dir}
+update_path "${tabix_dir}"
+update_path "${samtools_dir}"
+
+cd $start_dir
+
+# Install perl dependencies
+cpanm Dist::Zilla
+dzil authordeps --missing | cpanm
+dzil listdeps --missing | cpanm
+
+set +x
+set +e
diff --git a/lib/Bio/Tradis.pm b/lib/Bio/Tradis.pm
new file mode 100644
index 0000000..454714e
--- /dev/null
+++ b/lib/Bio/Tradis.pm
@@ -0,0 +1,31 @@
+use strict;
+use warnings;
+package Bio::Tradis;
+
+# ABSTRACT: Bio-Tradis contains a set of tools to analyse the output from TraDIS analyses. For more information on the TraDIS method, see http://genome.cshlp.org/content/19/12/2308
+
+=head1 SYNOPSIS
+
+Bio-Tradis provides functionality to:
+
+=over
+
+=item * detect TraDIS tags in a BAM file - L<Bio::Tradis::DetectTags>
+
+=item * add the tags to the reads - L<Bio::Tradis::AddTagsToSeq>
+
+=item * filter reads in a FastQ file containing a user defined tag - L<Bio::Tradis::FilterTags>
+
+=item * remove tags - L<Bio::Tradis::RemoveTags>
+
+=item * map to a reference genome - L<Bio::Tradis::Map>
+
+=item * create an insertion site plot file - L<Bio::Tradis::TradisPlot>
+
+=back
+
+Most of these functions are available as standalone scripts or as perl modules.
+
+
+=cut
+1;
diff --git a/lib/Bio/Tradis/AddTagsToSeq.pm b/lib/Bio/Tradis/AddTagsToSeq.pm
new file mode 100644
index 0000000..a4a1dd6
--- /dev/null
+++ b/lib/Bio/Tradis/AddTagsToSeq.pm
@@ -0,0 +1,203 @@
+package Bio::Tradis::AddTagsToSeq;
+
+# ABSTRACT: Takes a BAM file and creates a new BAM with tr and tq tags added to the sequence and quality strings.
+
+=head1 NAME
+
+Bio::Tradis::AddTagsToSeq
+
+=head1 SYNOPSIS
+
+Bio::Tradis::AddTagsToSeq parses BAM files, adds given tags to the start of the sequence and creates temporary SAM file,
+which is then converted to BAM
+
+ use Bio::Tradis::AddTagsToSeq;
+
+ my $pipeline = Bio::Tradis::AddTagsToSeq->new(bamfile => 'abc');
+ $pipeline->add_tags_to_seq();
+
+=head1 PARAMETERS
+
+=head2 Required
+
+C<bamfile> - path to/name of file containing reads and tags
+
+=head2 Optional
+
+C<outfile> - name to assign to output BAM. Defaults to C<file.tr.bam> for an input file named C<file.bam>
+
+=head1 METHODS
+
+C<add_tags_to_seq> - add TraDIS tags to reads. For unmapped reads, the tag
+ is added to the start of the read sequence and quality
+ strings. For reads where the flag indicates that it is
+ mapped and reverse complemented, the reverse complemented
+ tags are added to the end of the read strings.
+ This is because many conversion tools (e.g. picard) takes
+ the read orientation into account and will re-reverse the
+ mapped/rev comp reads during conversion, leaving all tags
+ in the correct orientation at the start of the sequences
+ in the resulting FastQ file.
+
+=cut
+
+use Moose;
+use Bio::Seq;
+use Bio::Tradis::Parser::Bam;
+use File::Basename;
+
+no warnings qw(uninitialized);
+
+has 'verbose' => ( is => 'rw', isa => 'Bool', default => 0 );
+has 'samtools_exec' => ( is => 'rw', isa => 'Str', default => 'samtools' );
+has 'bamfile' => ( is => 'rw', isa => 'Str', required => 1 );
+has 'outfile' => (
+ is => 'rw',
+ isa => 'Str',
+ required => 0,
+ default => sub {
+ my ($self) = @_;
+ my $o = $self->bamfile;
+ $o =~ s/\.bam/\.tr\.bam/;
+ $o =~ s/\.cram/\.tr\.cram/;
+ return $o;
+ }
+);
+
+has '_file_extension' => ( is => 'rw', isa => 'Str', lazy => 1, builder => '_build__file_extension' );
+has 'extension_to_output_switch' => ( is => 'rw', isa => 'HashRef', default => sub{ {cram => '-C', bam => '-b'} } );
+
+sub _build__file_extension
+{
+ my ($self) = @_;
+ my($filename, $dirs, $suffix) = fileparse($self->bamfile,qr/[^.]*/);
+ return lc($suffix);
+}
+
+sub add_tags_to_seq {
+ my ($self) = @_;
+
+ #set up BAM parser
+ my $filename = $self->bamfile;
+ my $outfile = $self->outfile;
+
+ #open temp file in SAM format and output headers from current BAM to it
+ print STDERR "Reading ".uc($self->_file_extension)." header\n" if($self->verbose);
+ system($self->samtools_exec." view -H $filename > tmp.sam");
+ open( TMPFILE, '>>tmp.sam' );
+
+ #open BAM file
+ print STDERR "Reading ".uc($self->_file_extension)." file\n" if($self->verbose);
+ my $pars = Bio::Tradis::Parser::Bam->new( file => $filename, samtools_exec => $self->samtools_exec );
+ my $read_info = $pars->read_info;
+
+ while ( $pars->next_read ) {
+ my $read_info = $pars->read_info;
+ my $line = ${$read_info}{READ};
+
+ # get tags, seq, qual and cigar str
+ my $trtag = ${$read_info}{tr};
+ my $tqtag = ${$read_info}{tq};
+
+ my $seq_tagged = ${$read_info}{SEQ};
+ my $qual_tagged = ${$read_info}{QUAL};
+ my $cigar_update = ${$read_info}{CIGAR};
+
+ #Check if seq is mapped & rev complement. If so, reformat.
+ my $mapped = $pars->is_mapped;
+ my $rev = $pars->is_reverse;
+ if ( $mapped && $rev ) {
+
+ # The transposon is not reverse complimented but the genomic read is
+
+ # reverse the genomic quality scores.
+ $qual_tagged = reverse($qual_tagged);
+
+ # Add the transposon quality score on the beginning
+ $qual_tagged = $tqtag . $qual_tagged;
+
+ # Reverse the whole quality string.
+ $qual_tagged = reverse($qual_tagged);
+
+ # Reverse the genomic sequence
+ my $genomic_seq_obj =
+ Bio::Seq->new( -seq => $seq_tagged, -alphabet => 'dna' );
+ my $reversed_genomic_seq_obj = $genomic_seq_obj->revcom;
+
+ # Add on the tag sequence
+ $seq_tagged = $trtag . $reversed_genomic_seq_obj->seq;
+
+ # Reverse the tag+genomic sequence to get it back into the correct orentation.
+ my $genomic_and_tag_seq_obj =
+ Bio::Seq->new( -seq => $seq_tagged, -alphabet => 'dna' );
+ $seq_tagged = $genomic_and_tag_seq_obj->revcom->seq;
+
+ }
+ else {
+ #print STDERR "$line\n" if(!defined($tqtag));
+ $seq_tagged = $trtag . $seq_tagged;
+ $qual_tagged = $tqtag . $qual_tagged;
+ }
+
+ if ($mapped) {
+ my $cigar = length($seq_tagged);
+ $cigar_update = $cigar . 'M';
+ }
+ else {
+ $cigar_update = '*';
+ }
+
+ # replace updated fields and print to TMPFILE
+ my @cols = split( " ", $line );
+ $cols[5] = $cigar_update;
+ $cols[9] = $seq_tagged;
+ $cols[10] = $qual_tagged;
+
+ print TMPFILE join( "\t", @cols ) . "\n";
+ }
+ $pars->close_file_handle;
+ close TMPFILE;
+
+ #convert tmp.sam to bam
+ print STDERR "Convert SAM to ".uc($self->_file_extension)."\n" if($self->verbose);
+
+
+ system($self->samtools_exec." view -h -S ".$self->_output_switch." -o $outfile tmp.sam");
+
+ if ( $self->_number_of_lines_in_bam_file($outfile) !=
+ $self->_number_of_lines_in_bam_file($filename) )
+ {
+ die
+"The number of lines in the input and output files don't match, so something's gone wrong\n";
+ }
+
+ #remove tmp file
+ unlink("tmp.sam");
+ return 1;
+}
+
+sub _output_switch
+{
+ my ( $self ) = @_;
+ if(defined($self->extension_to_output_switch->{$self->_file_extension}))
+ {
+ return $self->extension_to_output_switch->{$self->_file_extension};
+ }
+ else
+ {
+ return '';
+ }
+}
+
+sub _number_of_lines_in_bam_file {
+ my ( $self, $filename ) = @_;
+ open( my $fh, '-|', $self->samtools_exec." view $filename | wc -l" )
+ or die "Couldn't open file :" . $filename;
+ my $number_of_lines_in_file = <$fh>;
+ $number_of_lines_in_file =~ s!\W!!gi;
+ return $number_of_lines_in_file;
+}
+
+__PACKAGE__->meta->make_immutable;
+no Moose;
+1;
diff --git a/lib/Bio/Tradis/Analysis/Exceptions.pm b/lib/Bio/Tradis/Analysis/Exceptions.pm
new file mode 100644
index 0000000..6f1a9a4
--- /dev/null
+++ b/lib/Bio/Tradis/Analysis/Exceptions.pm
@@ -0,0 +1,20 @@
+package Bio::Tradis::Analysis::Exceptions;
+# ABSTRACT: Custom exceptions
+
+=head1 SYNOPSIS
+
+Basic exception catcher
+
+=cut
+
+use Exception::Class (
+ Bio::Tradis::Analysis::Exceptions::FailedToOpenAlignmentSlice => { description => 'Couldnt get reads from alignment slice. Error with Samtools or BAM' },
+ Bio::Tradis::Analysis::Exceptions::FailedToOpenExpressionResultsSpreadsheetForWriting => { description => 'Couldnt write out the results for expression' },
+ Bio::Tradis::Analysis::Exceptions::InvalidInputFiles => { description => 'Invalid inputs, sequence names or lengths are incorrect' },
+ Bio::Tradis::Analysis::Exceptions::FailedToCreateNewBAM => { description => 'Couldnt create a new bam file' },
+ Bio::Tradis::Analysis::Exceptions::FailedToCreateMpileup => { description => 'Couldnt create an mpileup' },
+ Bio::Tradis::Analysis::Exceptions::FailedToOpenFeaturesTabFileForWriting => { description => 'Couldnt write tab file' },
+ Bio::Tradis::Analysis::Exceptions::FileNotFound => { description => 'Couldnt find file' },
+);
+
+1;
diff --git a/lib/Bio/Tradis/Analysis/InsertSite.pm b/lib/Bio/Tradis/Analysis/InsertSite.pm
new file mode 100644
index 0000000..9c4eff1
--- /dev/null
+++ b/lib/Bio/Tradis/Analysis/InsertSite.pm
@@ -0,0 +1,207 @@
+package Bio::Tradis::Analysis::InsertSite;
+# ABSTRACT: Take in a bam file and plot the start position of each read
+
+=head1 NAME
+
+InsertSite.pm - Take in a bam file and plot the start position of each read
+
+=head1 SYNOPSIS
+
+Takes in a mapped BAM file and plot the start position of each read
+
+ use Bio::Tradis::Analysis::InsertSite;
+ my $insertsite_plots_from_bam = Bio::Tradis::Analysis::InsertSite->new(
+ filename => 'my_file.bam',
+ output_base_filename => 'my_output_file'
+ );
+ $insertsite_plots_from_bam->create_plots();
+
+
+=cut
+
+
+use Moose;
+use Bio::Tradis::Parser::Bam;
+use Bio::Tradis::Parser::Cigar;
+
+has 'filename' => ( is => 'rw', isa => 'Str', required => 1 );
+has 'output_base_filename' => ( is => 'rw', isa => 'Str', required => 1 );
+has 'mapping_score' => ( is => 'ro', isa => 'Int', required => 1 );
+has 'samtools_exec' => ( is => 'ro', isa => 'Str', default => 'samtools' );
+has '_output_file_handles' => ( is => 'rw', isa => 'HashRef', lazy_build => 1 );
+has '_sequence_names' => ( is => 'rw', isa => 'ArrayRef', lazy_build => 1 );
+has '_sequence_base_counters' =>
+ ( is => 'rw', isa => 'HashRef', lazy_build => 1 );
+has '_sequence_information' =>
+ ( is => 'rw', isa => 'HashRef', lazy_build => 1 );
+
+has '_frequency_of_read_start' => (
+ is => 'rw',
+ isa => 'HashRef',
+ lazy => 1,
+ builder => '_build__frequency_of_read_start'
+);
+
+sub _build__sequence_information {
+ my ($self) = @_;
+ my %all_sequences_info =
+ Bio::Tradis::Parser::Bam->new( file => $self->filename, samtools_exec => $self->samtools_exec )->seq_info;
+ return \%all_sequences_info;
+}
+
+sub _build__sequence_names {
+ my ($self) = @_;
+ my @sequence_names = keys %{ $self->_sequence_information };
+ return \@sequence_names;
+}
+
+sub _build__sequence_base_counters {
+ my ($self) = @_;
+ my %sequence_base_counters;
+ for my $sequence_name ( @{ $self->_sequence_names } ) {
+ $sequence_base_counters{$sequence_name} = 0;
+ }
+ return \%sequence_base_counters;
+}
+
+sub _build__output_file_handles {
+ my ($self) = @_;
+ my $out = $self->output_base_filename;
+ chomp $out;
+
+ my %output_file_handles;
+ for my $sequence_name ( @{ $self->_sequence_names } ) {
+ my $file_sequence_name = $sequence_name;
+ $file_sequence_name =~ s/[^\w\d\.]/_/g;
+ my $cmd = "gzip > $out.$file_sequence_name.insert_site_plot.gz";
+ open( $output_file_handles{$sequence_name}, '|-', $cmd )
+ || Bio::Tradis::Analysis::Exceptions::FailedToCreateOutputFileHandle
+ ->throw( error =>
+"Couldnt create output file handle for saving insertsite plot results for "
+ . $sequence_name . " in "
+ . $self->filename
+ . " and output base "
+ . $self->output_base_filename );
+ }
+
+ return \%output_file_handles;
+}
+
+sub _number_of_forward_reads {
+ my ( $self, $sequence_name, $read_coord ) = @_;
+ return $self->_number_of_reads( $sequence_name, $read_coord, 1 );
+}
+
+sub _number_of_reverse_reads {
+ my ( $self, $sequence_name, $read_coord ) = @_;
+ return $self->_number_of_reads( $sequence_name, $read_coord, -1 );
+}
+
+sub _number_of_reads {
+ my ( $self, $sequence_name, $read_coord, $direction ) = @_;
+ if (
+ defined(
+ $self->_frequency_of_read_start->{$sequence_name}{$read_coord}
+ )
+ && defined(
+ $self->_frequency_of_read_start->{$sequence_name}{$read_coord}
+ {$direction}
+ )
+ )
+ {
+ return $self->_frequency_of_read_start->{$sequence_name}{$read_coord}
+ {$direction};
+ }
+ return 0;
+}
+
+# work out if padding is needed and return it as a formatted string
+sub _create_padding_string {
+ my ( $self, $previous_counter, $current_counter ) = @_;
+ my $padding_string = "";
+ for ( my $i = $previous_counter + 1 ; $i < $current_counter ; $i++ ) {
+ $padding_string .= "0 0\n";
+ }
+ return $padding_string;
+}
+
+sub _print_padding_at_end_of_sequence {
+ my ($self) = @_;
+ for my $sequence_name ( @{ $self->_sequence_names } ) {
+ my $sequence_length =
+ $self->_sequence_information->{$sequence_name}->{'LN'};
+ next unless ( $sequence_length =~ /^[\d]+$/ );
+ $sequence_length++;
+ my $padding_string =
+ $self->_create_padding_string(
+ $self->_sequence_base_counters->{$sequence_name},
+ $sequence_length );
+ $self->_sequence_base_counters->{$sequence_name} = $sequence_length;
+ print { $self->_output_file_handles->{$sequence_name} } $padding_string;
+ }
+}
+
+sub _close_output_file_handles {
+ my ($self) = @_;
+ for my $output_file_handle ( values %{ $self->_output_file_handles } ) {
+ close($output_file_handle);
+ }
+ return;
+}
+
+sub _build__frequency_of_read_start {
+ my ($self) = @_;
+ my %frequency_of_read_start;
+ my $samtools_command = join(' ', ($self->samtools_exec, 'view', '-F', 4, '-q', $self->mapping_score, $self->filename));
+
+ open(my $samtools_view_fh,"-|" ,$samtools_command);
+ while(<$samtools_view_fh>)
+ {
+ my $sam_line = $_;
+
+ my @read_details = split("\t", $sam_line);
+ my $seqid = $read_details[2];
+ my $cigar_parser = Bio::Tradis::Parser::Cigar->new(cigar => $read_details[5], coordinate => $read_details[3]);
+ my $strand = 1;
+ $strand = -1 if(($read_details[1] & 0x10) == 0x10);
+
+ if ( $strand == 1 ) {
+ $frequency_of_read_start{$seqid}{ $cigar_parser->start }
+ { $strand }++;
+ }
+ else {
+ $frequency_of_read_start{$seqid}{ $cigar_parser->end }
+ { $strand }++;
+ }
+ }
+ return \%frequency_of_read_start;
+}
+
+sub create_plots {
+ my ($self) = @_;
+ my %read_starts = %{ $self->_frequency_of_read_start };
+ for my $sequence_name ( keys %read_starts ) {
+ my %sequence_read_coords = %{ $read_starts{$sequence_name} };
+ for my $read_coord ( sort { $a <=> $b } ( keys %sequence_read_coords ) )
+ {
+ my $padding_string =
+ $self->_create_padding_string(
+ $self->_sequence_base_counters->{$sequence_name}, $read_coord );
+ $self->_sequence_base_counters->{$sequence_name} = $read_coord;
+
+ my $forward_reads =
+ $self->_number_of_forward_reads( $sequence_name, $read_coord );
+ my $reverse_reads =
+ $self->_number_of_reverse_reads( $sequence_name, $read_coord );
+
+ print { $self->_output_file_handles->{$sequence_name} }
+ $padding_string . $forward_reads . " " . $reverse_reads . "\n";
+ }
+ }
+
+ $self->_print_padding_at_end_of_sequence;
+ $self->_close_output_file_handles;
+ return 1;
+}
+
+1;
diff --git a/lib/Bio/Tradis/CombinePlots.pm b/lib/Bio/Tradis/CombinePlots.pm
new file mode 100644
index 0000000..09d2750
--- /dev/null
+++ b/lib/Bio/Tradis/CombinePlots.pm
@@ -0,0 +1,327 @@
+package Bio::Tradis::CombinePlots;
+
+# ABSTRACT: Combine multiple plotfiles and generate updated statistics for the combined files
+
+=head1 SYNOPSIS
+
+Takes a tab-delimited file with an ID as the first column followed by
+a list of plotfiles to combine per row. The ID will be used to name the new
+plotfile and as an identifier in the stats file, so ensure these are unique.
+
+For example, an input file named plots_to_combine.txt:
+
+ tradis1 plot1.1.gz plot1.2.gz plot1.3.gz
+ tradis2 plot2.1.gz plot2.2.gz
+ tradis3 plot3.1.gz plot3.2.gz plot3.3.gz plot3.4.gz
+
+will produce
+=over
+
+=item 1. a directory named combined with 3 files - tradis1.insertion_site_plot.gz,
+tradis2.insertion_site_plot.gz, tradis3.insertion_site_plot.gz
+=item 2. a stats file named plots_to_combine.stats
+
+=back
+
+=head1 USAGE
+
+ use Bio::Tradis::CombinePlots;
+
+ my $pipeline = Bio::Tradis::CombinePlots->new(plotfile => 'abc');
+ $pipeline->combine;
+
+=cut
+
+use Moose;
+use strict;
+use warnings;
+use File::Temp;
+use File::Path qw( remove_tree );
+use Data::Dumper;
+use Cwd;
+use Bio::Tradis::Analysis::Exceptions;
+
+has 'plotfile' => ( is => 'rw', isa => 'Str', required => 1 );
+has 'combined_dir' => ( is => 'rw', isa => 'Str', default => 'combined' );
+has '_plot_handle' => (
+ is => 'ro',
+ isa => 'FileHandle',
+ required => 0,
+ lazy => 1,
+ builder => '_build__plot_handle'
+);
+has '_stats_handle' => (
+ is => 'ro',
+ isa => 'FileHandle',
+ required => 0,
+ lazy => 1,
+ builder => '_build__stats_handle'
+);
+has '_ordered_plot_ids' => (
+ is => 'rw',
+ isa => 'ArrayRef',
+ required => 0,
+ lazy => 1,
+ builder => '_build__ordered_plot_ids'
+);
+has '_destination' => (
+ is => 'rw',
+ isa => 'Str',
+ required => 0,
+ lazy => 1,
+ builder => '_build__destination'
+);
+
+sub _build__destination {
+ my $tmp_dir = File::Temp->newdir( DIR=> getcwd, CLEANUP => 0 );
+ return $tmp_dir->dirname;
+}
+
+sub _build__stats_handle {
+ my ($self) = @_;
+ my $filelist = $self->plotfile;
+ $filelist =~ s/([^\/]+$)//;
+ my $filename = $1;
+ $filename =~ s/[^\.]+$/stats/;
+ open( my $stats, ">", $filename );
+ return $stats;
+}
+
+sub _build__plot_handle {
+ my ($self) = @_;
+ my $plot = $self->plotfile;
+ open( my $plot_h, "<", $plot );
+ return $plot_h;
+}
+
+sub _build__ordered_plot_ids {
+ my ($self) = @_;
+ my $filelist = $self->plotfile;
+
+ my @id_order = `awk '{print \$1}' $filelist`;
+ foreach my $id (@id_order) {
+ chomp($id);
+ }
+ return \@id_order;
+}
+
+sub combine {
+ my ($self) = @_;
+ my $ordered_keys = $self->_ordered_plot_ids;
+ my $plot_handle = $self->_plot_handle;
+ my $combined_dir = $self->combined_dir;
+
+ $self->_write_stats_header;
+
+
+ system("mkdir $combined_dir") unless ( -d "$combined_dir" );
+ my @tabix_plot;
+
+ while ( my $line = <$plot_handle> ) {
+ #parse line into hash. keys = id, len, files. unzips files if needed.
+ my %plothash = $self->_parse_line($line);
+ my $id = $plothash{'id'};
+
+ #create output plot file
+ my $comb_plot_name = "$combined_dir/$id.insert_site_plot";
+ my $filelen = $plothash{'len'};
+ my ( @currentlines, $this_line );
+
+ my @full_plot;
+ foreach my $i ( 0 .. $filelen ) {
+ @currentlines = ();
+
+ foreach my $curr_fh ( @{ $plothash{'files'} } ) {
+ $this_line = <$curr_fh>;
+ push( @currentlines, $this_line ) if( defined $line && $line ne "");
+ }
+
+ my $comb_line = $self->_combine_lines( \@currentlines );
+
+ my $plot_values_tabix = $comb_line;
+ $plot_values_tabix =~ s/\s/\t/ if(defined $plot_values_tabix && $plot_values_tabix ne "");
+
+ my $tabix_line;
+ if ($id !~ m/^zip_combined/) {
+ my $tabix_line = "$id\t$i\t" . $plot_values_tabix if( defined $plot_values_tabix && $plot_values_tabix ne "");
+ push( @tabix_plot, $tabix_line ) if( $comb_line ne "");
+ }
+
+ push(@full_plot, $comb_line) if ( $comb_line ne '' );
+ }
+
+ open( CPLOT, '>', $comb_plot_name );
+ print CPLOT join("\n", @full_plot);
+ close(CPLOT);
+
+ $self->_write_stats($id, $filelen);
+ system("gzip -f $comb_plot_name");
+ }
+
+
+ if (@tabix_plot) {
+ $self->_prepare_and_create_tabix_for_combined_plots(\@tabix_plot);
+ }
+
+ File::Temp::cleanup();
+ # double check tmp dir is deleted. cleanup not working properly
+ remove_tree($self->_destination);
+ return 1;
+}
+
+sub _prepare_and_create_tabix_for_combined_plots {
+
+ my ($self, $tabix_plot) = @_;
+
+ my $tabix_plot_name = "combined/tabix.insert_site_plot.gz";
+ my $sorted_tabix_plot_name = "combined/tabix_sorted.insert_site_plot.gz";
+
+ open(my $tabix_plot_fh , '|-', " gzip >". $tabix_plot_name) or warn "Couldn't create the initial plot file for tabix";
+ print $tabix_plot_fh join( "\n", @{ $tabix_plot } );
+ close($tabix_plot_fh);
+
+ `cat $tabix_plot_name | gunzip - | sort -k1,1 -k2,2n | bgzip > $sorted_tabix_plot_name && tabix -b 2 -e 2 $sorted_tabix_plot_name`;
+ unlink($tabix_plot_name);
+
+}
+
+
+sub _parse_line {
+ my ( $self, $line ) = @_;
+ chomp $line;
+ my @fields = split( /\s+/, $line );
+ my $id = shift @fields;
+ my @files = @{ $self->_unzip_plots(\@fields) };
+ my $len = $self->_get_file_len( \@files );
+ if ( $len == 0 ){
+ die "\nPlots with ID $id not of equal length.\n";
+ }
+ #build file handles for each file
+ my @file_hs;
+ foreach my $f (@files){
+ open(my $fh, "<", $f);
+ push(@file_hs, $fh);
+ }
+ return ( id => $id, len => $len, files => \@file_hs );
+}
+
+sub _get_file_len {
+ my ( $self, $files ) = @_;
+
+ #check all files are of equal lens and return len if true
+ #wc misses last line - return $l++
+ my @lens;
+ for my $f ( @{$files} ) {
+ my $wc = `wc $f | awk '{print \$1}'`;
+ chomp $wc;
+ push( @lens, $wc );
+ }
+
+ my $l = shift @lens;
+ for my $x (@lens) {
+ return 0 if ( $x != $l );
+ }
+ return $l+1;
+}
+
+sub _combine_lines {
+ my ( $self, $lines ) = @_;
+
+ my @totals = ( 0, 0 );
+ foreach my $l ( @{$lines} ) {
+ if(!defined($l)){
+ return "";
+ next;
+ }
+ my @cols = split( /\s+/, $l );
+ $totals[0] += $cols[0];
+ $totals[1] += $cols[1];
+ }
+ return join( " ", @totals );
+}
+
+sub _write_stats_header {
+ my ($self) = @_;
+ my @fields =
+ ( "ID", "Sequence Length", "Unique Insertion Sites", "Seq Len/UIS" );
+ print { $self->_stats_handle } join( ",", @fields ) . "\n";
+ return 1;
+}
+
+sub _write_stats {
+ my ( $self, $id, $seq_len ) = @_;
+ my $combined_dir = $self->combined_dir;
+ my $comb_plot = "$combined_dir/$id.insert_site_plot";
+
+ #my $seq_len = `wc $comb_plot | awk '{print \$1}'`;
+ #chomp($seq_len);
+ my $uis = `grep -c -v "0 0" $comb_plot`;
+ chomp($uis);
+ my $sl_per_uis = "NaN";
+ $sl_per_uis = $seq_len / $uis if($uis > 0);
+
+ my $stats = "$id,$seq_len,$uis,$sl_per_uis\n";
+ print { $self->_stats_handle } $stats;
+
+ return 1;
+}
+
+sub _abs_path_list {
+ my ( $self, $files ) = @_;
+ my $plot_path = $self->_get_plotfile_path;
+
+ my @pathlist;
+ foreach my $f ( @{$files} ) {
+ if ( $f =~ /^\// ) { push( @pathlist, $f ); }
+ else { push( @pathlist, $plot_path . $f ); }
+ }
+ return \@pathlist;
+}
+
+sub _get_plotfile_path {
+ my ($self) = @_;
+ my $plotfile = $self->plotfile;
+
+ my @dirs = split( '/', $plotfile );
+ pop(@dirs);
+ my $path2plot = join( '/', @dirs );
+ return "$path2plot/";
+}
+
+sub _is_gz {
+ my ( $self, $plotname ) = @_;
+
+ if ( $plotname =~ /\.gz$/ ) {
+ return 1;
+ }
+ else {
+ return 0;
+ }
+}
+
+sub _unzip_plots {
+ my ( $self, $files ) = @_;
+ my $destination_directory = $self->_destination;
+
+ my @filelist = @{ $self->_abs_path_list($files) };
+ my @unz_plots;
+ foreach my $plotname ( @filelist ) {
+ Bio::Tradis::Analysis::Exceptions::FileNotFound->throw("Cannot find $plotname\n") unless ( -e $plotname );
+ if ( $self->_is_gz($plotname) ) {
+ $plotname =~ /([^\/]+$)/;
+ my $unz = $1;
+ $unz =~ s/\.gz//;
+ my $unzip_cmd = "gunzip -c $plotname > $destination_directory/$unz";
+ system($unzip_cmd);
+ push(@unz_plots, "$destination_directory/$unz");
+ }
+ else {
+ push(@unz_plots, $plotname);
+ }
+ }
+ return \@unz_plots;
+}
+
+__PACKAGE__->meta->make_immutable;
+no Moose;
+1;
diff --git a/lib/Bio/Tradis/CommandLine/AddTags.pm b/lib/Bio/Tradis/CommandLine/AddTags.pm
new file mode 100644
index 0000000..ac2564c
--- /dev/null
+++ b/lib/Bio/Tradis/CommandLine/AddTags.pm
@@ -0,0 +1,84 @@
+package Bio::Tradis::CommandLine::AddTags;
+
+# ABSTRACT: Add given tags to the start of the sequence
+
+=head1 SYNOPSIS
+
+Adds given tags to the start of the sequence
+
+=cut
+
+use Moose;
+use Getopt::Long qw(GetOptionsFromArray);
+use Cwd 'abs_path';
+use Bio::Tradis::AddTagsToSeq;
+
+has 'args' => ( is => 'ro', isa => 'ArrayRef', required => 1 );
+has 'script_name' => ( is => 'ro', isa => 'Str', required => 1 );
+has 'bamfile' => ( is => 'rw', isa => 'Str', required => 0 );
+has 'help' => ( is => 'rw', isa => 'Bool', required => 0 );
+has 'outfile' => ( is => 'rw', isa => 'Str', required => 0 );
+
+has 'verbose' => ( is => 'rw', isa => 'Bool', default => 0 );
+has 'samtools_exec' => ( is => 'rw', isa => 'Str', default => 'samtools' );
+
+sub BUILD {
+ my ($self) = @_;
+
+ my ( $bamfile, $outfile, $help, $verbose, $samtools_exec);
+
+ GetOptionsFromArray(
+ $self->args,
+ 'b|bamfile=s' => \$bamfile,
+ 'o|outfile=s' => \$outfile,
+ 'h|help' => \$help,
+ 'v|verbose' => \$verbose,
+ 'samtools_exec=s' => \$samtools_exec,
+ );
+
+ $self->bamfile( abs_path($bamfile) ) if ( defined($bamfile) );
+ $self->outfile( abs_path($outfile) ) if ( defined($outfile) );
+ $self->help($help) if ( defined($help) );
+ $self->verbose($verbose) if ( defined($verbose) );
+ $self->samtools_exec($samtools_exec) if ( defined($samtools_exec) );
+
+ # print usage text if required parameters are not present
+ ($bamfile) or die $self->usage_text;
+}
+
+sub run {
+ my ($self) = @_;
+
+ if ( defined( $self->help ) ) {
+ #if ( scalar( @{ $self->args } ) == 0 ) {
+ $self->usage_text;
+ }
+
+ my $tagadd = Bio::Tradis::AddTagsToSeq->new(
+ bamfile => $self->bamfile,
+ outfile => $self->outfile,
+ verbose => $self->verbose,
+ samtools_exec => $self->samtools_exec
+ );
+ $tagadd->add_tags_to_seq;
+}
+
+sub usage_text {
+ print <<USAGE;
+Adds transposon sequence and quality tags to the read strings and
+outputs a BAM.
+
+Usage: add_tags -b file.bam [options]
+
+Options:
+-b : bam file with tradis tags
+-o : output BAM name (optional. default: <file>.tr.bam)
+-v : verbose debugging output
+
+USAGE
+ exit;
+}
+
+__PACKAGE__->meta->make_immutable;
+no Moose;
+1;
diff --git a/lib/Bio/Tradis/CommandLine/CheckTags.pm b/lib/Bio/Tradis/CommandLine/CheckTags.pm
new file mode 100644
index 0000000..46a55cb
--- /dev/null
+++ b/lib/Bio/Tradis/CommandLine/CheckTags.pm
@@ -0,0 +1,70 @@
+package Bio::Tradis::CommandLine::CheckTags;
+
+# ABSTRACT: Check for presence of tr tag in BAM file
+
+=head1 SYNOPSIS
+
+Check for presence of tr tag in BAM file
+
+=cut
+
+use Moose;
+use Getopt::Long qw(GetOptionsFromArray);
+use Cwd 'abs_path';
+use Bio::Tradis::DetectTags;
+
+has 'args' => ( is => 'ro', isa => 'ArrayRef', required => 1 );
+has 'script_name' => ( is => 'ro', isa => 'Str', required => 1 );
+has 'bamfile' => ( is => 'rw', isa => 'Str', required => 0 );
+has 'help' => ( is => 'rw', isa => 'Bool', required => 0 );
+has 'samtools_exec' => ( is => 'rw', isa => 'Str', default => 'samtools' );
+
+sub BUILD {
+ my ($self) = @_;
+
+ my (
+ $bamfile, $help, $samtools_exec
+ );
+
+ GetOptionsFromArray(
+ $self->args,
+ 'b|bamfile=s' => \$bamfile,
+ 'h|help' => \$help,
+ 'samtools_exec=s' => \$samtools_exec,
+ );
+
+ $self->bamfile(abs_path($bamfile)) if ( defined($bamfile) );
+ $self->help($help) if ( defined($help) );
+ $self->samtools_exec($samtools_exec) if ( defined($samtools_exec) );
+
+ # print usage text if required parameters are not present
+ ($bamfile) or die $self->usage_text;
+}
+
+sub run {
+ my ($self) = @_;
+
+ if ( defined( $self->help ) ) {
+ $self->usage_text;
+ }
+
+ my $tagcheck = Bio::Tradis::DetectTags->new(bamfile => $self->bamfile, samtools_exec => $self->samtools_exec );
+ print $tagcheck->tags_present . "\n";
+}
+
+sub usage_text {
+ print <<USAGE;
+Check for the existence of tradis tags in a bam
+
+Usage: check_tags -b file.bam
+
+Options:
+-b : bam file with tradis tags
+
+USAGE
+ exit;
+}
+
+__PACKAGE__->meta->make_immutable;
+no Moose;
+1;
\ No newline at end of file
diff --git a/lib/Bio/Tradis/CommandLine/FilterFastqTags.pm b/lib/Bio/Tradis/CommandLine/FilterFastqTags.pm
new file mode 100644
index 0000000..9908f4d
--- /dev/null
+++ b/lib/Bio/Tradis/CommandLine/FilterFastqTags.pm
@@ -0,0 +1,84 @@
+package Bio::Tradis::CommandLine::FilterFastqTags;
+
+# ABSTRACT: Remove given tags from the start of the sequence
+
+=head1 SYNOPSIS
+
+Removes tags from the sequence and quality strings
+
+=cut
+
+use Moose;
+use Getopt::Long qw(GetOptionsFromArray);
+use Cwd 'abs_path';
+use Bio::Tradis::FilterTags;
+
+has 'args' => ( is => 'ro', isa => 'ArrayRef', required => 1 );
+has 'script_name' => ( is => 'ro', isa => 'Str', required => 1 );
+has 'fastqfile' => ( is => 'rw', isa => 'Str', required => 0 );
+has 'tag' => ( is => 'rw', isa => 'Str', required => 0 );
+has 'mismatch' => ( is => 'rw', isa => 'Int', required => 0, default => 0 );
+has 'help' => ( is => 'rw', isa => 'Bool', required => 0 );
+has 'outfile' => ( is => 'rw', isa => 'Str', required => 0 );
+
+sub BUILD {
+ my ($self) = @_;
+
+ my ( $fastqfile, $tag, $mismatch, $outfile, $help );
+
+ GetOptionsFromArray(
+ $self->args,
+ 'f|fastqfile=s' => \$fastqfile,
+ 't|tag=s' => \$tag,
+ 'm|mismatch=i' => \$mismatch,
+ 'o|outfile=s' => \$outfile,
+ 'h|help' => \$help
+ );
+
+ $self->fastqfile( abs_path($fastqfile) ) if ( defined($fastqfile) );
+ $self->tag($tag) if ( defined($tag) );
+ $self->mismatch($mismatch) if ( defined($mismatch) );
+ $self->outfile( abs_path($outfile) ) if ( defined($outfile) );
+ $self->help($help) if ( defined($help) );
+
+ # print usage text if required parameters are not present
+ ($fastqfile && $tag) or die $self->usage_text;
+}
+
+sub run {
+ my ($self) = @_;
+
+ if ( defined( $self->help ) ) {
+
+ #if ( scalar( @{ $self->args } ) == 0 ) {
+ $self->usage_text;
+ }
+
+ my $tag_filter = Bio::Tradis::FilterTags->new(
+ fastqfile => $self->fastqfile,
+ tag => $self->tag,
+ mismatch => $self->mismatch,
+ outfile => $self->outfile
+ );
+ $tag_filter->filter_tags;
+}
+
+sub usage_text {
+ print <<USAGE;
+Filters a BAM file and outputs reads with tag matching -t option
+
+Usage: filter_tags -b file.bam -t tag [options]
+
+Options:
+-f : fastq file with tradis tags attached
+-t : tag to search for
+-m : number of mismatches to allow when matching tag (optional. default = 0)
+-o : output file name (optional. default: <file>.tag.fastq)
+
+USAGE
+ exit;
+}
+
+__PACKAGE__->meta->make_immutable;
+no Moose;
+1;
diff --git a/lib/Bio/Tradis/CommandLine/PlotCombine.pm b/lib/Bio/Tradis/CommandLine/PlotCombine.pm
new file mode 100644
index 0000000..8cd4d3d
--- /dev/null
+++ b/lib/Bio/Tradis/CommandLine/PlotCombine.pm
@@ -0,0 +1,101 @@
+package Bio::Tradis::CommandLine::PlotCombine;
+
+# ABSTRACT: Combine multiple plotfiles and generate updated statistics for the combined files
+
+=head1 SYNOPSIS
+
+Takes a tab-delimited file with an ID as the first column followed by
+a list of plotfiles to combine per row. The ID will be used to name the new
+plotfile and as an identifier in the stats file, so ensure these are unique.
+
+For example, an input file named plots_to_combine.txt:
+
+ tradis1 plot1.1.gz plot1.2.gz plot1.3.gz
+ tradis2 plot2.1.gz plot2.2.gz
+ tradis3 plot3.1.gz plot3.2.gz plot3.3.gz plot3.4.gz
+
+will produce:
+
+=over
+
+=item 1. a directory named combined with 3 files - tradis1.insertion_site_plot.gz,
+tradis2.insertion_site_plot.gz, tradis3.insertion_site_plot.gz
+
+=item 2. a stats file named plots_to_combine.stats
+
+=back
+
+=cut
+
+use Moose;
+use Getopt::Long qw(GetOptionsFromArray);
+use Cwd 'abs_path';
+use Bio::Tradis::CombinePlots;
+
+has 'args' => ( is => 'ro', isa => 'ArrayRef', required => 1 );
+has 'script_name' => ( is => 'ro', isa => 'Str', required => 1 );
+has 'plotfile' => ( is => 'rw', isa => 'Str', required => 0 );
+has 'output_dir' => ( is => 'rw', isa => 'Str', default => 'combined' );
+has 'help' => ( is => 'rw', isa => 'Bool', required => 0 );
+
+sub BUILD {
+ my ($self) = @_;
+
+ my ( $plotfile, $output_dir, $help );
+
+ GetOptionsFromArray(
+ $self->args,
+ 'p|plotfile=s' => \$plotfile,
+ 'o|output_dir' => \$output_dir,
+ 'h|help' => \$help
+ );
+
+ $self->plotfile( abs_path($plotfile) ) if ( defined($plotfile) );
+ $self->help($help) if ( defined($help) );
+
+ # print usage text if required parameters are not present
+ ($plotfile) or die $self->usage_text;
+}
+
+sub run {
+ my ($self) = @_;
+
+ $self->usage_text if ( defined( $self->help ) );
+
+ Bio::Tradis::CombinePlots->new(
+ plotfile => $self->plotfile,
+ combined_dir => $self->output_dir,
+ )->combine;
+}
+
+sub usage_text {
+ print <<USAGE;
+Combine multiple plotfiles and generate updated statistics for the combined
+files. Takes a tab-delimited file with an ID as the first column followed by
+a list of plotfiles to combine per row. The ID will be used to name the new
+plotfile and as an identifier in the stats file, so ensure these are unique.
+
+For example, an input file named plots_to_combine.txt:
+
+tradis1 plot1.1.gz plot1.2.gz plot1.3.gz
+tradis2 plot2.1.gz plot2.2.gz
+tradis3 plot3.1.gz plot3.2.gz plot3.3.gz plot3.4.gz
+
+will produce
+1. a directory named combined with 3 files - tradis1.insertion_site_plot.gz,
+tradis2.insertion_site_plot.gz, tradis3.insertion_site_plot.gz
+2. a stats file named plots_to_combine.stats
+
+Usage: combine_tradis_plots -p plots.txt
+
+Options:
+-p|plotfile : file with plots to be combined
+-o|output_dir : name of directory for output (default: combined)
+
+USAGE
+ exit;
+}
+
+__PACKAGE__->meta->make_immutable;
+no Moose;
+1;
diff --git a/lib/Bio/Tradis/CommandLine/PlotTradis.pm b/lib/Bio/Tradis/CommandLine/PlotTradis.pm
new file mode 100644
index 0000000..1bc5cd9
--- /dev/null
+++ b/lib/Bio/Tradis/CommandLine/PlotTradis.pm
@@ -0,0 +1,79 @@
+package Bio::Tradis::CommandLine::PlotTradis;
+
+# ABSTRACT: Generate plots as part of a tradis analysis
+
+=head1 SYNOPSIS
+
+Generate insertion plots for Artemis from a mapped fastq file and
+a reference in GFF format
+
+=cut
+
+use Moose;
+use Getopt::Long qw(GetOptionsFromArray);
+use Cwd 'abs_path';
+use Bio::Tradis::TradisPlot;
+
+has 'args' => ( is => 'ro', isa => 'ArrayRef', required => 1 );
+has 'script_name' => ( is => 'ro', isa => 'Str', required => 1 );
+has 'mappedfile' => ( is => 'rw', isa => 'Str', required => 0 );
+has 'mapping_score' => ( is => 'rw', isa => 'Int', required => 0, default => 30);
+has 'help' => ( is => 'rw', isa => 'Bool', required => 0 );
+has 'outfile' => ( is => 'rw', isa => 'Str', required => 0, default => 'tradis.plot' );
+
+sub BUILD {
+ my ($self) = @_;
+
+ my ( $mappedfile, $outfile, $mapping_score, $help );
+
+ GetOptionsFromArray(
+ $self->args,
+ 'f|mappedfile=s' => \$mappedfile,
+ 'o|outfile=s' => \$outfile,
+ 'm|mapping_score=i' => \$mapping_score,
+ 'h|help' => \$help
+ );
+
+ $self->mappedfile( abs_path($mappedfile) ) if ( defined($mappedfile) );
+ $self->outfile( abs_path($outfile) ) if ( defined($outfile) );
+ $self->mapping_score($mapping_score) if ( defined($mapping_score) );
+ $self->help($help) if ( defined($help) );
+
+ # print usage text if required parameters are not present
+ ($mappedfile) or die $self->usage_text;
+}
+
+sub run {
+ my ($self) = @_;
+
+ if ( defined( $self->help ) ) {
+ #if ( scalar( @{ $self->args } ) == 0 ) {
+ $self->usage_text;
+ }
+
+ my $plot = Bio::Tradis::TradisPlot->new(
+ mappedfile => $self->mappedfile,
+ outfile => $self->outfile,
+ mapping_score => $self->mapping_score
+ );
+ $plot->plot;
+}
+
+sub usage_text {
+ print <<USAGE;
+Create insertion site plot for Artemis
+
+Usage: tradis_plot -f file.bam [options]
+
+Options:
+-f : mapped, sorted bam file
+-m : mapping quality must be greater than X (optional. default: 30)
+-o : output base name for plot (optional. default: tradis.plot)
+
+USAGE
+ exit;
+}
+
+__PACKAGE__->meta->make_immutable;
+no Moose;
+1;
diff --git a/lib/Bio/Tradis/CommandLine/RemoveFastqTags.pm b/lib/Bio/Tradis/CommandLine/RemoveFastqTags.pm
new file mode 100644
index 0000000..b3c35b7
--- /dev/null
+++ b/lib/Bio/Tradis/CommandLine/RemoveFastqTags.pm
@@ -0,0 +1,84 @@
+package Bio::Tradis::CommandLine::RemoveFastqTags;
+
+# ABSTRACT: Remove given tags from the start of the sequence
+
+=head1 SYNOPSIS
+
+Removes tags from the sequence and quality strings
+
+=cut
+
+use Moose;
+use Getopt::Long qw(GetOptionsFromArray);
+use Cwd 'abs_path';
+use Bio::Tradis::RemoveTags;
+
+has 'args' => ( is => 'ro', isa => 'ArrayRef', required => 1 );
+has 'script_name' => ( is => 'ro', isa => 'Str', required => 1 );
+has 'fastqfile' => ( is => 'rw', isa => 'Str', required => 0 );
+has 'tag' => ( is => 'rw', isa => 'Str', required => 0 );
+has 'mismatch' => ( is => 'rw', isa => 'Int', required => 0, default => 0 );
+has 'help' => ( is => 'rw', isa => 'Bool', required => 0 );
+has 'outfile' => ( is => 'rw', isa => 'Str', required => 0 );
+
+sub BUILD {
+ my ($self) = @_;
+
+ my ( $fastqfile, $tag, $mismatch, $outfile, $help );
+
+ GetOptionsFromArray(
+ $self->args,
+ 'f|fastqfile=s' => \$fastqfile,
+ 't|tag=s' => \$tag,
+ 'm|mismatch=i' => \$mismatch,
+ 'o|outfile=s' => \$outfile,
+ 'h|help' => \$help
+ );
+
+ $self->fastqfile( abs_path($fastqfile) ) if ( defined($fastqfile) );
+ $self->tag($tag) if ( defined($tag) );
+ $self->mismatch($mismatch) if ( defined($mismatch) );
+ $self->outfile( abs_path($outfile) ) if ( defined($outfile) );
+ $self->help($help) if ( defined($help) );
+
+ # print usage text if required parameters are not present
+ ($fastqfile && $tag) or die $self->usage_text;
+}
+
+sub run {
+ my ($self) = @_;
+
+ if ( defined( $self->help ) ) {
+
+ #if ( scalar( @{ $self->args } ) == 0 ) {
+ $self->usage_text;
+ }
+
+ my $tag_rm = Bio::Tradis::RemoveTags->new(
+ fastqfile => $self->fastqfile,
+ tag => $self->tag,
+ mismatch => $self->mismatch,
+ outfile => $self->outfile
+ );
+ $tag_rm->remove_tags;
+}
+
+sub usage_text {
+ print <<USAGE;
+Removes transposon sequence and quality tags from the read strings
+
+Usage: remove_tags -f file.fastq [options]
+
+Options:
+-f : fastq file with tradis tags
+-t : tag to remove
+-m : number of mismatches to allow when matching tag (optional. default = 0)
+-o : output file name (optional. default: <file>.rmtag.fastq)
+
+USAGE
+ exit;
+}
+
+__PACKAGE__->meta->make_immutable;
+no Moose;
+1;
diff --git a/lib/Bio/Tradis/CommandLine/RunMapping.pm b/lib/Bio/Tradis/CommandLine/RunMapping.pm
new file mode 100644
index 0000000..df15cc7
--- /dev/null
+++ b/lib/Bio/Tradis/CommandLine/RunMapping.pm
@@ -0,0 +1,118 @@
+package Bio::Tradis::CommandLine::RunMapping;
+
+# ABSTRACT: Perform mapping
+
+=head1 SYNOPSIS
+
+Takes a reference genome and indexes it.
+Maps given fastq files to ref.
+
+=cut
+
+use Moose;
+use Getopt::Long qw(GetOptionsFromArray);
+use Cwd 'abs_path';
+use Bio::Tradis::Map;
+
+has 'args' => ( is => 'ro', isa => 'ArrayRef', required => 1 );
+has 'script_name' => ( is => 'ro', isa => 'Str', required => 1 );
+has 'fastqfile' => ( is => 'rw', isa => 'Str', required => 0 );
+has 'reference' => ( is => 'rw', isa => 'Str', required => 0 );
+has 'help' => ( is => 'rw', isa => 'Bool', required => 0 );
+has 'refname' =>
+ ( is => 'rw', isa => 'Str', required => 0, default => 'ref.index' );
+has 'outfile' =>
+ ( is => 'rw', isa => 'Str', required => 0, default => 'mapped.sam' );
+has 'smalt_k' => ( is => 'rw', isa => 'Maybe[Int]', required => 0 );
+has 'smalt_s' => ( is => 'rw', isa => 'Maybe[Int]', required => 0 );
+has 'smalt_y' => ( is => 'rw', isa => 'Maybe[Num]', required => 0, default => 0.96 );
+has 'smalt_r' => ( is => 'rw', isa => 'Maybe[Int]', required => 0, default => -1 );
+has 'smalt_n' => ( is => 'rw', isa => 'Maybe[Int]', required => 0, default => 1 );
+
+sub BUILD {
+ my ($self) = @_;
+
+ my ( $fastqfile, $ref, $refname, $outfile, $smalt_k, $smalt_s, $smalt_y, $smalt_r,$smalt_n, $help );
+
+ GetOptionsFromArray(
+ $self->args,
+ 'f|fastqfile=s' => \$fastqfile,
+ 'r|reference=s' => \$ref,
+ 'rn|refname=s' => \$refname,
+ 'o|outfile=s' => \$outfile,
+ 'sk|smalt_k=i' => \$smalt_k,
+ 'ss|smalt_s=i' => \$smalt_s,
+ 'sy|smalt_y=f' => \$smalt_y,
+ 'sr|smalt_r=i' => \$smalt_r,
+ 'n|smalt_n=i' => \$smalt_n,
+ 'h|help' => \$help
+ );
+
+ $self->fastqfile( abs_path($fastqfile) ) if ( defined($fastqfile) );
+ $self->reference( abs_path($ref) ) if ( defined($ref) );
+ $self->refname($refname) if ( defined($refname) );
+ $self->outfile( abs_path($outfile) ) if ( defined($outfile) );
+ $self->smalt_k( $smalt_k ) if ( defined($smalt_k) );
+ $self->smalt_s( $smalt_s ) if ( defined($smalt_s) );
+ $self->smalt_y( $smalt_y ) if ( defined($smalt_y) );
+ $self->smalt_r( $smalt_r ) if ( defined($smalt_r) );
+ $self->smalt_n( $smalt_n ) if ( defined($smalt_n) );
+ $self->help($help) if ( defined($help) );
+
+ # print usage text if required parameters are not present
+ ($fastqfile && $ref) or die $self->usage_text;
+}
+
+sub run {
+ my ($self) = @_;
+
+ if ( defined( $self->help ) ) {
+ #if ( scalar( @{ $self->args } ) == 0 ) {
+ $self->usage_text;
+ }
+
+ my $mapping = Bio::Tradis::Map->new(
+ fastqfile => $self->fastqfile,
+ reference => $self->reference,
+ refname => $self->refname,
+ outfile => $self->outfile,
+ smalt_k => $self->smalt_k,
+ smalt_s => $self->smalt_s,
+ smalt_y => $self->smalt_y,
+ smalt_r => $self->smalt_r
+ );
+ $mapping->index_ref;
+ $mapping->do_mapping;
+}
+
+sub usage_text {
+ print <<USAGE;
+Indexes the reference genome and maps the given fastq file.
+-k and -s options for indexing are calculated for the length of
+the read as follows unless otherwise specified ( --smalt_k &
+--smalt_s options )
+Read length | k | s
+---------------+----+-----
+<70 | 13 | 4
+>70 & <100 | 13 | 6
+>100 | 20 | 13
+
+Usage: run_mapping -f file.fastq -r ref.fa [options]
+
+Options:
+-f : fastq file to map
+-r : reference in fasta format
+-rn : reference index name (optional. default: ref.index)
+-o : mapped SAM output name (optional. default: mapped.sam)
+--smalt_k : custom k-mer value for SMALT mapping
+--smalt_s : custom step size for SMALT mapping
+--smalt_r : custom r value for SMALT mapping
+-n : number of threads to use for SMALT and samtools sort (optional. default = 1)
+
+USAGE
+ exit;
+}
+
+__PACKAGE__->meta->make_immutable;
+no Moose;
+1;
diff --git a/lib/Bio/Tradis/CommandLine/TradisAnalysis.pm b/lib/Bio/Tradis/CommandLine/TradisAnalysis.pm
new file mode 100644
index 0000000..12449b4
--- /dev/null
+++ b/lib/Bio/Tradis/CommandLine/TradisAnalysis.pm
@@ -0,0 +1,271 @@
+package Bio::Tradis::CommandLine::TradisAnalysis;
+
+# ABSTRACT: Perform full tradis analysis
+
+=head1 SYNOPSIS
+
+Takes a fastq, reference and a tag and generates insertion
+site plots for use in Artemis
+
+=cut
+
+use Moose;
+use Getopt::Long qw(GetOptionsFromArray);
+use Cwd qw(abs_path cwd);
+use Bio::Tradis::RunTradis;
+use TryCatch;
+
+has 'args' => ( is => 'ro', isa => 'ArrayRef', required => 1 );
+has 'script_name' => ( is => 'ro', isa => 'Str', required => 1 );
+has 'fastqfile' => ( is => 'rw', isa => 'Str', required => 0 );
+has 'tag' => ( is => 'rw', isa => 'Str', required => 0 );
+has 'mismatch' => ( is => 'rw', isa => 'Int', required => 0, default => 0 );
+has 'tagdirection' =>
+ ( is => 'rw', isa => 'Str', required => 0, default => '3' );
+has 'reference' => ( is => 'rw', isa => 'Str', required => 0 );
+has 'help' => ( is => 'rw', isa => 'Bool', required => 0 );
+has 'mapping_score' =>
+ ( is => 'rw', isa => 'Int', required => 0, default => 30 );
+has 'smalt_k' => ( is => 'rw', isa => 'Maybe[Int]', required => 0 );
+has 'smalt_s' => ( is => 'rw', isa => 'Maybe[Int]', required => 0 );
+has 'smalt_y' => ( is => 'rw', isa => 'Maybe[Num]', required => 0, default => 0.96 );
+has 'smalt_r' => ( is => 'rw', isa => 'Maybe[Int]', required => 0, default => -1 );
+has 'smalt_n' => ( is => 'rw', isa => 'Maybe[Int]', required => 0, default => 1 );
+has 'essentiality' => ( is => 'rw', isa => 'Bool', required => 0, default => 0);
+
+has 'verbose' => ( is => 'rw', isa => 'Bool', default => 0 );
+has 'samtools_exec' => ( is => 'rw', isa => 'Str', default => 'samtools' );
+
+has '_output_directory' => (
+ is => 'rw',
+ isa => 'Str',
+ required => 0,
+ lazy => 1,
+ builder => '_build__output_directory'
+);
+
+has '_stats_handle' => (
+ is => 'ro',
+ isa => 'FileHandle',
+ required => 0,
+ lazy => 1,
+ builder => '_build__stats_handle'
+);
+
+sub BUILD {
+ my ($self) = @_;
+
+ my (
+ $fastqfile, $tag, $td, $mismatch, $ref,$smalt_n, $essentiality,
+ $map_score, $smalt_k, $smalt_s, $smalt_y, $smalt_r, $help, $verbose,$samtools_exec
+ );
+
+ GetOptionsFromArray(
+ $self->args,
+ 'f|fastqfile=s' => \$fastqfile,
+ 't|tag=s' => \$tag,
+ 'td|tagdirection=i' => \$td,
+ 'mm|mismatch=i' => \$mismatch,
+ 'r|reference=s' => \$ref,
+ 'm|mapping_score=i' => \$map_score,
+ 'sk|smalt_k=i' => \$smalt_k,
+ 'ss|smalt_s=i' => \$smalt_s,
+ 'sy|smalt_y=f' => \$smalt_y,
+ 'n|smalt_n=i' => \$smalt_n,
+ 'sr|smalt_r=i' => \$smalt_r,
+ 'v|verbose' => \$verbose,
+ 'samtools_exec=s' => \$samtools_exec,
+ 'e|essentiality' => \$essentiality,
+ 'h|help' => \$help
+ );
+
+ #Essentiality analysis requires different defaults.
+ if(!defined($smalt_r) && !defined($map_score) && defined($essentiality))
+ {
+ $self->essentiality($essentiality) if ( defined($essentiality));
+ $smalt_r = 0;
+ $map_score = 0;
+ }
+
+ $self->fastqfile( abs_path($fastqfile) ) if ( defined($fastqfile) );
+ $self->tag( uc($tag) ) if ( defined($tag) );
+ $self->tagdirection($td) if ( defined($td) );
+ $self->mismatch($mismatch) if ( defined($mismatch) );
+ $self->reference( abs_path($ref) ) if ( defined($ref) );
+ $self->mapping_score($map_score) if ( defined($map_score) );
+ $self->smalt_k($smalt_k) if ( defined($smalt_k) );
+ $self->smalt_s($smalt_s) if ( defined($smalt_s) );
+ $self->smalt_y($smalt_y) if ( defined($smalt_y) );
+ $self->smalt_r($smalt_r) if ( defined($smalt_r) );
+ $self->smalt_n($smalt_n) if ( defined($smalt_n) );
+ $self->help($help) if ( defined($help) );
+ $self->verbose($verbose) if ( defined($verbose));
+ $self->samtools_exec($samtools_exec) if ( defined($samtools_exec) );
+
+ # print usage text if required parameters are not present
+ ( $fastqfile && $tag && $ref ) or die $self->usage_text;
+}
+
+sub run {
+ my ($self) = @_;
+
+ if ( defined( $self->help ) ) {
+
+ #if ( scalar( @{ $self->args } ) == 0 ) {
+ $self->usage_text;
+ }
+
+ #parse list of files and run pipeline for each one if they all exist
+ my $fq = $self->fastqfile;
+ open( FILES, "<", $fq ) or die "Cannot find $fq";
+ my @filelist = <FILES>;
+ my $file_dir = $self->get_file_dir;
+
+ #check files exist before running
+ my $line_no = 0;
+ my $full_path;
+ foreach my $f1 (@filelist) {
+ chomp($f1);
+ $line_no++;
+ if ( $f1 =~ /^\// ) { $full_path = $f1; }
+ else { $full_path = "$file_dir/$f1"; }
+ unless ( -e $full_path ) {
+ die "File $full_path does not exist ($fq, line $line_no)\n";
+ }
+ }
+
+ #if all files exist, continue with analysis
+ my $at_least_one_good_fastq = 0;
+ foreach my $f2 (@filelist) {
+ chomp($f2);
+ if ( $f2 =~ /^\// ) { $full_path = $f2; }
+ else { $full_path = "$file_dir/$f2"; }
+ my $analysis = Bio::Tradis::RunTradis->new(
+ fastqfile => $full_path,
+ tag => $self->tag,
+ tagdirection => $self->tagdirection,
+ mismatch => $self->mismatch,
+ reference => $self->reference,
+ mapping_score => $self->mapping_score,
+ output_directory => $self->_output_directory,
+ _stats_handle => $self->_stats_handle,
+ smalt_k => $self->smalt_k,
+ smalt_s => $self->smalt_s,
+ smalt_y => $self->smalt_y,
+ smalt_r => $self->smalt_r,
+ smalt_n => $self->smalt_n,
+ verbose => $self->verbose,
+ samtools_exec => $self->samtools_exec
+ );
+ try {
+ $analysis->run_tradis;
+ $at_least_one_good_fastq = 1;
+ }
+ catch (Bio::Tradis::Exception::TagFilterError $e) {
+ my $tag = $self->tag;
+ warn "There was a problem filtering '$full_path' by '$tag'; it looks like the tag was not found in any read\n";
+ }
+ }
+ if ( ! $at_least_one_good_fastq ) {
+ Bio::Tradis::Exception::TagFilterError->throw( error => "None of the input files contained the specified tag. Please check that your inputs are valid fastq files and that at least one read in one of them starts with the specified tag\n" );
+ }
+
+ $self->_tidy_stats;
+ close(FILES);
+
+ #$self->_combine_plots;
+}
+
+sub _build__output_directory {
+ return cwd();
+}
+
+sub _stats_filename {
+ my ($self) = @_;
+ my $dir = $self->get_file_dir;
+ my $output_directory = $self->_output_directory;
+ my $stats_filename = $self->fastqfile;
+ $stats_filename =~ s/$dir\///;
+ $stats_filename =~ s/[^\.]+$/stats/;
+ return "$output_directory/$stats_filename";
+}
+
+sub _build__stats_handle {
+ my ($self) = @_;
+ my $stats_filename = $self->_stats_filename();
+ open( my $stats, ">", $stats_filename );
+ return $stats;
+}
+
+sub _tidy_stats {
+ my ($self) = @_;
+ my $output_directory = $self->_output_directory;
+ my $stats_filename = $self->_stats_filename();
+ open( STATS, '<', $stats_filename );
+ open( TMP, '>', "$output_directory/tmp.stats" );
+
+ my $header = 0;
+ while ( my $line = <STATS> ) {
+ if ( $line =~ /^File/ ) {
+ if ( $header == 0 ) {
+ print TMP "$line";
+ $header = 1;
+ }
+ }
+ else {
+ print TMP "$line";
+ }
+ }
+ close(TMP);
+ close(STATS);
+ system("mv $output_directory/tmp.stats $stats_filename");
+}
+
+sub _combine_plots {
+ my ($self) = @_;
+ my $filelist = $self->fastqfile;
+
+ return 1;
+}
+
+sub get_file_dir {
+ my ($self) = @_;
+ my $fq = $self->fastqfile;
+
+ my @dirs = split( '/', $fq );
+ pop(@dirs);
+ return join( '/', @dirs );
+}
+
+sub usage_text {
+ print <<USAGE;
+Run a TraDIS analysis. This involves:
+1: filtering the data with tags matching that passed via -t option
+2: removing the tags from the sequences
+3: mapping
+4: creating an insertion site plot
+5: creating a stats summary
+
+Usage: bacteria_tradis [options]
+
+Options:
+-f : text file listing fastq files with tradis tags attached
+-t : tag to search for
+-r : reference genome in fasta format (.fa)
+-td : tag direction - 3 or 5 (optional. default = 3)
+-mm : number of mismatches allowed when matching tag (optional. default = 0)
+-m : mapping quality cutoff score (optional. default = 30)
+--smalt_k : custom k-mer value for SMALT mapping (optional)
+--smalt_s : custom step size for SMALT mapping (optional)
+--smalt_y : custom y parameter for SMALT (optional. default = 0.96)
+--smalt_r : custom r parameter for SMALT (optional. default = -1)
+-n : number of threads to use for SMALT and samtools sort (optional. default = 1)
+-e : set defaults for essentiality experiment (smalt_r = 0, -m = 0)
+-v : verbose debugging output
+USAGE
+ exit;
+}
+
+__PACKAGE__->meta->make_immutable;
+no Moose;
+1;
diff --git a/lib/Bio/Tradis/CommandLine/TradisBam.pm b/lib/Bio/Tradis/CommandLine/TradisBam.pm
new file mode 100644
index 0000000..2c80835
--- /dev/null
+++ b/lib/Bio/Tradis/CommandLine/TradisBam.pm
@@ -0,0 +1,99 @@
+package Bio::Tradis::CommandLine::TradisBam;
+
+# ABSTRACT: Adds tags to sequences if tags are present
+
+=head1 SYNOPSIS
+
+Checks for tradis tags in the BAM and outputs processed TraDIS BAM file
+with tags attached
+
+=cut
+
+use Moose;
+use Getopt::Long qw(GetOptionsFromArray);
+use Cwd 'abs_path';
+use Bio::Tradis::DetectTags;
+use Bio::Tradis::AddTagsToSeq;
+
+has 'args' => ( is => 'ro', isa => 'ArrayRef', required => 1 );
+has 'script_name' => ( is => 'ro', isa => 'Str', required => 1 );
+has 'bamfile' => ( is => 'rw', isa => 'Str', required => 1 );
+has 'outfile' => (
+ is => 'rw',
+ isa => 'Str',
+ required => 0,
+ default => sub {
+ my $o = $self->bamfile;
+ $o =~ s/\.bam/\.tr\.bam/;
+ return $o;
+ }
+);
+has 'help' => ( is => 'rw', isa => 'Bool', required => 0 );
+has 'verbose' => ( is => 'rw', isa => 'Bool', default => 0 );
+has 'samtools_exec' => ( is => 'rw', isa => 'Str', default => 'samtools' );
+
+sub BUILD {
+ my ($self) = @_;
+
+ my ( $bamfile, $help, $outfile, $verbose, $samtools_exec );
+
+ GetOptionsFromArray(
+ $self->args,
+ 'b|bamfile=s' => \$bamfile,
+ 'o|outfile=s' => \$outfile,
+ 'h|help' => \$help,
+ 'v|verbose' => \$verbose,
+ 'samtools_exec=s' => \$samtools_exec,
+ );
+
+ $self->bamfile( abs_path($bamfile) ) if ( defined($bamfile) );
+ $self->outfile( abs_path($outfile) ) if ( defined($outfile) );
+ $self->help($help) if ( defined($help) );
+ $self->verbose($verbose) if ( defined($verbose) );
+ $self->samtools_exec($samtools_exec) if ( defined($samtools_exec) );
+
+ # print usage text if required parameters are not present
+ ($bamfile) or die $self->usage_text;
+}
+
+sub run {
+ my ($self) = @_;
+
+ if ( defined( $self->help ) ) {
+ $self->usage_text;
+ }
+
+ my $is_tradis =
+ Bio::Tradis::DetectTags->new(
+ bamfile => $self->bamfile,
+ samtools_exec => $self->samtools_exec
+ )->tags_present;
+ if ( defined($is_tradis) && $is_tradis == 1 ) {
+ my $add_tag_obj = Bio::Tradis::AddTagsToSeq->new(
+ bamfile => $self->bamfile,
+ outfile => $self->outfile,
+ verbose => $self->verbose,
+ samtools_exec => $self->samtools_exec
+ );
+ $add_tag_obj->add_tags_to_seq;
+ }
+}
+
+sub usage_text {
+ print <<USAGE;
+Checks for tradis tags in the BAM and outputs processed TraDIS BAM file
+with tags attached
+
+Usage: bam_to_tradis_bam -b file.bam [options]
+
+Options:
+-b : bam file
+-o : output BAM name (optional. default: <file>.tr.bam)
+-v : verbose debugging output
+USAGE
+ exit;
+}
+
+__PACKAGE__->meta->make_immutable;
+no Moose;
+1;
diff --git a/lib/Bio/Tradis/DetectTags.pm b/lib/Bio/Tradis/DetectTags.pm
new file mode 100644
index 0000000..fc24b5e
--- /dev/null
+++ b/lib/Bio/Tradis/DetectTags.pm
@@ -0,0 +1,54 @@
+package Bio::Tradis::DetectTags;
+
+# ABSTRACT: Detect tr tags in BAM file
+
+=head1 NAME
+
+Bio::Tradis::DetectTags
+
+=head1 SYNOPSIS
+
+Detects presence of tr/tq tags in BAM files from Tradis analyses
+ use Bio::Tradis::DetectTags;
+
+ my $pipeline = Bio::Tradis::DetectTags->new(bamfile => 'abc');
+ $pipeline->tags_present();
+
+=head1 PARAMETERS
+
+=head2 Required
+
+C<bamfile> - path to/name of file to check
+
+=head1 METHODS
+
+C<tags_present> - returns true if TraDIS tags are detected in C<bamfile>
+
+=cut
+
+use Moose;
+use Bio::Tradis::Parser::Bam
+
+has 'bamfile' => ( is => 'ro', isa => 'Str', required => 1 );
+has 'samtools_exec' => ( is => 'rw', isa => 'Str', default => 'samtools' );
+
+sub tags_present {
+ my ($self) = @_;
+ my $pars = Bio::Tradis::Parser::Bam->new( file => $self->bamfile, samtools_exec => $self->samtools_exec );
+ my $read_info = $pars->read_info;
+ $pars->next_read;
+ $read_info = $pars->read_info;
+ if(defined(${$read_info}{tr}))
+ {
+ return 1;
+ }
+ else
+ {
+ return 0;
+ }
+
+}
+
+__PACKAGE__->meta->make_immutable;
+no Moose;
+1;
diff --git a/lib/Bio/Tradis/Exception.pm b/lib/Bio/Tradis/Exception.pm
new file mode 100644
index 0000000..3f18620
--- /dev/null
+++ b/lib/Bio/Tradis/Exception.pm
@@ -0,0 +1,16 @@
+package Bio::Tradis::Exception;
+# ABSTRACT: Exceptions for input data
+
+=head1 SYNOPSIS
+
+Exceptions for input data
+
+=cut
+
+
+use Exception::Class (
+ Bio::Tradis::Exception::RefNotFound => { description => 'Cannot find the reference file' },
+ Bio::Tradis::Exception::TagFilterError => { description => 'Problem filtering the Fastq by tag' }
+);
+
+1;
diff --git a/lib/Bio/Tradis/FilterTags.pm b/lib/Bio/Tradis/FilterTags.pm
new file mode 100644
index 0000000..9566f8a
--- /dev/null
+++ b/lib/Bio/Tradis/FilterTags.pm
@@ -0,0 +1,162 @@
+package Bio::Tradis::FilterTags;
+
+# ABSTRACT: Filter tags in a fastq file
+
+=head1 SYNOPSIS
+
+Reads in a fastq file with tradis tags already attached to the start of the sequence
+Filters reads that contain the provided tag
+Outputs a file *.tag.fastq unless an alternative outfile name is specified
+
+ use Bio::Tradis::FilterTags;
+
+ my $pipeline = Bio::Tradis::FilterTags->new(fastqfile => 'abc', tag => 'abc');
+ $pipeline->filter_tags();
+
+=head1 PARAMETERS
+
+=head2 Required
+
+=over
+
+=item * C<fastqfile> - path to/name of file to filter. This may be a gzipped fastq file, in which case a temporary unzipped version is used and removed on completion.
+
+=item * C<tag> - TraDIS tag to match
+
+=back
+
+=head2 Optional
+
+=over
+
+=item * C<mismatch> - number of mismatches to allow when matching the tag. Default = 0
+
+=item * C<outfile> - output file name. Defaults to C<file.tag.fastq> for an input file named C<file.fastq>
+
+=back
+
+=head1 METHODS
+
+C<filter_tags> - outputs all reads containing the provided tag to C<outfile>
+
+=cut
+
+use Moose;
+use Bio::Tradis::Parser::Fastq;
+
+has 'fastqfile' => ( is => 'rw', isa => 'Str', required => 1 );
+has '_unzipped_fastq' =>
+ ( is => 'rw', isa => 'Str', lazy => 1, builder => '_build__unzipped_fastq' );
+has 'tag' => ( is => 'rw', isa => 'Str', required => 1 );
+has 'mismatch' => ( is => 'rw', isa => 'Int', required => 0 );
+has 'outfile' => (
+ is => 'rw',
+ isa => 'Str',
+ required => 0,
+ default => sub {
+ my ($self) = @_;
+ my $o = $self->fastqfile;
+ $o =~ s/\.fastq/\.tag\.fastq/;
+ return $o;
+ }
+);
+has '_currentread' => (
+ is => 'rw',
+ isa => 'ArrayRef',
+ required => 0,
+ writer => '_set_currentread'
+);
+
+sub _is_gz {
+ my ($self) = @_;
+ my $fq = $self->fastqfile;
+
+ if ( $fq =~ /\.gz/ ) {
+ return 1;
+ }
+ else {
+ return 0;
+ }
+}
+
+sub _build__unzipped_fastq {
+ my ($self) = @_;
+ my $fq = $self->fastqfile;
+
+ if ( $self->_is_gz ) {
+ $fq =~ /([^\/]+)$/;
+ my $newfq = $1;
+ $newfq =~ s/\.gz//;
+ if ( !-e $newfq ) {
+ `gunzip -c $fq > $newfq`;
+ }
+ return $newfq;
+ }
+ else {
+ return $fq;
+ }
+}
+
+sub filter_tags {
+ my ($self) = @_;
+ my $tag = uc( $self->tag );
+ my $outfile = $self->outfile;
+
+ #set up fastq parser
+ my $filename = $self->_unzipped_fastq;
+ my $pars = Bio::Tradis::Parser::Fastq->new( file => $filename );
+
+ open( OUTFILE, ">$outfile" );
+
+ while ( $pars->next_read ) {
+ my @read = $pars->read_info;
+ $self->_set_currentread( \@read );
+ my $id = $read[0];
+ my $seq_string = $read[1];
+ my $qual_string = $read[2];
+
+ my $print_out = 0;
+ if ( $self->mismatch == 0 ) {
+ if ( $seq_string =~ /^$tag/ ) {
+ $print_out = 1;
+ }
+ }
+ else {
+ my $mm = $self->_tag_mismatch($seq_string);
+ if ( $mm <= $self->mismatch ) {
+ $print_out = 1;
+ }
+ }
+
+ if ($print_out) {
+ print OUTFILE "\@$id\n";
+ print OUTFILE $seq_string . "\n+\n";
+ print OUTFILE $qual_string . "\n";
+ }
+ }
+ if ( $self->_is_gz ) {
+ unlink( $self->_unzipped_fastq );
+ }
+ close OUTFILE;
+ return 1;
+}
+
+sub _tag_mismatch {
+ my ($self) = @_;
+ my $tag_len = length( $self->tag );
+ my $seq_string = ${ $self->_currentread }[1];
+
+ my @tag = split( "", $self->tag );
+ my @seq = split( "", substr( $seq_string, 0, $tag_len ) );
+ my $mismatches = 0;
+ foreach my $i ( 0 .. ( $tag_len - 1 ) ) {
+ if ( $tag[$i] ne $seq[$i] ) {
+ $mismatches++;
+ }
+ }
+ return $mismatches;
+}
+
+__PACKAGE__->meta->make_immutable;
+no Moose;
+1;
diff --git a/lib/Bio/Tradis/Map.pm b/lib/Bio/Tradis/Map.pm
new file mode 100644
index 0000000..726f882
--- /dev/null
+++ b/lib/Bio/Tradis/Map.pm
@@ -0,0 +1,143 @@
+package Bio::Tradis::Map;
+
+# ABSTRACT: Perform mapping
+
+=head1 SYNOPSIS
+
+Takes a reference genome and indexes it.
+Maps given fastq files to ref.
+
+ use Bio::Tradis::Map;
+
+ my $pipeline = Bio::Tradis::Map->new(fastqfile => 'abc', reference => 'abc');
+ $pipeline->index_ref();
+ $pipeline->do_mapping();
+
+=head1 PARAMETERS
+
+=head2 Required
+
+=over
+
+=item * C<fastqfile> - path to/name of file containing reads to map to the reference
+
+=item * C<reference> - path to/name of reference genome in fasta format (.fa)
+
+=back
+
+=head2 Optional
+
+=over
+
+=item * C<refname> - name to assign to the reference index files. Default = ref.index
+
+=item * C<outfile> - name to assign to the mapped SAM file. Default = mapped.sam
+
+=back
+
+=head1 METHODS
+
+=over
+
+=item * C<index_ref> - create index files of the reference genome. These are required
+ for the mapping step. Only skip this step if index files already
+ exist. -k and -s options for referencing are calculated based
+ on the length of the reads being mapped as per table:
+
+=begin html
+
+<table>
+<tr><th>Read length</th><th>k</th><th>s</th></tr>
+<tr><td><70</td><td>13</td><td>4<td></tr>
+<tr><td>>70 and <100</td><td>13</td><td>6<td></tr>
+<tr><td>>100</td><td>20</td><td>6<td></tr>
+</table>
+
+=end html
+
+=item * C<do_mapping> - map C<fastqfile> to C<reference>. Options used for mapping are: C<-r -1 -x -y 0.96>
+
+=back
+
+For more information on the mapping and indexing options discussed here, see the L<SMALT manual|ftp://ftp.sanger.ac.uk/pub4/resources/software/smalt/smalt-manual-0.7.4.pdf>
+
+=cut
+
+use Moose;
+use Bio::Tradis::Parser::Fastq;
+
+has 'fastqfile' => ( is => 'rw', isa => 'Str', required => 1 );
+has 'reference' => ( is => 'rw', isa => 'Str', required => 1 );
+has 'refname' =>
+ ( is => 'rw', isa => 'Str', required => 0, default => 'ref.index' );
+has 'outfile' =>
+ ( is => 'rw', isa => 'Str', required => 0, default => 'mapped.sam' );
+has 'smalt_k' => ( is => 'rw', isa => 'Maybe[Int]', required => 0 );
+has 'smalt_s' => ( is => 'rw', isa => 'Maybe[Int]', required => 0 );
+has 'smalt_y' => ( is => 'rw', isa => 'Maybe[Num]', required => 0, default => 0.96 );
+has 'smalt_r' => ( is => 'rw', isa => 'Maybe[Int]', required => 0, default => -1 );
+has 'smalt_n' => ( is => 'rw', isa => 'Maybe[Int]', required => 0, default => 1 );
+
+sub index_ref {
+ my ($self) = @_;
+ my $ref = $self->reference;
+ my $refname = $self->refname;
+
+ # Calculate index parameters
+ my $pars = Bio::Tradis::Parser::Fastq->new( file => $self->fastqfile );
+ $pars->next_read;
+ my @read = $pars->read_info;
+ my $read_len = length($read[1]);
+ my ( $k, $s ) = $self->_calculate_index_parameters($read_len);
+
+ my $cmd = "smalt index -k $k -s $s $refname $ref > /dev/null 2>&1";
+ system($cmd);
+ return $cmd;
+}
+
+sub _calculate_index_parameters {
+ my ($self, $read_len) = @_;
+ my ( $k, $s );
+
+ if( defined $self->smalt_k ){ $k = $self->smalt_k; }
+ else{ $k = $self->_smalt_k_default($read_len); }
+
+ if( defined $self->smalt_s ){ $s = $self->smalt_s; }
+ else{ $s = $self->_smalt_s_default($read_len); }
+
+ return ( $k, $s );
+}
+
+sub _smalt_k_default {
+ my ($self, $read_len) = @_;
+ if($read_len < 100){ return 13; }
+ else{ return 20; }
+}
+
+sub _smalt_s_default {
+ my ( $self, $read_len ) = @_;
+ if( $read_len < 70 ){ return 4; }
+ elsif( $read_len > 100 ){ return 13; }
+ else{ return 6; }
+}
+
+sub do_mapping {
+ my ($self) = @_;
+ my $fqfile = $self->fastqfile;
+ my $refname = $self->refname;
+ my $outfile = $self->outfile;
+ my $y = $self->smalt_y;
+ my $r = $self->smalt_r;
+ my $n = $self->smalt_n;
+
+ my $smalt = "smalt map -n $n -x -r $r -y $y $refname $fqfile 1> $outfile 2> smalt.stderr";
+
+ system($smalt);
+ unlink('smalt.stderr');
+
+ return $smalt;
+}
+
+__PACKAGE__->meta->make_immutable;
+no Moose;
+1;
diff --git a/lib/Bio/Tradis/Parser/Bam.pm b/lib/Bio/Tradis/Parser/Bam.pm
new file mode 100644
index 0000000..05aa6c4
--- /dev/null
+++ b/lib/Bio/Tradis/Parser/Bam.pm
@@ -0,0 +1,192 @@
+package Bio::Tradis::Parser::Bam;
+
+# ABSTRACT: Very basic BAM parser. Limited functionality.
+
+=head1 SYNOPSIS
+
+Parses BAM files and gives access to basic info in them.
+
+ use Bio::Tradis::Parser::Bam;
+
+ my $pipeline = Bio::Tradis::Parser::Bam->new(file => 'abc');
+ $pipeline->read_info;
+ $pipeline->next_read;
+ $pipeline->seq_info;
+ $pipeline->is_mapped;
+ $pipeline->is_reverse;
+
+=cut
+
+use Moose;
+
+has 'samtools_exec' => ( is => 'rw', isa => 'Str', default => 'samtools' );
+has 'file' => ( is => 'rw', isa => 'Str', required => 1 );
+has '_bam_handle' => (
+ is => 'ro',
+ isa => 'FileHandle',
+ required => 0,
+ lazy => 1,
+ builder => '_build__bam_handle'
+);
+has '_currentread' => (
+ is => 'rw',
+ isa => 'HashRef',
+ required => 0,
+ writer => '_set_currentread'
+);
+
+### Private methods ###
+
+sub _build__bam_handle {
+ my ($self) = @_;
+ my $bamfile = $self->file;
+
+ open( my $bamh, "-|", $self->samtools_exec." view $bamfile" )
+ or die "Cannot open $bamfile";
+ return $bamh;
+}
+
+sub _binary_flag {
+ my ( $self, $flag ) = @_;
+ my $bin_flag = sprintf( "%b", int($flag) );
+ return $bin_flag;
+}
+
+sub _parse_read {
+ my ( $self, $line ) = @_;
+ chomp($line);
+
+ # Parse and return as a hash ref
+ my @fields = qw(QNAME FLAG RNAME POS MAPQ CIGAR RNEXT PNEXT TLEN SEQ QUAL);
+ my @cols = split( '\t', $line );
+ my %read;
+ $read{'READ'} = $line;
+ foreach my $i ( 0 .. ( scalar(@cols) - 1 ) ) {
+ if ( $i < scalar(@fields) ) {
+ $read{ $fields[$i] } = $cols[$i];
+ if ( $fields[$i] eq 'FLAG' ) {
+ $read{'BINARY_FLAG'} = $self->_binary_flag( int( $cols[$i] ) );
+ }
+ }
+ else {
+ $cols[$i] =~ /^([^:]+):[AifZHB]:(.+)/;
+ #my @tagged = split( ':', $cols[$i] );
+ #my $tag_key = shift @tagged;
+ #shift @tagged;
+ #$read{ $tag_key } = join(':', @tagged);
+ $read{ $1 } = $2;
+ }
+ }
+ return \%read;
+}
+
+### Public methods ###
+
+=seq_info
+Reads BAM header and returns a hash (keys are sequence ids, values are hash
+refs with keys as tags (like LN and M5))
+=cut
+
+sub seq_info {
+ my ($self) = @_;
+ my $bamfile = $self->file;
+
+ my ( %all_seq_info, $seq_name, %this_seq_info );
+ open( SINFO, "-|", $self->samtools_exec." view -H $bamfile | grep ^\@SQ | cut -f 2-" );
+ while ( my $line = <SINFO> ) {
+ chomp($line);
+ my @fields = split( '\t', $line );
+ $seq_name = shift(@fields);
+ $seq_name =~ s/SN://;
+ foreach my $item (@fields) {
+ my @parts = split( ':', $item );
+ my $tag = shift(@parts);
+ $this_seq_info{$tag} = join( ':', @parts );
+ foreach my $k (keys %this_seq_info){
+ $all_seq_info{$seq_name}->{$k} = $this_seq_info{$k};
+ }
+ }
+
+ }
+ return %all_seq_info;
+}
+
+=next_read
+Moves _currentread to the next entry in the BAM. Returns 0 if EOF.
+=cut
+
+sub next_read {
+ my ($self) = @_;
+ my $bh = $self->_bam_handle;
+ my $line = <$bh>;
+ if ( defined($line) ) {
+ chomp($line);
+ my $read = $self->_parse_read($line);
+ $self->_set_currentread($read);
+ return 1;
+ }
+ else {
+ return 0;
+ }
+}
+
+sub close_file_handle{
+ my ($self) = @_;
+ close $self->_bam_handle;
+}
+
+=read_info
+Returns info from _currentread = hash reference with field name as key.
+Standard fields are named as per the SAM format specification:
+1 : QNAME
+2 : FLAG
+3 : RNAME
+4 : POS
+5 : MAPQ
+6 : CIGAR
+7 : RNEXT
+8 : PNEXT
+9 : TLEN
+10 : SEQ
+11 : QUAL
+Additional fields will use their tag names.
+Complete line is returned with key READ
+=cut
+
+sub read_info {
+ my ($self) = @_;
+ return $self->_currentread;
+}
+
+=is_mapped
+Parses the flag for the current read and determines if mapped.
+Returns 0 or 1.
+=cut
+
+sub is_mapped {
+ my ($self) = @_;
+ my $flag = ${ $self->_currentread }{BINARY_FLAG};
+ my @flag_array = split( '', $flag );
+ my $resl;
+ if ( $flag_array[-3] ) { $resl = 0; }
+ else { $resl = 1; }
+ return $resl;
+}
+
+=is_reverse
+Parses the flag for the current read and determines if reverse
+complemented. Returns 0 or 1.
+=cut
+
+sub is_reverse {
+ my ($self) = @_;
+ my $flag = ${ $self->_currentread }{BINARY_FLAG};
+ my @flag_array = split( '', $flag );
+
+ #print @flag_array;
+ return $flag_array[-5];
+}
+
+__PACKAGE__->meta->make_immutable;
+no Moose;
+1;
diff --git a/lib/Bio/Tradis/Parser/Cigar.pm b/lib/Bio/Tradis/Parser/Cigar.pm
new file mode 100644
index 0000000..beae275
--- /dev/null
+++ b/lib/Bio/Tradis/Parser/Cigar.pm
@@ -0,0 +1,71 @@
+package Bio::Tradis::Parser::Cigar;
+
+# ABSTRACT: Take in a cigar string and output start and end relative to the reference sequence
+
+=head1 SYNOPSIS
+
+Take in a cigar string and output start and end relative to the reference sequence
+
+ use Bio::Tradis::Parser::Cigar;
+
+ my $cigar = Bio::Tradis::Parser::Cigar->new(coordinate => 123, cigar => '10S90M');
+ $cigar->start;
+ $cigar->end;
+
+=cut
+
+use Moose;
+
+has 'cigar' => ( is => 'ro', isa => 'Str', required => 1 );
+has 'coordinate' => ( is => 'ro', isa => 'Num', required => 1 );
+
+has '_results' => (is => 'ro', isa => 'HashRef', lazy => 1, builder => '_build__results');
+
+sub _build__results
+{
+ my($self) = @_;
+ my %results = ( start => 0, end => 0);
+ my $current_coordinate = $self->coordinate;
+
+ my @cigar_parts = $self->cigar =~ /(\d+[MIDNSHP=X])/g;
+ for my $cigar_item (@cigar_parts)
+ {
+ if( $cigar_item =~ /(\d+)([MIDNSHP=X])/)
+ {
+ my $number = $1;
+ my $action = $2;
+
+ if($action eq 'M' || $action eq 'X' || $action eq '=' )
+ {
+ $results{start} = $current_coordinate if($results{start} == 0);
+ $current_coordinate += $number;
+ $results{end} = $current_coordinate -1 if($results{end} < $current_coordinate);
+ }
+ elsif($action eq 'S' || $action eq 'D' || $action eq 'N')
+ {
+ $current_coordinate += $number;
+ }
+ elsif($action eq 'I' )
+ {
+ # do nothing
+ }
+ }
+ }
+
+ return \%results;
+}
+
+sub start
+{
+ my($self) = @_;
+ return $self->_results->{start};
+}
+
+sub end
+{
+ my($self) = @_;
+ return $self->_results->{end};
+}
+__PACKAGE__->meta->make_immutable;
+no Moose;
+1;
diff --git a/lib/Bio/Tradis/Parser/Fastq.pm b/lib/Bio/Tradis/Parser/Fastq.pm
new file mode 100644
index 0000000..88b9e68
--- /dev/null
+++ b/lib/Bio/Tradis/Parser/Fastq.pm
@@ -0,0 +1,101 @@
+package Bio::Tradis::Parser::Fastq;
+
+# ABSTRACT: Basic FastQ parser.
+
+=head1 SYNOPSIS
+
+Parses fastq files.
+
+ use Bio::Tradis::Parser::Fastq;
+
+ my $pipeline = Bio::Tradis::Parser::Fastq->new(file => 'abc');
+ $pipeline->next_read;
+ $pipeline->read_info;
+
+=cut
+
+use Moose;
+
+has 'file' => ( is => 'rw', isa => 'Str', required => 1 );
+has '_fastq_handle' => (
+ is => 'ro',
+ isa => 'FileHandle',
+ required => 0,
+ lazy => 1,
+ builder => '_build__fastq_handle'
+);
+has '_currentread' => (
+ is => 'rw',
+ isa => 'Str',
+ required => 0,
+ writer => '_set_currentread'
+);
+### Private methods ###
+
+sub _build__fastq_handle {
+ my ($self) = @_;
+ my $fastqfile = $self->file;
+
+ open( my $fqh, "<", $fastqfile ) or die "Cannot open $fastqfile";
+ return $fqh;
+}
+
+### Public methods ###
+
+=next_read
+Moves to the next read. Returns 1 if read exists, returns 0
+if EOF
+=cut
+
+sub next_read {
+ my ($self) = @_;
+ my $fqh = $self->_fastq_handle;
+
+ my $read = <$fqh>;
+ if ( defined($read) ) {
+ $self->_set_currentread($read);
+ return 1;
+ }
+ else {
+ return 0;
+ }
+}
+
+=read_info
+Returns an array of info for the read in an array.
+0 = id
+1 = sequence
+2 = quality string
+=cut
+sub read_info {
+ my ($self) = @_;
+ my $fqh = $self->_fastq_handle;
+
+ my @fastq_read;
+
+ # get id
+ my $id = $self->_currentread;
+ chomp($id);
+ $id =~ s/^\@//;
+ push( @fastq_read, $id );
+
+ # get sequence
+ my $seq = <$fqh>;
+ chomp($seq);
+ push( @fastq_read, $seq );
+
+ # skip + line
+ my $skip = <$fqh>;
+
+ # get quality
+ my $qual = <$fqh>;
+ chomp($qual);
+ push( @fastq_read, $qual );
+
+ return @fastq_read;
+
+}
+
+__PACKAGE__->meta->make_immutable;
+no Moose;
+1;
diff --git a/lib/Bio/Tradis/RemoveTags.pm b/lib/Bio/Tradis/RemoveTags.pm
new file mode 100644
index 0000000..7e00789
--- /dev/null
+++ b/lib/Bio/Tradis/RemoveTags.pm
@@ -0,0 +1,122 @@
+package Bio::Tradis::RemoveTags;
+
+# ABSTRACT: Remove tags from seqs a fastq file
+
+=head1 SYNOPSIS
+
+Reads in a fastq file with tradis tags already attached to the start of the sequence
+Removes tags from the sequence and quality strings
+Outputs a file *.rmtag.fastq unless an out file is specified
+
+ use Bio::Tradis::RemoveTags;
+
+ my $pipeline = Bio::Tradis::RemoveTags->new(fastqfile => 'abc', tag => 'abc');
+ $pipeline->remove_tags();
+
+=head1 PARAMETERS
+
+=head2 Required
+
+=over
+
+=item * C<fastqfile> - path to/name of file to filter
+
+=item * C<tag> - TraDIS tag to remove
+
+=back
+
+=head2 Optional
+
+=over
+
+=item * C<mismatch> - number of mismatches to allow when removing the tag. Default = 0
+
+=item * C<outfile> - defaults to C<file.rmtag.fastq> for and input file named C<file.fastq>
+
+=back
+
+=head1 METHODS
+
+C<remove_tags> - output all reads with the tags removed to C<outfile>
+
+=cut
+
+use Moose;
+use Bio::Tradis::Parser::Fastq;
+
+has 'fastqfile' => ( is => 'rw', isa => 'Str', required => 1 );
+has 'tag' => ( is => 'rw', isa => 'Str', required => 1 );
+has 'mismatch' => ( is => 'rw', isa => 'Int', required => 0 );
+has 'outfile' => (
+ is => 'rw',
+ isa => 'Str',
+ required => 0,
+ default => sub {
+ my ($self) = @_;
+ my $o = $self->bamfile;
+ $o =~ s/\.fastq/\.rmtag\.fastq/;
+ return $o;
+ }
+);
+
+sub remove_tags {
+ my ($self) = @_;
+ my $tag = uc( $self->tag );
+ my $outfile = $self->outfile;
+
+ #set up fastq parser
+ my $filename = $self->fastqfile;
+ my $pars = Bio::Tradis::Parser::Fastq->new( file => $filename );
+
+ # create file handle for output
+ open( OUTFILE, ">$outfile" );
+
+ # loop through fastq
+ while ( $pars->next_read ) {
+ my @read = $pars->read_info;
+ my $id = $read[0];
+ my $seq_string = $read[1];
+ my $qual_string = $read[2];
+
+ # remove the tag
+ my $rm = 0;
+ if ( $self->mismatch == 0 ) {
+ if ( $seq_string =~ m/^$tag/ ) { $rm = 1; }
+ }
+ else {
+ my $mm = $self->_tag_mismatch($seq_string);
+ if ( $mm <= $self->mismatch ) { $rm = 1; }
+ }
+
+ if ($rm) {
+ my $l = length($tag);
+ $seq_string = substr( $seq_string, $l );
+ $qual_string = substr( $qual_string, $l );
+ }
+
+ print OUTFILE "\@$id\n";
+ print OUTFILE $seq_string . "\n+\n";
+ print OUTFILE $qual_string . "\n";
+ }
+ close OUTFILE;
+ return 1;
+}
+
+sub _tag_mismatch {
+ my ( $self, $seq_string ) = @_;
+ my $tag_len = length( $self->tag );
+
+ my @tag = split( "", $self->tag );
+ my @seq = split( "", substr( $seq_string, 0, $tag_len ) );
+ my $mismatches = 0;
+ foreach my $i ( 0 .. ( $tag_len - 1 ) ) {
+ if ( $tag[$i] ne $seq[$i] ) {
+ $mismatches++;
+ }
+ }
+ return $mismatches;
+}
+
+__PACKAGE__->meta->make_immutable;
+no Moose;
+1;
diff --git a/lib/Bio/Tradis/RunTradis.pm b/lib/Bio/Tradis/RunTradis.pm
new file mode 100644
index 0000000..e1fc6b8
--- /dev/null
+++ b/lib/Bio/Tradis/RunTradis.pm
@@ -0,0 +1,511 @@
+package Bio::Tradis::RunTradis;
+
+# ABSTRACT: Perform all steps required for a tradis analysis
+
+=head1 SYNOPSIS
+
+Takes a fastq file with tags already attached, filters the tags matching user input,
+removes the tags, maps to a reference (.fa) and generates insertion site plots for use in
+Artemis (or other genome browsers), mapped BAM files for each lane and a statistical summary of the analysis.
+
+ use Bio::Tradis::RunTradis;
+
+ my $pipeline = Bio::Tradis::RunTradis->new(
+ fastqfile => 'abc',
+ reference => 'abc',
+ tag => 'abc',
+ tagdirection => '5'|'3'
+ );
+ $pipeline->run_tradis();
+
+=head1 PARAMETERS
+
+=head2 Required
+
+=over
+
+=item * C<fastqfile> - file containing a list of fastqs (gzipped or raw) to run the
+ complete analysis on. This includes all (including
+ intermediary format conversion and sorting) steps starting from
+ filtering.
+
+=item * C<tag> - TraDIS tag to filter and then remove
+
+=item * C<reference> - path to/name of reference genome in fasta format (.fa)
+
+=back
+
+=head2 Optional
+
+=over
+
+=item * C<mismatch> - number of mismatches to allow when filtering/removing the tag. Default = 0
+
+=item * C<tagdirection> - direction of the tag, 5' or 3'. Default = 3
+
+=item * C<mapping_score> - cutoff value for mapping score when creating insertion site plots. Default = 30
+
+=back
+
+=head1 METHODS
+
+C<run_tradis> - run complete analysis with given parameters
+
+=cut
+
+use Cwd;
+use Moose;
+use File::Temp;
+use File::Path 'rmtree';
+use Bio::Tradis::FilterTags;
+use Bio::Tradis::RemoveTags;
+use Bio::Tradis::Map;
+use Bio::Tradis::TradisPlot;
+use Bio::Tradis::Exception;
+use Bio::Tradis::Samtools;
+
+has 'verbose' => ( is => 'rw', isa => 'Bool', default => 0 );
+has 'fastqfile' => ( is => 'rw', isa => 'Str', required => 1 );
+has '_unzipped_fastq' =>
+ ( is => 'rw', isa => 'Str', lazy => 1, builder => '_build__unzipped_fastq' );
+has 'tag' => ( is => 'ro', isa => 'Str', required => 1 );
+has 'tagdirection' =>
+ ( is => 'ro', isa => 'Str', required => 1, default => '3' );
+has 'mismatch' => ( is => 'rw', isa => 'Int', required => 1, default => 0 );
+has 'mapping_score' =>
+ ( is => 'ro', isa => 'Int', required => 1, default => 30 );
+has 'reference' => ( is => 'rw', isa => 'Str', required => 1 );
+has 'outfile' => (
+ is => 'rw',
+ isa => 'Str',
+ required => 0,
+ default => sub {
+ my ($self) = @_;
+ my @dirs = split( '/', $self->fastqfile );
+ my $o = pop(@dirs);
+ $o =~ s/fastq/out/;
+ return $o;
+ }
+);
+has 'smalt_k' => ( is => 'rw', isa => 'Maybe[Int]', required => 0 );
+has 'smalt_s' => ( is => 'rw', isa => 'Maybe[Int]', required => 0 );
+has 'smalt_y' => ( is => 'rw', isa => 'Maybe[Num]', required => 0, default => 0.96 );
+has 'smalt_r' => ( is => 'rw', isa => 'Maybe[Int]', required => 0, default => -1);
+has 'smalt_n' => ( is => 'rw', isa => 'Maybe[Int]', required => 0, default => 1);
+has 'samtools_exec' => ( is => 'rw', isa => 'Str', default => 'samtools' );
+
+has '_temp_directory' => (
+ is => 'rw',
+ isa => 'Str',
+ required => 0,
+ lazy => 1,
+ builder => '_build__temp_directory'
+);
+has 'output_directory' => (
+ is => 'rw',
+ isa => 'Str',
+ required => 0,
+ lazy => 1,
+ builder => '_build_output_directory'
+);
+has '_stats_handle' => ( is => 'ro', isa => 'FileHandle', required => 1 );
+has '_sequence_info' => (
+ is => 'rw',
+ isa => 'HashRef',
+ required => 0,
+ lazy => 1,
+ builder => '_build__sequence_info'
+);
+has '_current_directory' => (
+ is => 'rw',
+ isa => 'Str',
+ required => 0,
+ lazy => 1,
+ builder => '_build__current_directory'
+);
+
+sub _is_gz {
+ my ($self) = @_;
+ my $fq = $self->fastqfile;
+
+ if ( $fq =~ /\.gz/ ) {
+ return 1;
+ }
+ else {
+ return 0;
+ }
+}
+
+sub _build__unzipped_fastq {
+ my ($self) = @_;
+ my $fq = $self->fastqfile;
+ my $temporary_directory = $self->_temp_directory;
+
+ if ( $self->_is_gz ) {
+ $fq =~ /([^\/]+)$/;
+ my $newfq = $1;
+ $newfq =~ s/\.gz//;
+ if ( !-e "$temporary_directory/$newfq" ) {
+ `gunzip -c $fq > $temporary_directory/$newfq`;
+ }
+ return "$temporary_directory/$newfq";
+ }
+ else {
+ return $fq;
+ }
+}
+
+sub _build__stats_handle {
+ my ($self) = @_;
+ my $outfile = $self->outfile;
+
+ open( my $stats, ">", "$outfile.stats" );
+ return $stats;
+}
+
+sub _build__sequence_info {
+ my ($self) = @_;
+ my $temporary_directory = $self->_temp_directory;
+ open( GREP,
+ "grep \@SQ $temporary_directory/mapped.sam | awk '{print \$2, \$3}' |"
+ );
+ my %sns = ();
+ while ( my $sn = <GREP> ) {
+ chomp($sn);
+ $sn =~ /SN:(\S+)\s+LN:(\d+)/;
+ $sns{$1} = $2;
+ }
+ return \%sns;
+}
+
+sub _build__temp_directory {
+ my ($self) = @_;
+ my $tmp_dir = File::Temp->newdir( 'tmp_run_tradis_XXXXX',
+ CLEANUP => 0,
+ DIR => $self->output_directory );
+ return $tmp_dir->dirname;
+}
+
+sub _build_output_directory {
+ return cwd();
+}
+
+sub _build__current_directory {
+ my ($self) = @_;
+ my $fq = $self->fastqfile;
+
+ my @dirs = split( '/', $fq );
+ pop(@dirs);
+ return join( '/', @dirs );
+}
+
+sub run_tradis {
+ my ($self) = @_;
+ my $temporary_directory = $self->_temp_directory;
+ my $fq = $self->fastqfile;
+
+ my $ref = $self->reference;
+ Bio::Tradis::Exception::RefNotFound->throw( error => "$ref not found\n" ) unless( -e $ref );
+
+ print STDERR "::::::::::::::::::\n$fq\n::::::::::::::::::\n\n" if($self->verbose);
+
+ # Step 1: Filter tags that match user input tag
+ print STDERR "..........Step 1: Filter tags that match user input tag\n" if($self->verbose);
+ $self->_filter;
+
+ print STDERR "..........Step 1.1: Check that at least one read started with the tag\n" if($self->verbose);
+ $self->_check_filter;
+
+ # Step 2: Remove the tag from the sequence and quality strings
+ print STDERR
+"..........Step 2: Remove the tag from the sequence and quality strings\n" if($self->verbose);
+ $self->_remove;
+
+ # Step 3: Map file to reference
+ print STDERR "..........Step 3: Map file to reference\n" if($self->verbose);
+ $self->_map;
+
+ # Step 4: Convert output from SAM to BAM, sort and index
+ print STDERR
+ "..........Step 3.5: Convert output from SAM to BAM and sort\n" if($self->verbose);
+ $self->_sam2bam;
+ $self->_sort_bam;
+ $self->_bamcheck;
+
+ # Step 5: Generate plot
+ print STDERR "..........Step 4: Generate plot\n" if($self->verbose);
+ $self->_make_plot;
+
+ # Step 6: Generate statistics
+ print STDERR "..........Step 5: Generate statistics\n" if($self->verbose);
+ $self->_stats;
+
+ # Step 7: Move files to current directory
+ print STDERR "..........Step 6: Move files to current directory\n" if($self->verbose);
+ my $outfile = $self->outfile;
+ my $output_directory = $self->output_directory;
+ system("mv $temporary_directory/$outfile* $output_directory");
+ system("mv $temporary_directory/mapped.sort.bam $output_directory/$outfile.mapped.bam");
+ system("mv $temporary_directory/mapped.sort.bam.bai $output_directory/$outfile.mapped.bam.bai");
+ system("mv $temporary_directory/mapped.bamcheck $output_directory/$outfile.mapped.bamcheck");
+
+ # Clean up
+ print STDERR "..........Clean up\n" if($self->verbose);
+
+ rmtree($temporary_directory);
+
+ return 1;
+}
+
+sub _filter {
+ my ($self) = @_;
+ my $temporary_directory = $self->_temp_directory;
+ my $fqfile = $self->_unzipped_fastq;
+ my $tag = $self->tag;
+ my $mm = $self->mismatch;
+
+ my $filter = Bio::Tradis::FilterTags->new(
+ fastqfile => $fqfile,
+ tag => $tag,
+ mismatch => $mm,
+ outfile => "$temporary_directory/filter.fastq"
+ )->filter_tags;
+}
+
+sub _check_filter {
+ my ($self) = @_;
+ my $temporary_directory = $self->_temp_directory;
+ my $filtered_file_filename = "$temporary_directory/filter.fastq";
+ open my $filtered_file, '<', $filtered_file_filename or
+ Bio::Tradis::Exception::TagFilterError->throw( error => "There was a problem filtering reads by the specified tag. Please check all input files are Fastq formatted and that at least one read in each starts with the specified tag\n" );
+ my @first_read_data;
+ while( my $line = <$filtered_file> ) {
+ last if $. > 4;
+ chomp($line);
+ push @first_read_data, $line;
+ }
+ my $number_of_read_lines = scalar @first_read_data;
+ if ( $number_of_read_lines ne 4) {
+ # There wasn't enough data for a complete read
+ Bio::Tradis::Exception::TagFilterError->throw( error => "There was a problem filtering reads by the specified tag. Please check all input files are Fastq formatted and that at least one read in each starts with the specified tag\n" );
+ }
+ my $read_plus_sign = $first_read_data[2];
+ if ( $read_plus_sign ne '+' ) {
+ # The first 'read' didn't have a '+' on the third line, suspicious
+ Bio::Tradis::Exception::TagFilterError->throw( error => "There was a problem filtering reads by the specified tag. Please check all input files are Fastq formatted and that at least one read in each starts with the specified tag\n" );
+ }
+ # I'm not proposing further (more detailed) validation here
+ close $filtered_file;
+}
+
+sub _remove {
+ my ($self) = @_;
+ my $temporary_directory = $self->_temp_directory;
+ my $tag = $self->tag;
+ my $mm = $self->mismatch;
+
+ my $rm_tags = Bio::Tradis::RemoveTags->new(
+ fastqfile => "$temporary_directory/filter.fastq",
+ tag => $tag,
+ mismatch => $mm,
+ outfile => "$temporary_directory/tags_removed.fastq"
+ )->remove_tags;
+}
+
+sub _map {
+ my ($self) = @_;
+ my $temporary_directory = $self->_temp_directory;
+
+ my $ref = $self->reference;
+
+ my $mapping = Bio::Tradis::Map->new(
+ fastqfile => "$temporary_directory/tags_removed.fastq",
+ reference => "$ref",
+ refname => "$temporary_directory/ref.index",
+ outfile => "$temporary_directory/mapped.sam",
+ smalt_k => $self->smalt_k,
+ smalt_s => $self->smalt_s,
+ smalt_y => $self->smalt_y,
+ smalt_r => $self->smalt_r,
+ smalt_n => $self->smalt_n
+ );
+ $mapping->index_ref;
+ $mapping->do_mapping;
+}
+
+sub _sam2bam {
+ my ($self) = @_;
+ my $temporary_directory = $self->_temp_directory;
+
+ system(
+$self->samtools_exec." view -b -o $temporary_directory/mapped.bam -S $temporary_directory/mapped.sam"
+ );
+ return 1;
+}
+
+sub _sort_bam {
+ my ($self) = @_;
+ my $temporary_directory = $self->_temp_directory;
+
+ my $samtools_obj = Bio::Tradis::Samtools->new(exec => $self->samtools_exec, threads => $self->smalt_n);
+ $samtools_obj->run_sort("$temporary_directory/mapped.bam","$temporary_directory/mapped.sort.bam");
+ $samtools_obj->run_index("$temporary_directory/mapped.sort.bam");
+ return 1;
+}
+
+sub _bamcheck {
+ my ($self) = @_;
+ my $temporary_directory = $self->_temp_directory;
+
+ system(
+$self->samtools_exec." stats $temporary_directory/mapped.sort.bam > $temporary_directory/mapped.bamcheck"
+ );
+ return 1;
+}
+
+sub _make_plot {
+ my ($self) = @_;
+ my $temporary_directory = $self->_temp_directory;
+ my $ref = $self->reference;
+ my $outfile = $self->outfile;
+ my $tr_d = $self->tagdirection;
+
+ my $plot = Bio::Tradis::TradisPlot->new(
+ mappedfile => "$temporary_directory/mapped.sort.bam",
+ mapping_score => $self->mapping_score,
+ outfile => "$temporary_directory/$outfile"
+ )->plot;
+
+ # if tag direction is 5, reverse plot columns
+ if ( $self->tagdirection eq '5' ) {
+ print STDERR "Tag direction = 5. Reversing plot..\n" if($self->verbose);
+ $self->_reverse_plots;
+ }
+ return 1;
+}
+
+sub _reverse_plots {
+ my ($self) = @_;
+ my $temporary_directory = $self->_temp_directory;
+ my $outfile = $self->outfile;
+ my @seqnames = keys %{ $self->_sequence_info };
+
+ my @current_plots =
+ glob("$temporary_directory/$outfile.*.insert_site_plot.gz");
+
+ foreach my $plotname (@current_plots) {
+ print STDERR "Reversing $plotname\n" if($self->verbose);
+
+ #my $plotname = $self->_plotname($sn);
+ system("gunzip -c $plotname > $temporary_directory/tmp.plot");
+ system(
+"awk '{ t = \$1; \$1 = \$2; \$2 = t; print; }' $temporary_directory/tmp.plot > rv_plot"
+ );
+ system("gzip -c rv_plot > $plotname");
+ }
+ unlink("$temporary_directory/tmp.plot");
+ unlink("rv_plot");
+}
+
+sub _stats {
+ my ($self) = @_;
+ my $outfile = $self->outfile;
+ my $temporary_directory = $self->_temp_directory;
+ my $fq = $self->_unzipped_fastq;
+ my $seq_info = $self->_sequence_info;
+
+ #write header to stats file
+ $self->_write_stats_header;
+
+ # Add file name and number of reads in it
+ my @fql = split( "/", $fq );
+ my $stats = "$fql[-1],";
+ my $total_reads = `wc $fq | awk '{print \$1/4}'`;
+ chomp($total_reads);
+ $stats .= "$total_reads,";
+
+ # Matching reads
+ my $matching =
+ `wc $temporary_directory/filter.fastq | awk '{print \$1/4}'`;
+ chomp($matching);
+ $stats .= "$matching,";
+ $stats .= ( $matching / $total_reads ) * 100 . ",";
+
+ # Mapped reads
+ my $mapped = $self->_number_of_mapped_reads;
+ $stats .= "$mapped,";
+ $stats .= ( $mapped / $matching ) * 100 . ",";
+
+ # Unique insertion sites
+ my ( $total_uis, $total_seq_len );
+ foreach my $si ( keys %{$seq_info} ) {
+ my $plotname = $self->_plotname($si);
+ system(
+"gunzip -c $temporary_directory/$plotname > $temporary_directory/tmp.plot"
+ );
+ my $uis = `grep -c -v "0 0" $temporary_directory/tmp.plot`;
+ chomp($uis);
+ $total_uis += $uis;
+ $stats .= "$uis,";
+ my $seqlen = ${$seq_info}{$si};
+ $total_seq_len += $seqlen;
+ my $uis_per_seqlen = "NaN";
+ $uis_per_seqlen = $seqlen / $uis if ( $uis > 0 );
+ chomp($uis_per_seqlen);
+ $stats .= "$uis_per_seqlen,";
+ }
+ $stats .= "$total_uis,";
+ my $t_uis_p_l = "NaN";
+ $t_uis_p_l = $total_seq_len / $total_uis if ( $total_uis > 0 );
+ $stats .= "$t_uis_p_l\n";
+ print { $self->_stats_handle } $stats;
+}
+
+sub _write_stats_header {
+ my ($self) = @_;
+ my @seqnames = keys %{ $self->_sequence_info };
+ my @fields = (
+ "File",
+ "Total Reads",
+ "Reads Matched",
+ "\% Matched",
+ "Reads Mapped",
+ "\% Mapped"
+ );
+ print { $self->_stats_handle } join( ",", @fields ) . ",";
+ foreach my $sn (@seqnames) {
+ print { $self->_stats_handle } "Unique Insertion Sites : $sn,";
+ print { $self->_stats_handle } "Seq Len/UIS : $sn,";
+ }
+ print { $self->_stats_handle } "Total Unique Insertion Sites,";
+ print { $self->_stats_handle } "Total Seq Len/Total UIS\n";
+}
+
+sub _plotname {
+ my ( $self, $seq_name ) = @_;
+ my $outfile = $self->outfile;
+
+ $seq_name =~ s/[^\w\d\.]/_/g;
+ my $plotfile_name = "$outfile.$seq_name.insert_site_plot.gz";
+ return $plotfile_name;
+}
+
+sub _number_of_mapped_reads {
+ my ($self) = @_;
+ my $temporary_directory = $self->_temp_directory;
+
+ my $pars =
+ Bio::Tradis::Parser::Bam->new(
+ file => "$temporary_directory/mapped.bam" );
+ my $c = 0;
+ while ( $pars->next_read ) {
+ if ( $pars->is_mapped ) {
+ $c++;
+ }
+ }
+ return $c;
+}
+
+__PACKAGE__->meta->make_immutable;
+no Moose;
+1;
diff --git a/lib/Bio/Tradis/Samtools.pm b/lib/Bio/Tradis/Samtools.pm
new file mode 100644
index 0000000..c15d626
--- /dev/null
+++ b/lib/Bio/Tradis/Samtools.pm
@@ -0,0 +1,102 @@
+package Bio::Tradis::Samtools;
+
+# ABSTRACT: Change samtools syntax depending on version found
+
+=head1 SYNOPSIS
+
+Change samtools syntax depending on version found
+ use Bio::Tradis::Samtools;
+
+ my $obj = Bio::Tradis::Samtools->new(
+ exec => 'samtools'
+ );
+
+ $obj->run_sort();
+
+=cut
+
+use Moose;
+use File::Spec;
+
+has 'exec' => ( is => 'ro', isa => 'Str', default => 'samtools' );
+has 'threads' => ( is => 'ro', isa => 'Int', default => 1 );
+has 'exec_version' => ( is => 'ro', isa => 'Str', lazy => 1, builder => '_build_exec_version' );
+
+sub _build_exec_version {
+ my ($self) = @_;
+
+ my $fp = $self->find_exe($self->exec);
+ if(!$fp)
+ {
+ exit("ERROR: Can't find required ".$self->exec." in your \$PATH");
+ }
+ my $cmd_version = $self->exec." 2>&1 | grep Version";
+ my ($version_string) = qx($cmd_version);
+
+ if(defined($version_string))
+ {
+ #Version: 0.1.19-44428cd
+ #Version: 1.2 (using htslib 1.2)
+ # we dont use 3rd number in version so just look for 0.1, 1.2
+ if($version_string =~ /Version:[\t\s]+(\d+)\.(\d+)/)
+ {
+ return $1.'.'.$2;
+ }
+ else
+ {
+ print STDERR "ERROR: Couldn't identify samtools version";
+ }
+ }
+ else
+ {
+ print STDERR "ERROR: Couldn't identify samtools version";
+ }
+ # reasonable fallback
+ return '0.1';
+}
+
+sub find_exe {
+ my ( $self, $bin ) = @_;
+ for my $dir ( File::Spec->path ) {
+ my $exe = File::Spec->catfile( $dir, $bin );
+ return $exe if -x $exe;
+ }
+ return;
+}
+
+sub _is_version_less_than_1 {
+ my ($self) = @_;
+ if($self->exec_version < 1.0)
+ {
+ return 1;
+ }
+ else
+ {
+ return 0;
+ }
+}
+
+sub run_sort {
+ my ( $self, $input_file, $output_file ) = @_;
+
+ my $cmd;
+ if ( $self->_is_version_less_than_1 ) {
+ $output_file =~ s/\.bam//i;
+ $cmd = join( ' ', ( $self->exec, 'sort', $input_file, $output_file) );
+ }
+ else {
+ $cmd = join( ' ', ( $self->exec, 'sort', '-@', $self->threads, '-O', 'bam', '-T', $input_file.'.tmp', '-o', $output_file, $input_file ) );
+ }
+ system($cmd);
+}
+
+sub run_index {
+ my ( $self, $input_file ) = @_;
+ system( $self->exec . " index $input_file" );
+}
+
+no Moose;
+__PACKAGE__->meta->make_immutable;
+
+1;
+
diff --git a/lib/Bio/Tradis/TradisPlot.pm b/lib/Bio/Tradis/TradisPlot.pm
new file mode 100644
index 0000000..a95ec0a
--- /dev/null
+++ b/lib/Bio/Tradis/TradisPlot.pm
@@ -0,0 +1,60 @@
+package Bio::Tradis::TradisPlot;
+
+# ABSTRACT: Generate plots as part of a tradis analysis
+
+=head1 SYNOPSIS
+
+Generate insertion plots for Artemis from a mapped fastq file and a reference
+in GFF format
+
+ use Bio::Tradis::TradisPlot;
+
+ my $pipeline = Bio::Tradis::TradisPlot->new(mappedfile => 'abc');
+ $pipeline->plot();
+
+=head1 PARAMETERS
+
+=head2 Required
+
+C<mappedfile> - mapped and sorted BAM file
+
+=head2 Optional
+
+=over
+
+=item * C<outfile> - base name to assign to the resulting insertion site plot. Default = tradis.plot
+
+=item * C<mapping_score> - cutoff value for mapping score. Default = 30
+
+=back
+
+=head1 METHODS
+
+C<plot> - create insertion site plots for reads in `mappedfile`. This file will be readable by the L<Artemis genome browser|http://www.sanger.ac.uk/resources/software/artemis/>
+
+=cut
+
+use Moose;
+use Bio::Tradis::Analysis::InsertSite;
+
+has 'mappedfile' => ( is => 'rw', isa => 'Str', required => 1 );
+has 'outfile' =>
+ ( is => 'rw', isa => 'Str', required => 1, default => 'tradis.plot' );
+has 'mapping_score' =>
+ ( is => 'rw', isa => 'Int', required => 1, default => 30 );
+
+sub plot {
+ my ($self) = @_;
+
+ Bio::Tradis::Analysis::InsertSite->new(
+ filename => $self->mappedfile,
+ output_base_filename => $self->outfile,
+ mapping_score => $self->mapping_score
+ )->create_plots;
+
+ return 1;
+}
+
+__PACKAGE__->meta->make_immutable;
+no Moose;
+1;
diff --git a/recipes/Tradis_SR_RR_12dark_42r1_rehyb12_index8.xml b/recipes/Tradis_SR_RR_12dark_42r1_rehyb12_index8.xml
new file mode 100644
index 0000000..bd4b9b4
--- /dev/null
+++ b/recipes/Tradis_SR_RR_12dark_42r1_rehyb12_index8.xml
@@ -0,0 +1,461 @@
+<?xml version="1.0"?>
+<RecipeFile xmlns:xsd="http://www.w3.org/2001/XMLSchema" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
+ <Protocol>
+ <ChemistryRef Description="Cluster Generation SR" ChemistryName="ClusterGenerationSR" />
+ <ChemistryRef Description="Skip Base 1" ChemistryName="FirstBase"/>
+ <ChemistryRef Description="Skip Base 2" ChemistryName="CompleteCycle_Low"/>
+ <ChemistryRef Description="Skip Base 3" ChemistryName="CompleteCycle_Low"/>
+ <ChemistryRef Description="Skip Base 4" ChemistryName="CompleteCycle_Low"/>
+ <ChemistryRef Description="Skip Base 5" ChemistryName="CompleteCycle_Low"/>
+ <ChemistryRef Description="Skip Base 6" ChemistryName="CompleteCycle_Low"/>
+ <ChemistryRef Description="Skip Base 7" ChemistryName="CompleteCycle_Low"/>
+ <ChemistryRef Description="Skip Base 8" ChemistryName="CompleteCycle_Low"/>
+ <ChemistryRef Description="Skip Base 9" ChemistryName="CompleteCycle_Low"/>
+ <ChemistryRef Description="Skip Base 10" ChemistryName="CompleteCycle_Low"/>
+ <ChemistryRef Description="Skip Base 11" ChemistryName="CompleteCycle_Low"/>
+ <ChemistryRef Description="Skip Base 12" ChemistryName="CompleteCycle_Low"/>
+ <ChemistryRef Description="End Deblock" ChemistryName="EndDeblock" />
+ <ReadRef Description="Read #1" ReadName="Read1" />
+ <ChemistryRef Description="Rehyb Read1 Primer" ChemistryName="RehybRead1Primer"/>
+ <ReadRef Description="Read initial 12" ReadName="ReadInitial" />
+ <ChemistryRef Description="Index Preparation i7" ChemistryName="IndexPreparation-i7" />
+ <ReadRef Description="IndexRead i7" ReadName="IndexRead-i7" />
+ <ChemistryRef Description="End Deblock" ChemistryName="EndDeblock" />
+ <ChemistryRef Description="Post Run Step" ChemistryName="PostRunForOnBoardClustering" />
+ </Protocol>
+ <ChemistryDefinitions>
+ <ChemistryDefinition Name="CompleteCycle">
+ <ChemistryStep Description="Deblock" Repeat="1">
+ <PumpToFlowcell Solution="0" ReagentName="USB" AspirationRate="1500" DispenseRate="2500" Volume="120" Duration="0" ToPosition="0" />
+ <Temp Temperature="60" Duration="0" />
+ <PumpToFlowcell Solution="0" ReagentName="CRM" AspirationRate="1000" DispenseRate="2500" Volume="110" Duration="0" ToPosition="0" />
+ <Wait Duration="5000" />
+ <DispenseAndWait Solution="0" AspirationRate="0" DispenseRate="0" Volume="0" Duration="10000" ToPosition="0" />
+ <PumpToFlowcell Solution="0" ReagentName="USB" AspirationRate="1000" DispenseRate="2500" Volume="24" Duration="0" ToPosition="0" />
+ <Wait Duration="5000" />
+ <DispenseAndWait Solution="0" AspirationRate="0" DispenseRate="0" Volume="0" Duration="5000" ToPosition="0" />
+ </ChemistryStep>
+ <ChemistryStep Description="Buffer Wash" Repeat="1">
+ <PumpToFlowcell Solution="0" ReagentName="USB" AspirationRate="1500" DispenseRate="2500" Volume="250" Duration="0" ToPosition="0" />
+ </ChemistryStep>
+ <ChemistryStep Description="Incorporation" Repeat="1">
+ <PumpToFlowcell Solution="0" ReagentName="IMM" AspirationRate="1000" DispenseRate="2500" Volume="110" Duration="0" ToPosition="0" />
+ <Temp Temperature="65" Duration="0" />
+ <Wait Duration="25000" />
+ <PumpToFlowcell Solution="0" ReagentName="USB" AspirationRate="1000" DispenseRate="2500" Volume="24" Duration="0" ToPosition="0" />
+ <Wait Duration="5000" />
+ <DispenseAndWait Solution="0" AspirationRate="0" DispenseRate="0" Volume="0" Duration="15000" ToPosition="0" />
+ <PumpToFlowcell Solution="0" ReagentName="USB" AspirationRate="1500" DispenseRate="2500" Volume="120" Duration="0" ToPosition="0" />
+ <Temp Temperature="20" Duration="15000" />
+ <PumpToFlowcell Solution="0" ReagentName="SRM" AspirationRate="750" DispenseRate="2500" Volume="75" Duration="0" ToPosition="0" />
+ <Wait Duration="5000" />
+ <DispenseAndWait Solution="0" AspirationRate="0" DispenseRate="0" Volume="0" Duration="10000" ToPosition="0" />
+ </ChemistryStep>
+ </ChemistryDefinition>
+ <ChemistryDefinition Name="FirstBase">
+ <ChemistryStep Description="Incorporation" Repeat="1">
+ <DispenseAndWait Solution="0" AspirationRate="0" DispenseRate="0" Volume="0" Duration="1" ToPosition="0" />
+ <Temp Temperature="60" Duration="0" />
+ <PumpToFlowcell Solution="0" ReagentName="USB" AspirationRate="1500" DispenseRate="2500" Volume="120" Duration="0" ToPosition="0" />
+ <PumpToFlowcell Solution="0" ReagentName="IMM" AspirationRate="1000" DispenseRate="2500" Volume="110" Duration="0" ToPosition="0" />
+ <Temp Temperature="65" Duration="0" />
+ <Wait Duration="5000" />
+ <DispenseAndWait Solution="0" AspirationRate="0" DispenseRate="0" Volume="0" Duration="20000" ToPosition="0" />
+ <PumpToFlowcell Solution="0" ReagentName="USB" AspirationRate="1000" DispenseRate="2500" Volume="24" Duration="0" ToPosition="0" />
+ <Wait Duration="5000" />
+ <DispenseAndWait Solution="0" AspirationRate="0" DispenseRate="0" Volume="0" Duration="15000" ToPosition="0" />
+ <PumpToFlowcell Solution="0" ReagentName="USB" AspirationRate="1500" DispenseRate="2500" Volume="120" Duration="0" ToPosition="0" />
+ <Temp Temperature="20" Duration="15000" />
+ <PumpToFlowcell Solution="0" ReagentName="SRM" AspirationRate="750" DispenseRate="2500" Volume="75" Duration="0" ToPosition="0" />
+ <Wait Duration="5000" />
+ <DispenseAndWait Solution="0" AspirationRate="0" DispenseRate="0" Volume="0" Duration="10000" ToPosition="0" />
+ </ChemistryStep>
+ </ChemistryDefinition>
+ <ChemistryDefinition Name="EndDeblock">
+ <ChemistryStep Description="Deblock" Repeat="1">
+ <PumpToFlowcell Solution="0" ReagentName="USB" AspirationRate="1500" DispenseRate="2500" Volume="120" Duration="0" ToPosition="0" />
+ <Temp Temperature="60" Duration="0" />
+ <PumpToFlowcell Solution="0" ReagentName="CRM" AspirationRate="1000" DispenseRate="2500" Volume="110" Duration="0" ToPosition="0" />
+ <Wait Duration="5000" />
+ <DispenseAndWait Solution="0" AspirationRate="0" DispenseRate="0" Volume="0" Duration="40000" ToPosition="0" />
+ <PumpToFlowcell Solution="0" ReagentName="USB" AspirationRate="1000" DispenseRate="2500" Volume="24" Duration="0" ToPosition="0" />
+ <Wait Duration="5000" />
+ <DispenseAndWait Solution="0" AspirationRate="0" DispenseRate="0" Volume="0" Duration="35000" ToPosition="0" />
+ <PumpToFlowcell Solution="0" ReagentName="USB" AspirationRate="1500" DispenseRate="2500" Volume="120" Duration="0" ToPosition="0" />
+ <TempOff />
+ </ChemistryStep>
+ </ChemistryDefinition>
+ <ChemistryDefinition Name="CompleteCycle_Low">
+ <ChemistryStep Description="Deblock" Repeat="1">
+ <PumpToFlowcell Solution="0" ReagentName="USB" AspirationRate="1500" DispenseRate="2500" Volume="120" Duration="0" ToPosition="0" />
+ <Temp Temperature="60" Duration="0" />
+ <PumpToFlowcell Solution="0" ReagentName="CRM" AspirationRate="1000" DispenseRate="2500" Volume="110" Duration="0" ToPosition="0" />
+ <Wait Duration="5000" />
+ <DispenseAndWait Solution="0" AspirationRate="0" DispenseRate="0" Volume="0" Duration="10000" ToPosition="0" />
+ <PumpToFlowcell Solution="0" ReagentName="USB" AspirationRate="1000" DispenseRate="2500" Volume="24" Duration="0" ToPosition="0" />
+ <Wait Duration="5000" />
+ <DispenseAndWait Solution="0" AspirationRate="0" DispenseRate="0" Volume="0" Duration="5000" ToPosition="0" />
+ </ChemistryStep>
+ <ChemistryStep Description="Buffer Wash" Repeat="1">
+ <PumpToFlowcell Solution="0" ReagentName="USB" AspirationRate="1500" DispenseRate="2500" Volume="250" Duration="0" ToPosition="0" />
+ </ChemistryStep>
+ <ChemistryStep Description="Incorporation" Repeat="1">
+ <PumpToFlowcell Solution="0" ReagentName="IMM" AspirationRate="1000" DispenseRate="2500" Volume="110" Duration="0" ToPosition="0" />
+ <Temp Temperature="65" Duration="0" />
+ <Wait Duration="25000" />
+ <PumpToFlowcell Solution="0" ReagentName="USB" AspirationRate="1000" DispenseRate="2500" Volume="24" Duration="0" ToPosition="0" />
+ <Wait Duration="5000" />
+ <DispenseAndWait Solution="0" AspirationRate="0" DispenseRate="0" Volume="0" Duration="15000" ToPosition="0" />
+ <PumpToFlowcell Solution="0" ReagentName="USB" AspirationRate="1500" DispenseRate="2500" Volume="120" Duration="0" ToPosition="0" />
+ <Temp Temperature="20" Duration="15000" />
+ <PumpToFlowcell Solution="0" ReagentName="SRM" AspirationRate="1500" DispenseRate="2500" Volume="75" Duration="0" ToPosition="0" />
+ <Wait Duration="5000" />
+ <DispenseAndWait Solution="0" AspirationRate="0" DispenseRate="0" Volume="0" Duration="10000" ToPosition="0" />
+ </ChemistryStep>
+ </ChemistryDefinition>
+ <ChemistryDefinition Name="FirstBase_Low">
+ <ChemistryStep Description="Incorporation" Repeat="1">
+ <DispenseAndWait Solution="0" AspirationRate="0" DispenseRate="0" Volume="0" Duration="1" ToPosition="0" />
+ <Temp Temperature="60" Duration="0" />
+ <PumpToFlowcell Solution="0" ReagentName="USB" AspirationRate="1500" DispenseRate="2500" Volume="120" Duration="0" ToPosition="0" />
+ <PumpToFlowcell Solution="0" ReagentName="IMM" AspirationRate="1000" DispenseRate="2500" Volume="110" Duration="0" ToPosition="0" />
+ <Temp Temperature="65" Duration="0" />
+ <Wait Duration="5000" />
+ <DispenseAndWait Solution="0" AspirationRate="0" DispenseRate="0" Volume="0" Duration="20000" ToPosition="0" />
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+ <Wait Duration="5000" />
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+ <Temp Temperature="20" Duration="15000" />
+ <PumpToFlowcell Solution="0" ReagentName="SRM" AspirationRate="1500" DispenseRate="2500" Volume="75" Duration="0" ToPosition="0" />
+ <Wait Duration="5000" />
+ <DispenseAndWait Solution="0" AspirationRate="0" DispenseRate="0" Volume="0" Duration="10000" ToPosition="0" />
+ </ChemistryStep>
+ </ChemistryDefinition>
+ <ChemistryDefinition Name="EndDeblock_Low">
+ <ChemistryStep Description="Deblock" Repeat="1">
+ <PumpToFlowcell Solution="0" ReagentName="USB" AspirationRate="1500" DispenseRate="2500" Volume="120" Duration="0" ToPosition="0" />
+ <Temp Temperature="60" Duration="0" />
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+ <Wait Duration="5000" />
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+ <Wait Duration="5000" />
+ <DispenseAndWait Solution="0" AspirationRate="0" DispenseRate="0" Volume="0" Duration="35000" ToPosition="0" />
+ <PumpToFlowcell Solution="0" ReagentName="USB" AspirationRate="1500" DispenseRate="2500" Volume="120" Duration="0" ToPosition="0" />
+ <TempOff />
+ </ChemistryStep>
+ </ChemistryDefinition>
+ <ChemistryDefinition Name="ResumeChemistry">
+ <ChemistryStep Description="Prepare for scanning" Repeat="1">
+ <Temp Temperature="20" Duration="0" />
+ <PumpToFlowcell Solution="0" ReagentName="SRM" AspirationRate="750" DispenseRate="2500" Volume="75" Duration="0" ToPosition="0" />
+ <Temp Temperature="20" Duration="15000" />
+ </ChemistryStep>
+ </ChemistryDefinition>
+ <ChemistryDefinition Name="PauseChemistry">
+ <ChemistryStep Description="Pause flowcell" Repeat="1">
+ <PumpToFlowcell Solution="0" ReagentName="USB" AspirationRate="1500" DispenseRate="2500" Volume="100" Duration="0" ToPosition="0" />
+ <Temp Temperature="20" Duration="0" />
+ </ChemistryStep>
+ </ChemistryDefinition>
+ <ChemistryDefinition Name="PostRun">
+ <ChemistryStep Description="Post-Run Flush" Repeat="1">
+ <Temp Temperature="20" Duration="0" />
+ <PumpToFlowcell Solution="2" ReagentName="PW1" AspirationRate="1500" DispenseRate="2500" Volume="2250" Duration="0" ToPosition="0" />
+ </ChemistryStep>
+ </ChemistryDefinition>
+ <ChemistryDefinition Name="PostRunForOnBoardClustering">
+ <ChemistryStep Description="Post-Run Flush" Repeat="1">
+ <Temp Temperature="20" Duration="0" />
+ <PumpToFlowcell Solution="2" ReagentName="PW1" AspirationRate="1000" DispenseRate="2500" Volume="2250" Duration="0" ToPosition="0" />
+ <PumpToValvePosition Solution="2" ReagentName="PW1" AspirationRate="1000" DispenseRate="250" Volume="250" Duration="0" ToPosition="20" />
+ <PumpToFlowcell Solution="0" ReagentName="TMP" AspirationRate="1000" DispenseRate="2500" Volume="250" Duration="0" ToPosition="0" />
+ <PumpToFlowcell Solution="2" ReagentName="PW1" AspirationRate="1000" DispenseRate="2500" Volume="1000" Duration="0" ToPosition="0" />
+ <PumpToValvePosition Solution="2" ReagentName="PW1" AspirationRate="1000" DispenseRate="250" Volume="250" Duration="0" ToPosition="20" />
+ </ChemistryStep>
+ </ChemistryDefinition>
+ <ChemistryDefinition Name="IndexPreparation-i7">
+ <ChemistryStep Description="IndexPreparation-i7" Repeat="1">
+ <PumpToFlowcell Solution="0" ReagentName="FDR" AspirationRate="240" DispenseRate="2500" Volume="100" Duration="0" ToPosition="0" />
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+ <Temp Temperature="40" Duration="60000" />
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+ <Wait Duration="300000" />
+ <PumpToFlowcell Solution="0" ReagentName="USB" AspirationRate="1500" DispenseRate="2500" Volume="120" Duration="0" ToPosition="0" />
+ <Temp Temperature="20" Duration="0" />
+ </ChemistryStep>
+ </ChemistryDefinition>
+ <ChemistryDefinition Name="IndexPreparation-i5-SR">
+ <ChemistryStep Description="IndexPreparation-i5-SR" Repeat="1">
+ <PumpToFlowcell Solution="0" ReagentName="FDR" AspirationRate="240" DispenseRate="2500" Volume="100" Duration="0" ToPosition="0" />
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+ <Wait Duration="300000" />
+ <PumpToFlowcell Solution="0" ReagentName="USB" AspirationRate="1500" DispenseRate="2500" Volume="120" Duration="0" ToPosition="0" />
+ <Temp Temperature="20" Duration="0" />
+ </ChemistryStep>
+ </ChemistryDefinition>
+ <ChemistryDefinition Name="ClusterGenerationSR">
+ <ChemistryStep Description="Prime" Repeat="1">
+ <PumpToFlowcell Solution="0" ReagentName="FDR" AspirationRate="1000" DispenseRate="2500" Volume="500" Duration="0" ToPosition="0" />
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+ <PumpToFlowcell Solution="5" ReagentName="USB" AspirationRate="1500" DispenseRate="2500" Volume="500" Duration="0" ToPosition="0" />
+ <PumpToFlowcell Solution="6" ReagentName="USB" AspirationRate="1500" DispenseRate="2500" Volume="500" Duration="0" ToPosition="0" />
+ <PumpToFlowcell Solution="0" ReagentName="TMP" AspirationRate="1000" DispenseRate="2500" Volume="100" Duration="0" ToPosition="0" />
+ </ChemistryStep>
+ <ChemistryStep Description="TemplateHyb" Repeat="15">
+ <PumpToFlowcell Solution="0" ReagentName="TMP" AspirationRate="250" DispenseRate="2500" Volume="5" Duration="0" ToPosition="0" />
+ <Wait Duration="3000" />
+ </ChemistryStep>
+ <ChemistryStep Description="TemplateTemp" Repeat="1">
+ <Temp Temperature="85" Duration="60000" />
+ <Wait Duration="30000" />
+ <Temp Temperature="40" Duration="60000" />
+ </ChemistryStep>
+ <ChemistryStep Description="TemplateWash" Repeat="15">
+ <PumpToFlowcell Solution="0" ReagentName="USB" AspirationRate="250" DispenseRate="2500" Volume="5" Duration="0" ToPosition="0" />
+ <Wait Duration="18000" />
+ </ChemistryStep>
+ <ChemistryStep Description="FE" Repeat="15">
+ <PumpToFlowcell Solution="0" ReagentName="AMS" AspirationRate="250" DispenseRate="2500" Volume="5" Duration="0" ToPosition="0" />
+ <Wait Duration="3000" />
+ </ChemistryStep>
+ <ChemistryStep Description="FEWait" Repeat="1">
+ <Wait Duration="90000" />
+ </ChemistryStep>
+ <ChemistryStep Description="Amp-TempRamp" Repeat="1">
+ <Temp Temperature="55" Duration="0" />
+ </ChemistryStep>
+ <ChemistryStep Description="Amplification1" Repeat="28">
+ <PumpToFlowcell Solution="0" ReagentName="FDR" AspirationRate="120" DispenseRate="2500" Volume="28" Duration="0" ToPosition="0" />
+ <PumpToFlowcell Solution="0" ReagentName="FPM" AspirationRate="120" DispenseRate="2500" Volume="28" Duration="0" ToPosition="0" />
+ <PumpToFlowcell Solution="0" ReagentName="AMS" AspirationRate="120" DispenseRate="2500" Volume="72" Duration="0" ToPosition="0" />
+ </ChemistryStep>
+ <ChemistryStep Description="Postamplificationwash" Repeat="1">
+ <PumpToFlowcell Solution="0" ReagentName="USB" AspirationRate="1500" DispenseRate="2500" Volume="120" Duration="0" ToPosition="0" />
+ <Temp Temperature="20" Duration="0" />
+ </ChemistryStep>
+ <ChemistryStep Description="LinearizationSR" Repeat="1">
+ <Temp Temperature="20" Duration="0" />
+ <PumpToFlowcell Solution="0" ReagentName="FLS" AspirationRate="1500" DispenseRate="2500" Volume="500" Duration="0" ToPosition="0" />
+ <PumpToFlowcell Solution="0" ReagentName="FLS" AspirationRate="15" DispenseRate="2500" Volume="125" Duration="0" ToPosition="0" />
+ <PumpToFlowcell Solution="0" ReagentName="USB" AspirationRate="1500" DispenseRate="2500" Volume="120" Duration="0" ToPosition="0" />
+ </ChemistryStep>
+ <ChemistryStep Description="SBS Prime" Repeat="1">
+ <Temp Temperature="20" Duration="0" />
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diff --git a/recipes/Tradis_adapter_primers.xlsx b/recipes/Tradis_adapter_primers.xlsx
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index 0000000..9f3f10f
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diff --git a/recipes/Transposon10/Chemistry/Chemistry.xml b/recipes/Transposon10/Chemistry/Chemistry.xml
new file mode 100755
index 0000000..96dfceb
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+ </ChemistryStep>
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+ <PumpToFlowcell ReagentName="LMX1" AspirationRate="250" DispenseRate="7500" Volume="75" />
+ <Temp Temperature="46" />
+ <Wait Duration="300000" />
+ <PumpToFlowcell ReagentName="PR2" AspirationRate="2000" DispenseRate="7500" Volume="120" />
+ </ChemistryStep>
+ <ChemistryStep Description="SBS Prime">
+ <Temp Temperature="20" />
+ <PumpToFlowcell ReagentName="IMS" AspirationRate="2000" DispenseRate="7500" Volume="300" />
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+ <PumpToFlowcell ReagentName="PR2" AspirationRate="2000" DispenseRate="7500" Volume="250" />
+ </ChemistryStep>
+ </ChemistryDefinition>
+ <ChemistryDefinition Name="PairedEndTurnaround">
+ <ChemistryStep Description="Pre-resynthesis_tempramp">
+ <Temp Temperature="50" />
+ </ChemistryStep>
+ <ChemistryStep Description="Resynthesis" Repeat="8" >
+ <PumpToFlowcell ReagentName="LDR" AspirationRate="250" DispenseRate="7500" Volume="28" />
+ <PumpToFlowcell ReagentName="LPM" AspirationRate="250" DispenseRate="7500" Volume="28" />
+ <PumpToFlowcell ReagentName="AMS2" AspirationRate="250" DispenseRate="7500" Volume="72" />
+ <Wait Duration="15000" />
+ </ChemistryStep>
+ <ChemistryStep Description="Post-resynthesis_wash">
+ <PumpToFlowcell ReagentName="PR2" AspirationRate="2000" DispenseRate="7500" Volume="120" />
+ <Temp Temperature="20" Duration="45000" />
+ </ChemistryStep>
+ <ChemistryStep Description="Linearisation 2">
+ <PumpToFlowcell ReagentName="LMX2" AspirationRate="2000" DispenseRate="7500" Volume="300" />
+ <PumpToFlowcell ReagentName="LMX2" AspirationRate="250" DispenseRate="7500" Volume="75" />
+ <Temp Temperature="38" />
+ <Wait Duration="300000"/>
+ <PumpToFlowcell ReagentName="PR2" AspirationRate="2000" DispenseRate="7500" Volume="120" />
+ </ChemistryStep>
+ </ChemistryDefinition>
+ <ChemistryDefinition Name="FirstReadPreparation">
+ <ChemistryStep Description="FirstReadPreparation">
+ <PumpToFlowcell ReagentName="LDR" AspirationRate="250" DispenseRate="7500" Volume="75" />
+ <Temp Temperature="65" Duration="60000" />
+ <PumpToFlowcell ReagentName="C1" AspirationRate="2000" DispenseRate="7500" Volume="300" />
+ <PumpToFlowcell ReagentName="C1" AspirationRate="250" DispenseRate="7500" Volume="75" />
+ <Temp Temperature="40" Duration="60000" />
+ <PumpToFlowcell ReagentName="PR2" AspirationRate="2000" DispenseRate="7500" Volume="120" />
+ <TempOff />
+ </ChemistryStep>
+ </ChemistryDefinition>
+ <ChemistryDefinition Name="SecondReadPreparation">
+ <ChemistryStep Description="SecondReadPreparation">
+ <PumpToFlowcell ReagentName="LDR" AspirationRate="250" DispenseRate="7500" Volume="75" />
+ <Temp Temperature="65" Duration="60000" />
+ <PumpToFlowcell ReagentName="C3" AspirationRate="2000" DispenseRate="7500" Volume="300" />
+ <PumpToFlowcell ReagentName="C3" AspirationRate="250" DispenseRate="7500" Volume="75" />
+ <Temp Temperature="40" Duration="60000" />
+ <PumpToFlowcell ReagentName="PR2" AspirationRate="2000" DispenseRate="7500" Volume="120" />
+ <TempOff />
+ </ChemistryStep>
+ </ChemistryDefinition>
+ <ChemistryDefinition Name="Index1Preparation">
+ <ChemistryStep Description="Index1Preparation">
+ <Temp Temperature="20" Duration="25000" />
+ <PumpToFlowcell ReagentName="LDR" AspirationRate="250" DispenseRate="7500" Volume="75" />
+ <Temp Temperature="65" Duration="60000" />
+ <PumpToFlowcell ReagentName="C1" AspirationRate="2000" DispenseRate="7500" Volume="300" />
+ <PumpToFlowcell ReagentName="C1" AspirationRate="250" DispenseRate="7500" Volume="75" />
+ <Temp Temperature="40" Duration="60000" />
+ <PumpToFlowcell ReagentName="PR2" AspirationRate="2000" DispenseRate="7500" Volume="120" />
+ <TempOff />
+ </ChemistryStep>
+ </ChemistryDefinition>
+ <ChemistryDefinition Name="Deprotection">
+ <ChemistryStep Description="Deprotection">
+ <Temp Temperature="20" />
+ <Wait Duration="120000" />
+ <PumpToFlowcell ReagentName="RMF" AspirationRate="2000" DispenseRate="7500" Volume="300" />
+ <PumpToFlowcell ReagentName="RMF" AspirationRate="250" DispenseRate="7500" Volume="75" />
+ <Temp Temperature="38" />
+ <Wait Duration="300000"/>
+ <PumpToFlowcell ReagentName="PR2" AspirationRate="2000" DispenseRate="7500" Volume="120" />
+ </ChemistryStep>
+ <ChemistryStep Description="Denaturation">
+ <Temp Temperature="20" Duration="25000" />
+ <PumpToFlowcell ReagentName="LDR" AspirationRate="250" DispenseRate="7500" Volume="75" />
+ <Temp Temperature="65" Duration="60000" />
+ <PumpToFlowcell ReagentName="PR2" AspirationRate="2000" DispenseRate="7500" Volume="300" />
+ <PumpToFlowcell ReagentName="PR2" AspirationRate="250" DispenseRate="7500" Volume="75" />
+ <Temp Temperature="40" Duration="60000" />
+ <PumpToFlowcell ReagentName="PR2" AspirationRate="2000" DispenseRate="7500" Volume="120" />
+ <TempOff />
+ </ChemistryStep>
+ </ChemistryDefinition>
+
+ <ChemistryDefinition Name="Index2Preparation">
+ <ChemistryStep Description="Index2Preparation">
+ <Temp Temperature="20" Duration="25000" />
+ <PumpToFlowcell ReagentName="LDR" AspirationRate="250" DispenseRate="2500" Volume="75" />
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+ <TempOff />
+ </ChemistryStep>
+ </ChemistryDefinition>
+
+ <ChemistryDefinition Name="Index2FirstBaseDark">
+ <ChemistryStep Description="Incorporation" Repeat="1">
+ <Temp Temperature="60" Duration="0" />
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+ <PumpToFlowcell ReagentName="PR2" AspirationRate="2000" Solution="0" DispenseRate="7500" Volume="5" />
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+ <PumpToFlowcell ReagentName="PR2" AspirationRate="2000" Solution="0" DispenseRate="7500" Volume="20" />
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+ </ChemistryStep>
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+ <PumpToFlowcell ReagentName="PR2" AspirationRate="2000" Solution="0" DispenseRate="7500" Volume="5" />
+ <DispenseAndWait DispenseRate="7500" Duration="30000" />
+ </ChemistryStep>
+ <ChemistryStep Description="Buffer Wash" Repeat="1">
+ <PumpToFlowcell ReagentName="PR2" AspirationRate="2000" Solution="0" DispenseRate="7500" Volume="250" />
+ </ChemistryStep>
+ <ChemistryStep Description="Incorporation" Repeat="1">
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+ <PumpToFlowcell ReagentName="PR2" AspirationRate="2000" Solution="0" DispenseRate="7500" Volume="20" />
+ <Temp Temperature="65" Duration="0" />
+ <Wait Duration="45000" />
+ <PumpToFlowcell ReagentName="PR2" AspirationRate="2000" Solution="0" DispenseRate="7500" Volume="5" />
+ <DispenseAndWait Duration="40000" />
+ <Temp Temperature="22" Duration="0" />
+ <PumpToFlowcell ReagentName="PR2" AspirationRate="2000" Solution="0" DispenseRate="7500" Volume="120" />
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+ <PumpToFlowcell ReagentName="PR2" AspirationRate="2000" Solution="0" DispenseRate="7500" Volume="20" />
+ <DispenseAndWait DispenseRate="7500" Duration="15000" />
+ </ChemistryStep>
+ </ChemistryDefinition>
+ </ChemistryDefinitions>
\ No newline at end of file
diff --git a/recipes/Transposon10/Exposures/Sony.xml b/recipes/Transposon10/Exposures/Sony.xml
new file mode 100755
index 0000000..ed9e88d
--- /dev/null
+++ b/recipes/Transposon10/Exposures/Sony.xml
@@ -0,0 +1,7 @@
+<?xml version="1.0" encoding="utf-8" ?>
+<Exposures>
+ <Exposure Name="A" Start="1037" Ramp="0" />
+ <Exposure Name="T" Start="500" Ramp="0" />
+ <Exposure Name="C" Start="1037" Ramp="0" />
+ <Exposure Name="G" Start="500" Ramp="0" />
+</Exposures>
diff --git a/recipes/Transposon10/Exposures/SonyV2.xml b/recipes/Transposon10/Exposures/SonyV2.xml
new file mode 100755
index 0000000..b1f60d9
--- /dev/null
+++ b/recipes/Transposon10/Exposures/SonyV2.xml
@@ -0,0 +1,11 @@
+<?xml version="1.0" encoding="utf-8" ?>
+<Exposures>
+ <Exposure Name="A" Start="260" IsIndexed="false" Ramp="5.2" />
+ <Exposure Name="A" Start="1037" IsIndexed="true" Ramp="0" />
+ <Exposure Name="T" Start="125" IsIndexed="false" Ramp="2.5" />
+ <Exposure Name="T" Start="500" IsIndexed="true" Ramp="0" />
+ <Exposure Name="C" Start="260" IsIndexed="false" Ramp="5.2" />
+ <Exposure Name="C" Start="1037" IsIndexed="true" Ramp="0" />
+ <Exposure Name="G" Start="125" IsIndexed="false" Ramp="2.5" />
+ <Exposure Name="G" Start="500" IsIndexed="true" Ramp="0" />
+</Exposures>
diff --git a/recipes/Transposon10/Protocol/1Read1Index.xml b/recipes/Transposon10/Protocol/1Read1Index.xml
new file mode 100755
index 0000000..d10932c
--- /dev/null
+++ b/recipes/Transposon10/Protocol/1Read1Index.xml
@@ -0,0 +1,24 @@
+<?xml version="1.0"?>
+<Protocol Version="Fraise 0.7.1 Amplicon v1.1">
+ <ChemistryRef ChemistryName="OnBoardClusterGeneration" />
+ <ChemistryRef ChemistryName="FirstReadPreparation" />
+ <ChemistryRef ChemistryName="Index2CompleteCycleDark2" />
+ <ChemistryRef ChemistryName="Index2CompleteCycleDark2" />
+ <ChemistryRef ChemistryName="Index2CompleteCycleDark2" />
+ <ChemistryRef ChemistryName="Index2CompleteCycleDark2" />
+ <ChemistryRef ChemistryName="Index2CompleteCycleDark2" />
+ <ChemistryRef ChemistryName="Index2CompleteCycleDark2" />
+ <ChemistryRef ChemistryName="Index2CompleteCycleDark2" />
+ <ChemistryRef ChemistryName="Index2CompleteCycleDark2" />
+ <ChemistryRef ChemistryName="Index2CompleteCycleDark2" />
+ <ChemistryRef ChemistryName="Index2CompleteCycleDark2" />
+ <ChemistryRef ChemistryName="EndDeblock" />
+ <ReadRef ReadName="FirstRead" />
+ <ChemistryRef ChemistryName="EndDeblock" />
+ <ChemistryRef ChemistryName="Index1Preparation" />
+ <ReadRef ReadName="IndexRead1" />
+ <ChemistryRef ChemistryName="EndDeblock" />
+ <ChemistryRef ChemistryName="TemplateRinse" />
+ <ChemistryRef ChemistryName="End" />
+
+</Protocol>
\ No newline at end of file
diff --git a/recipes/Transposon10/Protocol/1Read2Index.xml b/recipes/Transposon10/Protocol/1Read2Index.xml
new file mode 100755
index 0000000..28dac13
--- /dev/null
+++ b/recipes/Transposon10/Protocol/1Read2Index.xml
@@ -0,0 +1,25 @@
+<?xml version="1.0"?>
+<Protocol Version="Fraise 0.7.1 Amplicon v1.1">
+ <ChemistryRef ChemistryName="OnBoardClusterGeneration" />
+ <ChemistryRef ChemistryName="FirstReadPreparation" />
+ <ChemistryRef ChemistryName="Index2CompleteCycleDark2" />
+ <ChemistryRef ChemistryName="Index2CompleteCycleDark2" />
+ <ChemistryRef ChemistryName="Index2CompleteCycleDark2" />
+ <ChemistryRef ChemistryName="Index2CompleteCycleDark2" />
+ <ChemistryRef ChemistryName="Index2CompleteCycleDark2" />
+ <ChemistryRef ChemistryName="Index2CompleteCycleDark2" />
+ <ChemistryRef ChemistryName="Index2CompleteCycleDark2" />
+ <ChemistryRef ChemistryName="Index2CompleteCycleDark2" />
+ <ChemistryRef ChemistryName="Index2CompleteCycleDark2" />
+ <ChemistryRef ChemistryName="Index2CompleteCycleDark2" />
+ <ChemistryRef ChemistryName="EndDeblock" />
+ <ReadRef ReadName="FirstRead" />
+ <ChemistryRef ChemistryName="EndDeblock" />
+ <ChemistryRef ChemistryName="Index1Preparation" />
+ <ReadRef ReadName="IndexRead1" />
+ <ChemistryRef ChemistryName="EndDeblock" />
+ <ChemistryRef ChemistryName="Index2Preparation" />
+ <ReadRef ReadName="IndexRead2" />
+ <ChemistryRef ChemistryName="TemplateRinse" />
+ <ChemistryRef ChemistryName="End" />
+ </Protocol>
\ No newline at end of file
diff --git a/recipes/Transposon10/Protocol/2Read1Index.xml b/recipes/Transposon10/Protocol/2Read1Index.xml
new file mode 100755
index 0000000..693c8e9
--- /dev/null
+++ b/recipes/Transposon10/Protocol/2Read1Index.xml
@@ -0,0 +1,28 @@
+<?xml version="1.0"?>
+<Protocol Version="Fraise 0.7.1 Amplicon v1.1">
+ <ChemistryRef ChemistryName="OnBoardClusterGeneration" />
+ <ChemistryRef ChemistryName="FirstReadPreparation" />
+ <ChemistryRef ChemistryName="Index2CompleteCycleDark2" />
+ <ChemistryRef ChemistryName="Index2CompleteCycleDark2" />
+ <ChemistryRef ChemistryName="Index2CompleteCycleDark2" />
+ <ChemistryRef ChemistryName="Index2CompleteCycleDark2" />
+ <ChemistryRef ChemistryName="Index2CompleteCycleDark2" />
+ <ChemistryRef ChemistryName="Index2CompleteCycleDark2" />
+ <ChemistryRef ChemistryName="Index2CompleteCycleDark2" />
+ <ChemistryRef ChemistryName="Index2CompleteCycleDark2" />
+ <ChemistryRef ChemistryName="Index2CompleteCycleDark2" />
+ <ChemistryRef ChemistryName="Index2CompleteCycleDark2" />
+ <ChemistryRef ChemistryName="EndDeblock" />
+ <ReadRef ReadName="FirstRead" />
+ <ChemistryRef ChemistryName="EndDeblock" />
+ <ChemistryRef ChemistryName="Index1Preparation" />
+ <ReadRef ReadName="IndexRead1" />
+ <ChemistryRef ChemistryName="EndDeblock" />
+ <ChemistryRef ChemistryName="Deprotection" />
+ <ChemistryRef ChemistryName="PairedEndTurnaround" />
+ <ChemistryRef ChemistryName="SecondReadPreparation" />
+ <ReadRef ReadName="SecondRead" />
+ <ChemistryRef ChemistryName="EndDeblock" />
+ <ChemistryRef ChemistryName="TemplateRinse" />
+ <ChemistryRef ChemistryName="End" />
+ </Protocol>
\ No newline at end of file
diff --git a/recipes/Transposon10/Protocol/2Read2Index.xml b/recipes/Transposon10/Protocol/2Read2Index.xml
new file mode 100755
index 0000000..07e3c69
--- /dev/null
+++ b/recipes/Transposon10/Protocol/2Read2Index.xml
@@ -0,0 +1,31 @@
+<?xml version="1.0"?>
+<Protocol Version="Fraise 0.7.1 Amplicon v1.1">
+ <ChemistryRef ChemistryName="OnBoardClusterGeneration" />
+ <ChemistryRef ChemistryName="FirstReadPreparation" />
+ <ChemistryRef ChemistryName="Index2CompleteCycleDark2" />
+ <ChemistryRef ChemistryName="Index2CompleteCycleDark2" />
+ <ChemistryRef ChemistryName="Index2CompleteCycleDark2" />
+ <ChemistryRef ChemistryName="Index2CompleteCycleDark2" />
+ <ChemistryRef ChemistryName="Index2CompleteCycleDark2" />
+ <ChemistryRef ChemistryName="Index2CompleteCycleDark2" />
+ <ChemistryRef ChemistryName="Index2CompleteCycleDark2" />
+ <ChemistryRef ChemistryName="Index2CompleteCycleDark2" />
+ <ChemistryRef ChemistryName="Index2CompleteCycleDark2" />
+ <ChemistryRef ChemistryName="Index2CompleteCycleDark2" />
+ <ChemistryRef ChemistryName="EndDeblock" />
+ <ReadRef ReadName="FirstRead" />
+ <ChemistryRef ChemistryName="EndDeblock" />
+ <ChemistryRef ChemistryName="Index1Preparation" />
+ <ReadRef ReadName="IndexRead1" />
+ <ChemistryRef ChemistryName="EndDeblock" />
+ <ChemistryRef ChemistryName="Index2Preparation" />
+ <ReadRef ReadName="IndexRead2" />
+ <ChemistryRef ChemistryName="EndDeblock" />
+ <ChemistryRef ChemistryName="Deprotection" />
+ <ChemistryRef ChemistryName="PairedEndTurnaround" />
+ <ChemistryRef ChemistryName="SecondReadPreparation" />
+ <ReadRef ReadName="SecondRead" />
+ <ChemistryRef ChemistryName="EndDeblock" />
+ <ChemistryRef ChemistryName="TemplateRinse" />
+ <ChemistryRef ChemistryName="End" />
+ </Protocol>
\ No newline at end of file
diff --git a/recipes/Transposon10/Reads/Reads.xml b/recipes/Transposon10/Reads/Reads.xml
new file mode 100755
index 0000000..3ced231
--- /dev/null
+++ b/recipes/Transposon10/Reads/Reads.xml
@@ -0,0 +1,23 @@
+<?xml version="1.0"?>
+<ReadDefinitions Version="Fraise 0.7.1 Amplicon v1.1">
+ <ReadDefinition Name="FirstRead">
+ <FirstBase ChemistryName="FirstBase" Cycles="1" />
+ <Imaging ChemistryName="CompleteCycle" Cycles="NumCycles - 1" />
+ <End ChemistryName="EndRead" />
+ </ReadDefinition>
+ <ReadDefinition Name="IndexRead1" IsIndexed="True" >
+ <FirstBase ChemistryName="FirstBase" Cycles="1" />
+ <Imaging ChemistryName="CompleteCycle" Cycles="NumCycles - 1" />
+ <End ChemistryName="EndRead" />
+ </ReadDefinition>
+ <ReadDefinition Name="SecondRead" IsIndexed="false">
+ <FirstBase ChemistryName="FirstBase" Cycles="1" />
+ <Imaging ChemistryName="CompleteCycle" Cycles="NumCycles - 1" />
+ <End ChemistryName="EndRead" />
+ </ReadDefinition>
+ <ReadDefinition Name="IndexRead2" IsIndexed="true">
+ <FirstBase ChemistryName="FirstBase" Cycles="1" />
+ <Imaging ChemistryName="CompleteCycle" Cycles="NumCycles - 1" />
+ <End ChemistryName="EndRead" />
+ </ReadDefinition>
+ </ReadDefinitions>
\ No newline at end of file
diff --git a/recipes/Transposon10/Reagents/MaintenanceWash.xml b/recipes/Transposon10/Reagents/MaintenanceWash.xml
new file mode 100755
index 0000000..f6d14da
--- /dev/null
+++ b/recipes/Transposon10/Reagents/MaintenanceWash.xml
@@ -0,0 +1,25 @@
+<?xml version="1.0" encoding="utf-8" ?>
+<Reagents Name="Bolt Avocado Reagents" Version="Selector Valve Positions v2.2">
+ <Reagent Name="PW1" Description="PW1" SelectorValvePosition="1" />
+ <Reagent Name="PW1" Description="PW1" SelectorValvePosition="2" />
+ <Reagent Name="PW1" Description="PW1" SelectorValvePosition="3" />
+ <Reagent Name="PW1" Description="PW1" SelectorValvePosition="4" />
+ <Reagent Name="PW1" Description="PW1" SelectorValvePosition="5" />
+ <Reagent Name="PW1" Description="PW1" SelectorValvePosition="6" />
+ <Reagent Name="PW1" Description="PW1" SelectorValvePosition="7" />
+ <Reagent Name="PW1" Description="PW1" SelectorValvePosition="8" />
+ <Reagent Name="PW1" Description="PW1" SelectorValvePosition="9" />
+ <Reagent Name="PW1" Description="PW1" SelectorValvePosition="10" />
+ <Reagent Name="PW1" Description="PW1" SelectorValvePosition="11" />
+ <Reagent Name="PW1" Description="PW1" SelectorValvePosition="12" />
+ <Reagent Name="PW1" Description="PW1" SelectorValvePosition="13" />
+ <Reagent Name="PW1" Description="PW1" SelectorValvePosition="14" />
+ <Reagent Name="PW1" Description="PW1" SelectorValvePosition="15" />
+ <Reagent Name="PW1" Description="PW1" SelectorValvePosition="16" />
+ <Reagent Name="PW1" Description="PW1" SelectorValvePosition="17" />
+ <Reagent Name="PW1" Description="PW1" SelectorValvePosition="18" />
+ <Reagent Name="PW1" Description="PW1" SelectorValvePosition="19" />
+ <Reagent Name="PW1" Description="PW1" SelectorValvePosition="20" />
+ <Reagent Name="PW1" Description="PW1" SelectorValvePosition="21" />
+ <Reagent Name="PW1" Description="PW1" SelectorValvePosition="22" />
+</Reagents>
diff --git a/recipes/Transposon10/Reagents/PostRunWash.xml b/recipes/Transposon10/Reagents/PostRunWash.xml
new file mode 100755
index 0000000..f6d14da
--- /dev/null
+++ b/recipes/Transposon10/Reagents/PostRunWash.xml
@@ -0,0 +1,25 @@
+<?xml version="1.0" encoding="utf-8" ?>
+<Reagents Name="Bolt Avocado Reagents" Version="Selector Valve Positions v2.2">
+ <Reagent Name="PW1" Description="PW1" SelectorValvePosition="1" />
+ <Reagent Name="PW1" Description="PW1" SelectorValvePosition="2" />
+ <Reagent Name="PW1" Description="PW1" SelectorValvePosition="3" />
+ <Reagent Name="PW1" Description="PW1" SelectorValvePosition="4" />
+ <Reagent Name="PW1" Description="PW1" SelectorValvePosition="5" />
+ <Reagent Name="PW1" Description="PW1" SelectorValvePosition="6" />
+ <Reagent Name="PW1" Description="PW1" SelectorValvePosition="7" />
+ <Reagent Name="PW1" Description="PW1" SelectorValvePosition="8" />
+ <Reagent Name="PW1" Description="PW1" SelectorValvePosition="9" />
+ <Reagent Name="PW1" Description="PW1" SelectorValvePosition="10" />
+ <Reagent Name="PW1" Description="PW1" SelectorValvePosition="11" />
+ <Reagent Name="PW1" Description="PW1" SelectorValvePosition="12" />
+ <Reagent Name="PW1" Description="PW1" SelectorValvePosition="13" />
+ <Reagent Name="PW1" Description="PW1" SelectorValvePosition="14" />
+ <Reagent Name="PW1" Description="PW1" SelectorValvePosition="15" />
+ <Reagent Name="PW1" Description="PW1" SelectorValvePosition="16" />
+ <Reagent Name="PW1" Description="PW1" SelectorValvePosition="17" />
+ <Reagent Name="PW1" Description="PW1" SelectorValvePosition="18" />
+ <Reagent Name="PW1" Description="PW1" SelectorValvePosition="19" />
+ <Reagent Name="PW1" Description="PW1" SelectorValvePosition="20" />
+ <Reagent Name="PW1" Description="PW1" SelectorValvePosition="21" />
+ <Reagent Name="PW1" Description="PW1" SelectorValvePosition="22" />
+</Reagents>
diff --git a/recipes/Transposon10/Reagents/Sequencing.xml b/recipes/Transposon10/Reagents/Sequencing.xml
new file mode 100755
index 0000000..87cac01
--- /dev/null
+++ b/recipes/Transposon10/Reagents/Sequencing.xml
@@ -0,0 +1,24 @@
+<?xml version="1.0" encoding="utf-8" ?>
+<Reagents Name="Shock Reagents" Version="Selector Valve Positions v2.2">
+ <Reagent Name="IMS" Description="Incorporation Mix" SelectorValvePosition="1" />
+ <Reagent Name="SRE" Description="Scan Mix" SelectorValvePosition="2" />
+ <Reagent Name="PR2" Description="Incorporation Buffer" SelectorValvePosition="3" />
+ <Reagent Name="CMS" Description="Cleavage Mix" SelectorValvePosition="4" />
+ <Reagent Name="AMS1" Description="Amplification Mix 1" SelectorValvePosition="5" />
+ <Reagent Name="AMS2" Description="Amplification Mix 2" SelectorValvePosition="6" />
+ <Reagent Name="LPM" Description="Lin Pre Mix" SelectorValvePosition="7" />
+ <Reagent Name="LDR" Description="Formamide" SelectorValvePosition="8" />
+ <Reagent Name="LMX1" Description="Linearization Mix" SelectorValvePosition="9" />
+ <Reagent Name="LMX2" Description="R2 Lin Mix" SelectorValvePosition="10" />
+ <Reagent Name="RMF" Description="Resynthesis Mix" SelectorValvePosition="11" />
+ <Reagent Name="HP10" Description="R1 Primer Mix" SelectorValvePosition="12" />
+ <Reagent Name="HP12" Description="Index Primer Mix" SelectorValvePosition="13" />
+ <Reagent Name="HP11" Description="R2 Primer Mix" SelectorValvePosition="14" />
+ <Reagent Name="PW1" Description="Water" SelectorValvePosition="15" />
+ <Reagent Name="PW2" Description="Water" SelectorValvePosition="16" />
+ <Reagent Name="TMP" Description="Template" SelectorValvePosition="17" />
+ <Reagent Name="C1" Description="Custom 1 Primer Mix" SelectorValvePosition="18" />
+ <Reagent Name="C2" Description="Custom 2 Primer Mix" SelectorValvePosition="19" />
+ <Reagent Name="C3" Description="Custom 3 Primer Mix" SelectorValvePosition="20" />
+ <Reagent Name="PW3" Description="Water" SelectorValvePosition="21" />
+</Reagents>
\ No newline at end of file
diff --git a/recipes/Transposon10/Wash/LineWash.xml b/recipes/Transposon10/Wash/LineWash.xml
new file mode 100755
index 0000000..ebfa1af
--- /dev/null
+++ b/recipes/Transposon10/Wash/LineWash.xml
@@ -0,0 +1,102 @@
+<?xml version="1.0"?>
+<Recipe xmlns:xsd="http://www.w3.org/2001/XMLSchema" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" Name="LineWash_v0.3">
+
+ <Protocol Version="LineWash">
+ <ChemistryRef ChemistryName="LineWash" Repeat="1" />
+ </Protocol>
+
+ <ChemistryDefinitions Version="LineWash_v0.3">
+ <ChemistryDefinition Name="CleanSyringe">
+ <ChemistryStep Description="CleanSyringe" Repeat="1"> <!--run water through syringe to reduce carryover since about to backflush-->
+ <AspirateFromBypass ReagentName="PW1" AspirationRate="2000" DispenseRate="2500" Volume="1000" />
+ <Wait Duration="10000" />
+ <AspirateFromBypass ReagentName="PW1" AspirationRate="500" DispenseRate="1000" Volume="500" />
+ <Wait Duration="10000" />
+ <AspirateFromBypass ReagentName="PW1" AspirationRate="2000" DispenseRate="2500" Volume="500" />
+ </ChemistryStep>
+ </ChemistryDefinition>
+ <ChemistryDefinition Name="Oscillate">
+ <ChemistryStep Description="Oscillate" Repeat="1">
+ <!--add airbubble, fill syringe, and slowly pump back and forth increasing pressure-->
+ <PumpToFlowcell Solution="23" AspirationRate="1000" DispenseRate="2500" Volume="15" />
+ <AspirateFromBypass ReagentName="PW1" AspirationRate="2000" Volume="250" />
+ </ChemistryStep>
+ <ChemistryStep Description="OscillateSubStep" Repeat="49">
+ <DispenseToFlowcell ReagentName="PW1" DispenseRate="2000" Volume="5"/>
+ <Wait Duration="1000" />
+ <Aspirate ReagentName="PW1" AspirationRate="2000" Volume="5" />
+ <Wait Duration="1000" />
+ <DispenseToFlowcell ReagentName="PW1" DispenseRate="2000" Volume="10"/>
+ <Wait Duration="1000" />
+ <Aspirate ReagentName="PW1" AspirationRate="2000" Volume="5" />
+ <Wait Duration="6000" />
+ </ChemistryStep>
+ </ChemistryDefinition>
+ <ChemistryDefinition Name="Reprime">
+ <ChemistryStep Description="Reprime" Repeat="1"> <!--prime line with 500uL-->
+ <PumpToFlowcell ReagentName="PW1" AspirationRate="2000" DispenseRate="2500" Volume="500" />
+ </ChemistryStep>
+ </ChemistryDefinition>
+ <ChemistryDefinition Name="Flush">
+ <ChemistryStep Description="Flush" Repeat="1"> <!--empty tube and refill from bypass-->
+ <PumpToFlowcell ReagentName="PW1" AspirationRate="5000" DispenseRate="5000" Volume="3000" />
+ <AspirateFromBypass ReagentName="PW1" AspirationRate="2000" Volume="250" />
+ <DispenseToFlowcell ReagentName="PW1" DispenseRate="2000" Volume="250" />
+ <AspirateFromBypass ReagentName="PW1" AspirationRate="2000" Volume="250" />
+ <DispenseToFlowcell ReagentName="PW1" DispenseRate="2000" Volume="250" />
+ <AspirateFromBypass ReagentName="PW1" AspirationRate="2000" Volume="250" />
+ <DispenseToFlowcell ReagentName="PW1" DispenseRate="2000" Volume="250" />
+ <AspirateFromBypass ReagentName="PW1" AspirationRate="2000" Volume="250" />
+ <DispenseToFlowcell ReagentName="PW1" DispenseRate="2000" Volume="250" />
+ <AspirateFromBypass ReagentName="PW1" AspirationRate="2000" Volume="250" />
+ <DispenseToFlowcell ReagentName="PW1" DispenseRate="2000" Volume="250" />
+ <AspirateFromBypass ReagentName="PW1" AspirationRate="2000" Volume="250" />
+ <DispenseToFlowcell ReagentName="PW1" DispenseRate="2000" Volume="250" />
+ <AspirateFromBypass ReagentName="PW1" AspirationRate="2000" Volume="250" />
+ <DispenseToFlowcell ReagentName="PW1" DispenseRate="2000" Volume="250" />
+ <AspirateFromBypass ReagentName="PW1" AspirationRate="2000" Volume="250" />
+ <DispenseToFlowcell ReagentName="PW1" DispenseRate="2000" Volume="250" />
+ <AspirateFromBypass ReagentName="PW1" AspirationRate="2000" Volume="250" />
+ <DispenseToFlowcell ReagentName="PW1" DispenseRate="2000" Volume="250" />
+ <AspirateFromBypass ReagentName="PW1" AspirationRate="2000" Volume="250" />
+ <DispenseToFlowcell ReagentName="PW1" DispenseRate="2000" Volume="250" />
+ <AspirateFromBypass ReagentName="PW1" AspirationRate="2000" Volume="250" />
+ <DispenseToFlowcell ReagentName="PW1" DispenseRate="2000" Volume="250" />
+ <AspirateFromBypass ReagentName="PW1" AspirationRate="2000" Volume="250" />
+ <DispenseToFlowcell ReagentName="PW1" DispenseRate="2000" Volume="250" />
+ </ChemistryStep>
+ </ChemistryDefinition>
+ <ChemistryDefinition Name="Wait180000">
+ <ChemistryStep Description="Wait180000" Repeat="1">
+ <Wait Duration="180000" />
+ </ChemistryStep>
+ </ChemistryDefinition>
+ </ChemistryDefinitions>
+
+ - <Reagents Name="ClogWashReagents" Version="Selector Valve Positions v2.2">
+ <Reagent Name="PW1" Description="Water" SelectorValvePosition="1" />
+ <Reagent Name="PW1" Description="Water" SelectorValvePosition="2" />
+ <Reagent Name="PW1" Description="Water" SelectorValvePosition="3" />
+ <Reagent Name="PW1" Description="Water" SelectorValvePosition="4" />
+ <Reagent Name="PW1" Description="Water" SelectorValvePosition="5" />
+ <Reagent Name="PW1" Description="Water" SelectorValvePosition="6" />
+ <Reagent Name="PW1" Description="Water" SelectorValvePosition="7" />
+ <Reagent Name="PW1" Description="Water" SelectorValvePosition="8" />
+ <Reagent Name="PW1" Description="Water" SelectorValvePosition="9" />
+ <Reagent Name="PW1" Description="Water" SelectorValvePosition="10" />
+ <Reagent Name="PW1" Description="Water" SelectorValvePosition="11" />
+ <Reagent Name="PW1" Description="Water" SelectorValvePosition="12" />
+ <Reagent Name="PW1" Description="Water" SelectorValvePosition="13" />
+ <Reagent Name="PW1" Description="Water" SelectorValvePosition="14" />
+ <Reagent Name="PW1" Description="Water" SelectorValvePosition="15" />
+ <Reagent Name="PW1" Description="Water" SelectorValvePosition="16" />
+ <Reagent Name="PW1" Description="Water" SelectorValvePosition="17" />
+ <Reagent Name="PW1" Description="Water" SelectorValvePosition="18" />
+ <Reagent Name="PW1" Description="Water" SelectorValvePosition="19" />
+ <Reagent Name="PW1" Description="Water" SelectorValvePosition="20" />
+ <Reagent Name="PW1" Description="Water" SelectorValvePosition="21" />
+ <Reagent Name="PW1" Description="Water" SelectorValvePosition="22" />
+ </Reagents>
+
+ <Name>LineWash_v0.3</Name>
+</Recipe>
diff --git a/recipes/Transposon10/Wash/MaintenanceWash.xml b/recipes/Transposon10/Wash/MaintenanceWash.xml
new file mode 100755
index 0000000..52d8301
--- /dev/null
+++ b/recipes/Transposon10/Wash/MaintenanceWash.xml
@@ -0,0 +1,115 @@
+<?xml version="1.0" ?>
+<Recipe xmlns:xsd="http://www.w3.org/2001/XMLSchema" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" Name="Maintenance Wash Recipe">
+ <Protocol>
+ <ChemistryRef Description="PostRun Wash" ChemistryName="Wash" />
+ </Protocol>
+ <ChemistryDefinitions>
+ <ChemistryDefinition Name="Wash">
+ <ChemistryStep Description="Wash">
+ <PumpToFlowcell Solution="4" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="3" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <Dispense DispenseRate="2500" Volume="250" />
+ <AspirateFromBypass ReagentName="PR2" AspirationRate="2000" Volume="250" />
+ <Dispense DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="2" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="1" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="5" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="6" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="7" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="17" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="18" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="19" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="20" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="8" AspirationRate="1000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="9" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="10" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="11" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="12" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="13" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="14" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="17" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="18" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="19" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="20" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="15" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="16" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="21" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="22" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="4" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="3" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <Dispense DispenseRate="2500" Volume="250" />
+ <AspirateFromBypass ReagentName="PR2" AspirationRate="2000" Volume="250" />
+ <Dispense DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="2" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="1" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="5" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="6" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="7" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="17" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="18" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="19" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="20" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="8" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="9" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="10" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="11" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="12" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="13" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="14" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="17" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="18" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="19" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="20" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="4" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="17" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="18" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="19" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="20" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="3" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <Dispense DispenseRate="2500" Volume="250" />
+ <AspirateFromBypass ReagentName="PR2" AspirationRate="2000" Volume="250" />
+ <Dispense DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="17" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="18" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="19" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="20" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="2" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="1" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="3" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <Dispense DispenseRate="2500" Volume="250" />
+ <AspirateFromBypass ReagentName="PR2" AspirationRate="2000" Volume="250" />
+ <Dispense DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="15" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="16" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="21" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="22" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ </ChemistryStep>
+ </ChemistryDefinition>
+ </ChemistryDefinitions>
+ <Reagents>
+ <Reagent Name="PW1" Description="Water" ViciPosition="1" />
+ <Reagent Name="PW1" Description="Water" ViciPosition="2" />
+ <Reagent Name="PW1" Description="Water" ViciPosition="3" />
+ <Reagent Name="PW1" Description="Water" ViciPosition="4" />
+ <Reagent Name="PW1" Description="Water" ViciPosition="5" />
+ <Reagent Name="PW1" Description="Water" ViciPosition="6" />
+ <Reagent Name="PW1" Description="Water" ViciPosition="7" />
+ <Reagent Name="PW1" Description="Water" ViciPosition="8" />
+ <Reagent Name="PW1" Description="Water" ViciPosition="9" />
+ <Reagent Name="PW1" Description="Water" ViciPosition="10" />
+ <Reagent Name="PW1" Description="Water" ViciPosition="11" />
+ <Reagent Name="PW1" Description="Water" ViciPosition="12" />
+ <Reagent Name="PW1" Description="Water" ViciPosition="13" />
+ <Reagent Name="PW1" Description="Water" ViciPosition="14" />
+ <Reagent Name="PW1" Description="Water" ViciPosition="15" />
+ <Reagent Name="PW1" Description="Water" ViciPosition="16" />
+ <Reagent Name="PW1" Description="Water" ViciPosition="17" />
+ <Reagent Name="PW1" Description="Water" ViciPosition="18" />
+ <Reagent Name="PW1" Description="Water" ViciPosition="19" />
+ <Reagent Name="PW1" Description="Water" ViciPosition="20" />
+ <Reagent Name="PW1" Description="Water" ViciPosition="21" />
+ <Reagent Name="PW1" Description="Water" ViciPosition="22" />
+
+ </Reagents>
+ <Name>PostRunWash_v1.0.1</Name>
+</Recipe>
\ No newline at end of file
diff --git a/recipes/Transposon10/Wash/PostRunWash.xml b/recipes/Transposon10/Wash/PostRunWash.xml
new file mode 100755
index 0000000..43bc4d8
--- /dev/null
+++ b/recipes/Transposon10/Wash/PostRunWash.xml
@@ -0,0 +1,180 @@
+<?xml version="1.0"?>
+<Recipe xmlns:xsd="http://www.w3.org/2001/XMLSchema" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" Name="PostRunWash_v1.0.0">
+ <Protocol>
+ <ChemistryRef Description="PostRun Wash" ChemistryName="Wash" />
+ </Protocol>
+
+ <ChemistryDefinitions>
+ <ChemistryDefinition Name="Wash">
+ <ChemistryStep Description="TemplateNaOClAspirate">
+ <PumpToFlowcell Solution="3" AspirationRate="2000" DispenseRate="7500" Volume="1000" />
+ <PumpToFlowcell Solution="17" AspirationRate="2000" DispenseRate="7500" Volume="1250" />
+ </ChemistryStep>
+ <ChemistryStep Description="Prime">
+ <PumpToFlowcell Solution="3" AspirationRate="2000" DispenseRate="7500" Volume="1000" />
+ <Dispense DispenseRate="7500" />
+ </ChemistryStep>
+ <ChemistryStep Description="Wash1" Repeat="8">
+ <Aspirate Solution="3" AspirationRate="2000" Volume="250" />
+ <DispenseToFlowcell Solution="17" DispenseRate="2000" Volume="250" />
+ </ChemistryStep>
+ <ChemistryStep Description="EmptyTube">
+ <PumpToFlowcell Solution="17" AspirationRate="2000" DispenseRate="7500" Volume="2000" />
+ </ChemistryStep>
+ <ChemistryStep Description="Prime">
+ <PumpToFlowcell Solution="3" AspirationRate="2000" DispenseRate="7500" Volume="1000" />
+ <Dispense DispenseRate="7500" />
+ </ChemistryStep>
+ <ChemistryStep Description="Wash2" Repeat="8">
+ <Aspirate Solution="3" AspirationRate="2000" Volume="250" />
+ <DispenseToFlowcell Solution="17" DispenseRate="2000" Volume="250" />
+ </ChemistryStep>
+ <ChemistryStep Description="EmptyTube">
+ <PumpToFlowcell Solution="17" AspirationRate="2000" DispenseRate="7500" Volume="2000" />
+ </ChemistryStep>
+ <ChemistryStep Description="Prime">
+ <PumpToFlowcell Solution="3" AspirationRate="2000" DispenseRate="7500" Volume="1000" />
+ <Dispense DispenseRate="7500" />
+ </ChemistryStep>
+ <ChemistryStep Description="Wash3" Repeat="8">
+ <Aspirate Solution="3" AspirationRate="2000" Volume="250" />
+ <DispenseToFlowcell Solution="17" DispenseRate="2000" Volume="250" />
+ </ChemistryStep>
+ <ChemistryStep Description="Wash">
+ <PumpToFlowcell Solution="4" AspirationRate="2000" DispenseRate="7500" Volume="250" />
+ <PumpToFlowcell Solution="3" AspirationRate="2000" DispenseRate="7500" Volume="250" />
+ <Dispense DispenseRate="7500" Volume="250" />
+ <AspirateFromBypass ReagentName="PR2" AspirationRate="2000" Volume="250" />
+ <Dispense DispenseRate="7500" Volume="250" />
+ <PumpToFlowcell Solution="2" AspirationRate="2000" DispenseRate="7500" Volume="250" />
+ <PumpToFlowcell Solution="1" AspirationRate="2000" DispenseRate="7500" Volume="250" />
+ <Dispense DispenseRate="7500" />
+ <PumpToFlowcell Solution="5" AspirationRate="2000" DispenseRate="7500" Volume="250" />
+ <PumpToFlowcell Solution="6" AspirationRate="2000" DispenseRate="7500" Volume="250" />
+ <Dispense DispenseRate="7500" />
+ <PumpToFlowcell Solution="7" AspirationRate="2000" DispenseRate="7500" Volume="250" />
+ <PumpToFlowcell Solution="17" AspirationRate="2000" DispenseRate="7500" Volume="250" />
+ <Dispense DispenseRate="7500" />
+ <PumpToFlowcell Solution="18" AspirationRate="2000" DispenseRate="7500" Volume="250" />
+ <PumpToFlowcell Solution="19" AspirationRate="2000" DispenseRate="7500" Volume="250" />
+ <Dispense DispenseRate="7500" />
+ <PumpToFlowcell Solution="20" AspirationRate="2000" DispenseRate="7500" Volume="250" />
+ <PumpToFlowcell Solution="8" AspirationRate="1000" DispenseRate="7500" Volume="250" />
+ <Dispense DispenseRate="7500" />
+ <PumpToFlowcell Solution="9" AspirationRate="2000" DispenseRate="7500" Volume="250" />
+ <PumpToFlowcell Solution="10" AspirationRate="2000" DispenseRate="7500" Volume="250" />
+ <Dispense DispenseRate="7500" />
+ <PumpToFlowcell Solution="11" AspirationRate="2000" DispenseRate="7500" Volume="250" />
+ <PumpToFlowcell Solution="12" AspirationRate="2000" DispenseRate="7500" Volume="250" />
+ <Dispense DispenseRate="7500" />
+ <PumpToFlowcell Solution="13" AspirationRate="2000" DispenseRate="7500" Volume="250" />
+ <PumpToFlowcell Solution="14" AspirationRate="2000" DispenseRate="7500" Volume="250" />
+ <Dispense DispenseRate="7500" />
+ <PumpToFlowcell Solution="17" AspirationRate="2000" DispenseRate="7500" Volume="250" />
+ <PumpToFlowcell Solution="18" AspirationRate="2000" DispenseRate="7500" Volume="250" />
+ <Dispense DispenseRate="7500" />
+ <PumpToFlowcell Solution="19" AspirationRate="2000" DispenseRate="7500" Volume="250" />
+ <PumpToFlowcell Solution="20" AspirationRate="2000" DispenseRate="7500" Volume="250" />
+ <Dispense DispenseRate="7500" />
+ <PumpToFlowcell Solution="15" AspirationRate="2000" DispenseRate="7500" Volume="250" />
+ <PumpToFlowcell Solution="16" AspirationRate="2000" DispenseRate="7500" Volume="250" />
+ <Dispense DispenseRate="7500" />
+ <PumpToFlowcell Solution="21" AspirationRate="2000" DispenseRate="7500" Volume="250" />
+ <PumpToFlowcell Solution="22" AspirationRate="2000" DispenseRate="7500" Volume="250" />
+ <Dispense DispenseRate="7500" />
+ <PumpToFlowcell Solution="4" AspirationRate="2000" DispenseRate="7500" Volume="250" />
+ <Dispense DispenseRate="7500" Volume="250" />
+ <PumpToFlowcell Solution="3" AspirationRate="2000" DispenseRate="7500" Volume="250" />
+ <Dispense DispenseRate="7500" Volume="250" />
+ <AspirateFromBypass ReagentName="PR2" AspirationRate="2000" Volume="250" />
+ <Dispense DispenseRate="7500" Volume="250" />
+ <PumpToFlowcell Solution="2" AspirationRate="2000" DispenseRate="7500" Volume="250" />
+ <PumpToFlowcell Solution="1" AspirationRate="2000" DispenseRate="7500" Volume="250" />
+ <Dispense DispenseRate="7500" />
+ <PumpToFlowcell Solution="5" AspirationRate="2000" DispenseRate="7500" Volume="250" />
+ <PumpToFlowcell Solution="6" AspirationRate="2000" DispenseRate="7500" Volume="250" />
+ <Dispense DispenseRate="7500" />
+ <PumpToFlowcell Solution="7" AspirationRate="2000" DispenseRate="7500" Volume="250" />
+ <PumpToFlowcell Solution="17" AspirationRate="2000" DispenseRate="7500" Volume="250" />
+ <Dispense DispenseRate="7500" />
+ <PumpToFlowcell Solution="18" AspirationRate="2000" DispenseRate="7500" Volume="250" />
+ <PumpToFlowcell Solution="19" AspirationRate="2000" DispenseRate="7500" Volume="250" />
+ <Dispense DispenseRate="7500" />
+ <PumpToFlowcell Solution="20" AspirationRate="2000" DispenseRate="7500" Volume="250" />
+ <PumpToFlowcell Solution="8" AspirationRate="2000" DispenseRate="7500" Volume="250" />
+ <Dispense DispenseRate="7500" />
+ <PumpToFlowcell Solution="9" AspirationRate="2000" DispenseRate="7500" Volume="250" />
+ <PumpToFlowcell Solution="10" AspirationRate="2000" DispenseRate="7500" Volume="250" />
+ <Dispense DispenseRate="7500" />
+ <PumpToFlowcell Solution="11" AspirationRate="2000" DispenseRate="7500" Volume="250" />
+ <PumpToFlowcell Solution="12" AspirationRate="2000" DispenseRate="7500" Volume="250" />
+ <Dispense DispenseRate="7500" />
+ <PumpToFlowcell Solution="13" AspirationRate="2000" DispenseRate="7500" Volume="250" />
+ <PumpToFlowcell Solution="14" AspirationRate="2000" DispenseRate="7500" Volume="250" />
+ <Dispense DispenseRate="7500" />
+ <PumpToFlowcell Solution="17" AspirationRate="2000" DispenseRate="7500" Volume="250" />
+ <PumpToFlowcell Solution="18" AspirationRate="2000" DispenseRate="7500" Volume="250" />
+ <Dispense DispenseRate="7500" />
+ <PumpToFlowcell Solution="19" AspirationRate="2000" DispenseRate="7500" Volume="250" />
+ <PumpToFlowcell Solution="20" AspirationRate="2000" DispenseRate="7500" Volume="250" />
+ <Dispense DispenseRate="7500" />
+ <PumpToFlowcell Solution="4" AspirationRate="2000" DispenseRate="7500" Volume="250" />
+ <PumpToFlowcell Solution="17" AspirationRate="2000" DispenseRate="7500" Volume="250" />
+ <Dispense DispenseRate="7500" />
+ <PumpToFlowcell Solution="18" AspirationRate="2000" DispenseRate="7500" Volume="250" />
+ <PumpToFlowcell Solution="19" AspirationRate="2000" DispenseRate="7500" Volume="250" />
+ <Dispense DispenseRate="7500" />
+ <PumpToFlowcell Solution="20" AspirationRate="2000" DispenseRate="7500" Volume="250" />
+ <Dispense DispenseRate="7500" Volume="250" />
+ <PumpToFlowcell Solution="3" AspirationRate="2000" DispenseRate="7500" Volume="250" />
+ <Dispense DispenseRate="7500" Volume="250" />
+ <AspirateFromBypass ReagentName="PR2" AspirationRate="2000" Volume="250" />
+ <Dispense DispenseRate="7500" Volume="250" />
+ <PumpToFlowcell Solution="17" AspirationRate="2000" DispenseRate="7500" Volume="250" />
+ <PumpToFlowcell Solution="18" AspirationRate="2000" DispenseRate="7500" Volume="250" />
+ <Dispense DispenseRate="7500" />
+ <PumpToFlowcell Solution="19" AspirationRate="2000" DispenseRate="7500" Volume="250" />
+ <PumpToFlowcell Solution="20" AspirationRate="2000" DispenseRate="7500" Volume="250" />
+ <Dispense DispenseRate="7500" />
+ <PumpToFlowcell Solution="2" AspirationRate="2000" DispenseRate="7500" Volume="250" />
+ <PumpToFlowcell Solution="1" AspirationRate="2000" DispenseRate="7500" Volume="250" />
+ <Dispense DispenseRate="7500" />
+ <PumpToFlowcell Solution="3" AspirationRate="2000" DispenseRate="7500" Volume="250" />
+ <Dispense DispenseRate="7500" Volume="250" />
+ <AspirateFromBypass ReagentName="PR2" AspirationRate="2000" Volume="250" />
+ <Dispense DispenseRate="7500" Volume="250" />
+ <PumpToFlowcell Solution="15" AspirationRate="2000" DispenseRate="7500" Volume="250" />
+ <PumpToFlowcell Solution="16" AspirationRate="2000" DispenseRate="7500" Volume="250" />
+ <Dispense DispenseRate="7500" />
+ <PumpToFlowcell Solution="21" AspirationRate="2000" DispenseRate="7500" Volume="250" />
+ <PumpToFlowcell Solution="22" AspirationRate="2000" DispenseRate="7500" Volume="250" />
+ </ChemistryStep>
+ </ChemistryDefinition>
+ </ChemistryDefinitions>
+ <Reagents>
+ <Reagent Name="PW1" Description="Water" ViciPosition="1" />
+ <Reagent Name="PW1" Description="Water" ViciPosition="2" />
+ <Reagent Name="PW1" Description="Water" ViciPosition="3" />
+ <Reagent Name="PW1" Description="Water" ViciPosition="4" />
+ <Reagent Name="PW1" Description="Water" ViciPosition="5" />
+ <Reagent Name="PW1" Description="Water" ViciPosition="6" />
+ <Reagent Name="PW1" Description="Water" ViciPosition="7" />
+ <Reagent Name="PW1" Description="Water" ViciPosition="8" />
+ <Reagent Name="PW1" Description="Water" ViciPosition="9" />
+ <Reagent Name="PW1" Description="Water" ViciPosition="10" />
+ <Reagent Name="PW1" Description="Water" ViciPosition="11" />
+ <Reagent Name="PW1" Description="Water" ViciPosition="12" />
+ <Reagent Name="PW1" Description="Water" ViciPosition="13" />
+ <Reagent Name="PW1" Description="Water" ViciPosition="14" />
+ <Reagent Name="PW1" Description="Water" ViciPosition="15" />
+ <Reagent Name="PW1" Description="Water" ViciPosition="16" />
+ <Reagent Name="PW1" Description="DiluteNaOCl" ViciPosition="17" />
+ <Reagent Name="PW1" Description="Water" ViciPosition="18" />
+ <Reagent Name="PW1" Description="Water" ViciPosition="19" />
+ <Reagent Name="PW1" Description="Water" ViciPosition="20" />
+ <Reagent Name="PW1" Description="Water" ViciPosition="21" />
+ <Reagent Name="PW1" Description="Water" ViciPosition="22" />
+
+ </Reagents>
+ <Name>PostRunWash_v1.0.1</Name>
+</Recipe>
\ No newline at end of file
diff --git a/recipes/Transposon10/Wash/PostRunWashOriginal.xml b/recipes/Transposon10/Wash/PostRunWashOriginal.xml
new file mode 100755
index 0000000..fc50905
--- /dev/null
+++ b/recipes/Transposon10/Wash/PostRunWashOriginal.xml
@@ -0,0 +1,115 @@
+<?xml version="1.0"?>
+<Recipe xmlns:xsd="http://www.w3.org/2001/XMLSchema" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" Name="PostRunWash_v1.0.0">
+ <Protocol>
+ <ChemistryRef Description="PostRun Wash" ChemistryName="Wash" />
+ </Protocol>
+ <ChemistryDefinitions>
+ <ChemistryDefinition Name="Wash">
+ <ChemistryStep Description="Wash">
+ <PumpToFlowcell Solution="4" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="3" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <Dispense DispenseRate="2500" Volume="250" />
+ <AspirateFromBypass ReagentName="PR2" AspirationRate="2000" Volume="250" />
+ <Dispense DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="2" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="1" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="5" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="6" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="7" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="17" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="18" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="19" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="20" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="8" AspirationRate="1000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="9" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="10" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="11" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="12" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="13" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="14" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="17" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="18" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="19" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="20" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="15" AspirationRate="2000" DispenseRate="2500" Volume="250" />
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+ <PumpToFlowcell Solution="22" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="4" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="3" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <Dispense DispenseRate="2500" Volume="250" />
+ <AspirateFromBypass ReagentName="PR2" AspirationRate="2000" Volume="250" />
+ <Dispense DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="2" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="1" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="5" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="6" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="7" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="17" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="18" AspirationRate="2000" DispenseRate="2500" Volume="250" />
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+ <PumpToFlowcell Solution="20" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="8" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="9" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="10" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="11" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="12" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="13" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="14" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="17" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="18" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="19" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="20" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="4" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="17" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="18" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="19" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="20" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="3" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <Dispense DispenseRate="2500" Volume="250" />
+ <AspirateFromBypass ReagentName="PR2" AspirationRate="2000" Volume="250" />
+ <Dispense DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="17" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="18" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="19" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="20" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="2" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="1" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="3" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <Dispense DispenseRate="2500" Volume="250" />
+ <AspirateFromBypass ReagentName="PR2" AspirationRate="2000" Volume="250" />
+ <Dispense DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="15" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="16" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="21" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="22" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ </ChemistryStep>
+ </ChemistryDefinition>
+ </ChemistryDefinitions>
+ <Reagents>
+ <Reagent Name="PW1" Description="Water" ViciPosition="1" />
+ <Reagent Name="PW1" Description="Water" ViciPosition="2" />
+ <Reagent Name="PW1" Description="Water" ViciPosition="3" />
+ <Reagent Name="PW1" Description="Water" ViciPosition="4" />
+ <Reagent Name="PW1" Description="Water" ViciPosition="5" />
+ <Reagent Name="PW1" Description="Water" ViciPosition="6" />
+ <Reagent Name="PW1" Description="Water" ViciPosition="7" />
+ <Reagent Name="PW1" Description="Water" ViciPosition="8" />
+ <Reagent Name="PW1" Description="Water" ViciPosition="9" />
+ <Reagent Name="PW1" Description="Water" ViciPosition="10" />
+ <Reagent Name="PW1" Description="Water" ViciPosition="11" />
+ <Reagent Name="PW1" Description="Water" ViciPosition="12" />
+ <Reagent Name="PW1" Description="Water" ViciPosition="13" />
+ <Reagent Name="PW1" Description="Water" ViciPosition="14" />
+ <Reagent Name="PW1" Description="Water" ViciPosition="15" />
+ <Reagent Name="PW1" Description="Water" ViciPosition="16" />
+ <Reagent Name="PW1" Description="Water" ViciPosition="17" />
+ <Reagent Name="PW1" Description="Water" ViciPosition="18" />
+ <Reagent Name="PW1" Description="Water" ViciPosition="19" />
+ <Reagent Name="PW1" Description="Water" ViciPosition="20" />
+ <Reagent Name="PW1" Description="Water" ViciPosition="21" />
+ <Reagent Name="PW1" Description="Water" ViciPosition="22" />
+
+ </Reagents>
+ <Name>PostRunWash_v1.0.1</Name>
+</Recipe>
\ No newline at end of file
diff --git a/recipes/Transposon10/Wash/StandbyWash.xml b/recipes/Transposon10/Wash/StandbyWash.xml
new file mode 100755
index 0000000..ce83571
--- /dev/null
+++ b/recipes/Transposon10/Wash/StandbyWash.xml
@@ -0,0 +1,70 @@
+<?xml version="1.0"?>
+<Recipe xmlns:xsd="http://www.w3.org/2001/XMLSchema" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" Name="StandbyWash_v1.0.0">
+ <Protocol>
+ <ChemistryRef Description="Standby Wash 1 of 8" ChemistryName="Wash" />
+ <ChemistryRef Description="Standby Wash 2 of 8" ChemistryName="Wash" />
+ <ChemistryRef Description="Standby Wash 3 of 8" ChemistryName="Wash" />
+ <ChemistryRef Description="Standby Wash 4 of 8" ChemistryName="Wash" />
+ <ChemistryRef Description="Standby Wash 5 of 8" ChemistryName="Wash" />
+ <ChemistryRef Description="Standby Wash 6 of 8" ChemistryName="Wash" />
+ <ChemistryRef Description="Standby Wash 7 of 8" ChemistryName="Wash" />
+ <ChemistryRef Description="Standby Wash 8 of 8" ChemistryName="Wash" />
+ </Protocol>
+ <ChemistryDefinitions>
+ <ChemistryDefinition Name="Wash">
+ <ChemistryStep Description="Wash">
+ <PumpToFlowcell Solution="4" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="3" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <Dispense DispenseRate="2500" Volume="250" />
+ <AspirateFromBypass ReagentName="PR2" AspirationRate="2000" Volume="250" />
+ <Dispense DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="2" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="1" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="5" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="6" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="7" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="17" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="18" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="19" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="20" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="8" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="9" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="10" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="11" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="12" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="13" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="14" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="15" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="16" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="21" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="22" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ </ChemistryStep>
+ </ChemistryDefinition>
+ </ChemistryDefinitions>
+ <Reagents>
+ <Reagent Name="PW1" Description="Water" ViciPosition="1" />
+ <Reagent Name="PW1" Description="Water" ViciPosition="2" />
+ <Reagent Name="PW1" Description="Water" ViciPosition="3" />
+ <Reagent Name="PW1" Description="Water" ViciPosition="4" />
+ <Reagent Name="PW1" Description="Water" ViciPosition="5" />
+ <Reagent Name="PW1" Description="Water" ViciPosition="6" />
+ <Reagent Name="PW1" Description="Water" ViciPosition="7" />
+ <Reagent Name="PW1" Description="Water" ViciPosition="8" />
+ <Reagent Name="PW1" Description="Water" ViciPosition="9" />
+ <Reagent Name="PW1" Description="Water" ViciPosition="10" />
+ <Reagent Name="PW1" Description="Water" ViciPosition="11" />
+ <Reagent Name="PW1" Description="Water" ViciPosition="12" />
+ <Reagent Name="PW1" Description="Water" ViciPosition="13" />
+ <Reagent Name="PW1" Description="Water" ViciPosition="14" />
+ <Reagent Name="PW1" Description="Water" ViciPosition="15" />
+ <Reagent Name="PW1" Description="Water" ViciPosition="16" />
+ <Reagent Name="PW1" Description="Water" ViciPosition="17" />
+ <Reagent Name="PW1" Description="Water" ViciPosition="18" />
+ <Reagent Name="PW1" Description="Water" ViciPosition="19" />
+ <Reagent Name="PW1" Description="Water" ViciPosition="20" />
+ <Reagent Name="PW1" Description="Water" ViciPosition="21" />
+ <Reagent Name="PW1" Description="Water" ViciPosition="22" />
+
+ </Reagents>
+ <Name>StandbyWash_v1.0.0</Name>
+</Recipe>
\ No newline at end of file
diff --git a/recipes/Transposon12/Chemistry/Chemistry.xml b/recipes/Transposon12/Chemistry/Chemistry.xml
new file mode 100644
index 0000000..96dfceb
--- /dev/null
+++ b/recipes/Transposon12/Chemistry/Chemistry.xml
@@ -0,0 +1,413 @@
+<?xml version="1.0"?>
+<ChemistryDefinitions Version="Calvados + AutoWashv4">
+
+ <ChemistryDefinition Name="CompleteCycle">
+ <ChemistryStep Description="Deblock" Repeat="1">
+ <Temp Duration="0" Temperature="60" />
+ <PumpToFlowcell ReagentName="PR2" AspirationRate="2000" Solution="0" DispenseRate="7500" Volume="120" />
+ <PumpToFlowcell ReagentName="CMS" AspirationRate="2000" Solution="0" DispenseRate="7500" Volume="60" />
+ <PumpToFlowcell ReagentName="PR2" AspirationRate="2000" Solution="0" DispenseRate="7500" Volume="22" />
+ <Wait Duration="10000" />
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+ <PumpToFlowcell ReagentName="PR2" AspirationRate="2000" Solution="0" DispenseRate="7500" Volume="20" />
+ <Wait Duration="35000" />
+ <PumpToFlowcell ReagentName="PR2" AspirationRate="2000" Solution="0" DispenseRate="7500" Volume="5" />
+ <DispenseAndWait DispenseRate="7500" Duration="30000" />
+ </ChemistryStep>
+ <ChemistryStep Description="Buffer Wash" Repeat="1">
+ <PumpToFlowcell ReagentName="PR2" AspirationRate="2000" Solution="0" DispenseRate="7500" Volume="250" />
+ </ChemistryStep>
+ <ChemistryStep Description="Incorporation" Repeat="1">
+ <PumpToFlowcell ReagentName="IMS" AspirationRate="2000" Solution="0" DispenseRate="7500" Volume="60" />
+ <PumpToFlowcell ReagentName="PR2" AspirationRate="2000" Solution="0" DispenseRate="7500" Volume="20" />
+ <Temp Temperature="65" Duration="0" />
+ <Wait Duration="45000" />
+ <PumpToFlowcell ReagentName="PR2" AspirationRate="2000" Solution="0" DispenseRate="7500" Volume="5" />
+ <DispenseAndWait Duration="40000" />
+ <Temp Temperature="22" Duration="0" />
+ <PumpToFlowcell ReagentName="PR2" AspirationRate="2000" Solution="0" DispenseRate="7500" Volume="120" />
+ <PumpToFlowcell ReagentName="SRE" AspirationRate="2000" Solution="0" DispenseRate="7500" Volume="60" />
+ <PumpToFlowcell ReagentName="PR2" AspirationRate="2000" Solution="0" DispenseRate="7500" Volume="20" />
+ <DispenseAndWait DispenseRate="7500" Duration="15000" />
+ </ChemistryStep>
+ </ChemistryDefinition>
+ </ChemistryDefinitions>
\ No newline at end of file
diff --git a/recipes/Transposon12/Exposures/Sony.xml b/recipes/Transposon12/Exposures/Sony.xml
new file mode 100644
index 0000000..ed9e88d
--- /dev/null
+++ b/recipes/Transposon12/Exposures/Sony.xml
@@ -0,0 +1,7 @@
+<?xml version="1.0" encoding="utf-8" ?>
+<Exposures>
+ <Exposure Name="A" Start="1037" Ramp="0" />
+ <Exposure Name="T" Start="500" Ramp="0" />
+ <Exposure Name="C" Start="1037" Ramp="0" />
+ <Exposure Name="G" Start="500" Ramp="0" />
+</Exposures>
diff --git a/recipes/Transposon12/Exposures/SonyV2.xml b/recipes/Transposon12/Exposures/SonyV2.xml
new file mode 100644
index 0000000..b1f60d9
--- /dev/null
+++ b/recipes/Transposon12/Exposures/SonyV2.xml
@@ -0,0 +1,11 @@
+<?xml version="1.0" encoding="utf-8" ?>
+<Exposures>
+ <Exposure Name="A" Start="260" IsIndexed="false" Ramp="5.2" />
+ <Exposure Name="A" Start="1037" IsIndexed="true" Ramp="0" />
+ <Exposure Name="T" Start="125" IsIndexed="false" Ramp="2.5" />
+ <Exposure Name="T" Start="500" IsIndexed="true" Ramp="0" />
+ <Exposure Name="C" Start="260" IsIndexed="false" Ramp="5.2" />
+ <Exposure Name="C" Start="1037" IsIndexed="true" Ramp="0" />
+ <Exposure Name="G" Start="125" IsIndexed="false" Ramp="2.5" />
+ <Exposure Name="G" Start="500" IsIndexed="true" Ramp="0" />
+</Exposures>
diff --git a/recipes/Transposon12/Protocol/1Read1Index.xml b/recipes/Transposon12/Protocol/1Read1Index.xml
new file mode 100644
index 0000000..7690874
--- /dev/null
+++ b/recipes/Transposon12/Protocol/1Read1Index.xml
@@ -0,0 +1,26 @@
+<?xml version="1.0"?>
+<Protocol Version="Fraise 0.7.1 Amplicon v1.1">
+ <ChemistryRef ChemistryName="OnBoardClusterGeneration" />
+ <ChemistryRef ChemistryName="FirstReadPreparation" />
+ <ChemistryRef ChemistryName="Index2CompleteCycleDark2" />
+ <ChemistryRef ChemistryName="Index2CompleteCycleDark2" />
+ <ChemistryRef ChemistryName="Index2CompleteCycleDark2" />
+ <ChemistryRef ChemistryName="Index2CompleteCycleDark2" />
+ <ChemistryRef ChemistryName="Index2CompleteCycleDark2" />
+ <ChemistryRef ChemistryName="Index2CompleteCycleDark2" />
+ <ChemistryRef ChemistryName="Index2CompleteCycleDark2" />
+ <ChemistryRef ChemistryName="Index2CompleteCycleDark2" />
+ <ChemistryRef ChemistryName="Index2CompleteCycleDark2" />
+ <ChemistryRef ChemistryName="Index2CompleteCycleDark2" />
+ <ChemistryRef ChemistryName="Index2CompleteCycleDark2" />
+ <ChemistryRef ChemistryName="Index2CompleteCycleDark2" />
+ <ChemistryRef ChemistryName="EndDeblock" />
+ <ReadRef ReadName="FirstRead" />
+ <ChemistryRef ChemistryName="EndDeblock" />
+ <ChemistryRef ChemistryName="Index1Preparation" />
+ <ReadRef ReadName="IndexRead1" />
+ <ChemistryRef ChemistryName="EndDeblock" />
+ <ChemistryRef ChemistryName="TemplateRinse" />
+ <ChemistryRef ChemistryName="End" />
+
+</Protocol>
\ No newline at end of file
diff --git a/recipes/Transposon12/Protocol/1Read2Index.xml b/recipes/Transposon12/Protocol/1Read2Index.xml
new file mode 100644
index 0000000..adacc5d
--- /dev/null
+++ b/recipes/Transposon12/Protocol/1Read2Index.xml
@@ -0,0 +1,27 @@
+<?xml version="1.0"?>
+<Protocol Version="Fraise 0.7.1 Amplicon v1.1">
+ <ChemistryRef ChemistryName="OnBoardClusterGeneration" />
+ <ChemistryRef ChemistryName="FirstReadPreparation" />
+ <ChemistryRef ChemistryName="Index2CompleteCycleDark2" />
+ <ChemistryRef ChemistryName="Index2CompleteCycleDark2" />
+ <ChemistryRef ChemistryName="Index2CompleteCycleDark2" />
+ <ChemistryRef ChemistryName="Index2CompleteCycleDark2" />
+ <ChemistryRef ChemistryName="Index2CompleteCycleDark2" />
+ <ChemistryRef ChemistryName="Index2CompleteCycleDark2" />
+ <ChemistryRef ChemistryName="Index2CompleteCycleDark2" />
+ <ChemistryRef ChemistryName="Index2CompleteCycleDark2" />
+ <ChemistryRef ChemistryName="Index2CompleteCycleDark2" />
+ <ChemistryRef ChemistryName="Index2CompleteCycleDark2" />
+ <ChemistryRef ChemistryName="Index2CompleteCycleDark2" />
+ <ChemistryRef ChemistryName="Index2CompleteCycleDark2" />
+ <ChemistryRef ChemistryName="EndDeblock" />
+ <ReadRef ReadName="FirstRead" />
+ <ChemistryRef ChemistryName="EndDeblock" />
+ <ChemistryRef ChemistryName="Index1Preparation" />
+ <ReadRef ReadName="IndexRead1" />
+ <ChemistryRef ChemistryName="EndDeblock" />
+ <ChemistryRef ChemistryName="Index2Preparation" />
+ <ReadRef ReadName="IndexRead2" />
+ <ChemistryRef ChemistryName="TemplateRinse" />
+ <ChemistryRef ChemistryName="End" />
+ </Protocol>
\ No newline at end of file
diff --git a/recipes/Transposon12/Protocol/2Read1Index.xml b/recipes/Transposon12/Protocol/2Read1Index.xml
new file mode 100644
index 0000000..23c8bbc
--- /dev/null
+++ b/recipes/Transposon12/Protocol/2Read1Index.xml
@@ -0,0 +1,30 @@
+<?xml version="1.0"?>
+<Protocol Version="Fraise 0.7.1 Amplicon v1.1">
+ <ChemistryRef ChemistryName="OnBoardClusterGeneration" />
+ <ChemistryRef ChemistryName="FirstReadPreparation" />
+ <ChemistryRef ChemistryName="Index2CompleteCycleDark2" />
+ <ChemistryRef ChemistryName="Index2CompleteCycleDark2" />
+ <ChemistryRef ChemistryName="Index2CompleteCycleDark2" />
+ <ChemistryRef ChemistryName="Index2CompleteCycleDark2" />
+ <ChemistryRef ChemistryName="Index2CompleteCycleDark2" />
+ <ChemistryRef ChemistryName="Index2CompleteCycleDark2" />
+ <ChemistryRef ChemistryName="Index2CompleteCycleDark2" />
+ <ChemistryRef ChemistryName="Index2CompleteCycleDark2" />
+ <ChemistryRef ChemistryName="Index2CompleteCycleDark2" />
+ <ChemistryRef ChemistryName="Index2CompleteCycleDark2" />
+ <ChemistryRef ChemistryName="Index2CompleteCycleDark2" />
+ <ChemistryRef ChemistryName="Index2CompleteCycleDark2" />
+ <ChemistryRef ChemistryName="EndDeblock" />
+ <ReadRef ReadName="FirstRead" />
+ <ChemistryRef ChemistryName="EndDeblock" />
+ <ChemistryRef ChemistryName="Index1Preparation" />
+ <ReadRef ReadName="IndexRead1" />
+ <ChemistryRef ChemistryName="EndDeblock" />
+ <ChemistryRef ChemistryName="Deprotection" />
+ <ChemistryRef ChemistryName="PairedEndTurnaround" />
+ <ChemistryRef ChemistryName="SecondReadPreparation" />
+ <ReadRef ReadName="SecondRead" />
+ <ChemistryRef ChemistryName="EndDeblock" />
+ <ChemistryRef ChemistryName="TemplateRinse" />
+ <ChemistryRef ChemistryName="End" />
+ </Protocol>
\ No newline at end of file
diff --git a/recipes/Transposon12/Protocol/2Read2Index.xml b/recipes/Transposon12/Protocol/2Read2Index.xml
new file mode 100644
index 0000000..b38a97f
--- /dev/null
+++ b/recipes/Transposon12/Protocol/2Read2Index.xml
@@ -0,0 +1,33 @@
+<?xml version="1.0"?>
+<Protocol Version="Fraise 0.7.1 Amplicon v1.1">
+ <ChemistryRef ChemistryName="OnBoardClusterGeneration" />
+ <ChemistryRef ChemistryName="FirstReadPreparation" />
+ <ChemistryRef ChemistryName="Index2CompleteCycleDark2" />
+ <ChemistryRef ChemistryName="Index2CompleteCycleDark2" />
+ <ChemistryRef ChemistryName="Index2CompleteCycleDark2" />
+ <ChemistryRef ChemistryName="Index2CompleteCycleDark2" />
+ <ChemistryRef ChemistryName="Index2CompleteCycleDark2" />
+ <ChemistryRef ChemistryName="Index2CompleteCycleDark2" />
+ <ChemistryRef ChemistryName="Index2CompleteCycleDark2" />
+ <ChemistryRef ChemistryName="Index2CompleteCycleDark2" />
+ <ChemistryRef ChemistryName="Index2CompleteCycleDark2" />
+ <ChemistryRef ChemistryName="Index2CompleteCycleDark2" />
+ <ChemistryRef ChemistryName="Index2CompleteCycleDark2" />
+ <ChemistryRef ChemistryName="Index2CompleteCycleDark2" />
+ <ChemistryRef ChemistryName="EndDeblock" />
+ <ReadRef ReadName="FirstRead" />
+ <ChemistryRef ChemistryName="EndDeblock" />
+ <ChemistryRef ChemistryName="Index1Preparation" />
+ <ReadRef ReadName="IndexRead1" />
+ <ChemistryRef ChemistryName="EndDeblock" />
+ <ChemistryRef ChemistryName="Index2Preparation" />
+ <ReadRef ReadName="IndexRead2" />
+ <ChemistryRef ChemistryName="EndDeblock" />
+ <ChemistryRef ChemistryName="Deprotection" />
+ <ChemistryRef ChemistryName="PairedEndTurnaround" />
+ <ChemistryRef ChemistryName="SecondReadPreparation" />
+ <ReadRef ReadName="SecondRead" />
+ <ChemistryRef ChemistryName="EndDeblock" />
+ <ChemistryRef ChemistryName="TemplateRinse" />
+ <ChemistryRef ChemistryName="End" />
+ </Protocol>
\ No newline at end of file
diff --git a/recipes/Transposon12/Reads/Reads.xml b/recipes/Transposon12/Reads/Reads.xml
new file mode 100644
index 0000000..3ced231
--- /dev/null
+++ b/recipes/Transposon12/Reads/Reads.xml
@@ -0,0 +1,23 @@
+<?xml version="1.0"?>
+<ReadDefinitions Version="Fraise 0.7.1 Amplicon v1.1">
+ <ReadDefinition Name="FirstRead">
+ <FirstBase ChemistryName="FirstBase" Cycles="1" />
+ <Imaging ChemistryName="CompleteCycle" Cycles="NumCycles - 1" />
+ <End ChemistryName="EndRead" />
+ </ReadDefinition>
+ <ReadDefinition Name="IndexRead1" IsIndexed="True" >
+ <FirstBase ChemistryName="FirstBase" Cycles="1" />
+ <Imaging ChemistryName="CompleteCycle" Cycles="NumCycles - 1" />
+ <End ChemistryName="EndRead" />
+ </ReadDefinition>
+ <ReadDefinition Name="SecondRead" IsIndexed="false">
+ <FirstBase ChemistryName="FirstBase" Cycles="1" />
+ <Imaging ChemistryName="CompleteCycle" Cycles="NumCycles - 1" />
+ <End ChemistryName="EndRead" />
+ </ReadDefinition>
+ <ReadDefinition Name="IndexRead2" IsIndexed="true">
+ <FirstBase ChemistryName="FirstBase" Cycles="1" />
+ <Imaging ChemistryName="CompleteCycle" Cycles="NumCycles - 1" />
+ <End ChemistryName="EndRead" />
+ </ReadDefinition>
+ </ReadDefinitions>
\ No newline at end of file
diff --git a/recipes/Transposon12/Reagents/MaintenanceWash.xml b/recipes/Transposon12/Reagents/MaintenanceWash.xml
new file mode 100644
index 0000000..f6d14da
--- /dev/null
+++ b/recipes/Transposon12/Reagents/MaintenanceWash.xml
@@ -0,0 +1,25 @@
+<?xml version="1.0" encoding="utf-8" ?>
+<Reagents Name="Bolt Avocado Reagents" Version="Selector Valve Positions v2.2">
+ <Reagent Name="PW1" Description="PW1" SelectorValvePosition="1" />
+ <Reagent Name="PW1" Description="PW1" SelectorValvePosition="2" />
+ <Reagent Name="PW1" Description="PW1" SelectorValvePosition="3" />
+ <Reagent Name="PW1" Description="PW1" SelectorValvePosition="4" />
+ <Reagent Name="PW1" Description="PW1" SelectorValvePosition="5" />
+ <Reagent Name="PW1" Description="PW1" SelectorValvePosition="6" />
+ <Reagent Name="PW1" Description="PW1" SelectorValvePosition="7" />
+ <Reagent Name="PW1" Description="PW1" SelectorValvePosition="8" />
+ <Reagent Name="PW1" Description="PW1" SelectorValvePosition="9" />
+ <Reagent Name="PW1" Description="PW1" SelectorValvePosition="10" />
+ <Reagent Name="PW1" Description="PW1" SelectorValvePosition="11" />
+ <Reagent Name="PW1" Description="PW1" SelectorValvePosition="12" />
+ <Reagent Name="PW1" Description="PW1" SelectorValvePosition="13" />
+ <Reagent Name="PW1" Description="PW1" SelectorValvePosition="14" />
+ <Reagent Name="PW1" Description="PW1" SelectorValvePosition="15" />
+ <Reagent Name="PW1" Description="PW1" SelectorValvePosition="16" />
+ <Reagent Name="PW1" Description="PW1" SelectorValvePosition="17" />
+ <Reagent Name="PW1" Description="PW1" SelectorValvePosition="18" />
+ <Reagent Name="PW1" Description="PW1" SelectorValvePosition="19" />
+ <Reagent Name="PW1" Description="PW1" SelectorValvePosition="20" />
+ <Reagent Name="PW1" Description="PW1" SelectorValvePosition="21" />
+ <Reagent Name="PW1" Description="PW1" SelectorValvePosition="22" />
+</Reagents>
diff --git a/recipes/Transposon12/Reagents/PostRunWash.xml b/recipes/Transposon12/Reagents/PostRunWash.xml
new file mode 100644
index 0000000..f6d14da
--- /dev/null
+++ b/recipes/Transposon12/Reagents/PostRunWash.xml
@@ -0,0 +1,25 @@
+<?xml version="1.0" encoding="utf-8" ?>
+<Reagents Name="Bolt Avocado Reagents" Version="Selector Valve Positions v2.2">
+ <Reagent Name="PW1" Description="PW1" SelectorValvePosition="1" />
+ <Reagent Name="PW1" Description="PW1" SelectorValvePosition="2" />
+ <Reagent Name="PW1" Description="PW1" SelectorValvePosition="3" />
+ <Reagent Name="PW1" Description="PW1" SelectorValvePosition="4" />
+ <Reagent Name="PW1" Description="PW1" SelectorValvePosition="5" />
+ <Reagent Name="PW1" Description="PW1" SelectorValvePosition="6" />
+ <Reagent Name="PW1" Description="PW1" SelectorValvePosition="7" />
+ <Reagent Name="PW1" Description="PW1" SelectorValvePosition="8" />
+ <Reagent Name="PW1" Description="PW1" SelectorValvePosition="9" />
+ <Reagent Name="PW1" Description="PW1" SelectorValvePosition="10" />
+ <Reagent Name="PW1" Description="PW1" SelectorValvePosition="11" />
+ <Reagent Name="PW1" Description="PW1" SelectorValvePosition="12" />
+ <Reagent Name="PW1" Description="PW1" SelectorValvePosition="13" />
+ <Reagent Name="PW1" Description="PW1" SelectorValvePosition="14" />
+ <Reagent Name="PW1" Description="PW1" SelectorValvePosition="15" />
+ <Reagent Name="PW1" Description="PW1" SelectorValvePosition="16" />
+ <Reagent Name="PW1" Description="PW1" SelectorValvePosition="17" />
+ <Reagent Name="PW1" Description="PW1" SelectorValvePosition="18" />
+ <Reagent Name="PW1" Description="PW1" SelectorValvePosition="19" />
+ <Reagent Name="PW1" Description="PW1" SelectorValvePosition="20" />
+ <Reagent Name="PW1" Description="PW1" SelectorValvePosition="21" />
+ <Reagent Name="PW1" Description="PW1" SelectorValvePosition="22" />
+</Reagents>
diff --git a/recipes/Transposon12/Reagents/Sequencing.xml b/recipes/Transposon12/Reagents/Sequencing.xml
new file mode 100644
index 0000000..87cac01
--- /dev/null
+++ b/recipes/Transposon12/Reagents/Sequencing.xml
@@ -0,0 +1,24 @@
+<?xml version="1.0" encoding="utf-8" ?>
+<Reagents Name="Shock Reagents" Version="Selector Valve Positions v2.2">
+ <Reagent Name="IMS" Description="Incorporation Mix" SelectorValvePosition="1" />
+ <Reagent Name="SRE" Description="Scan Mix" SelectorValvePosition="2" />
+ <Reagent Name="PR2" Description="Incorporation Buffer" SelectorValvePosition="3" />
+ <Reagent Name="CMS" Description="Cleavage Mix" SelectorValvePosition="4" />
+ <Reagent Name="AMS1" Description="Amplification Mix 1" SelectorValvePosition="5" />
+ <Reagent Name="AMS2" Description="Amplification Mix 2" SelectorValvePosition="6" />
+ <Reagent Name="LPM" Description="Lin Pre Mix" SelectorValvePosition="7" />
+ <Reagent Name="LDR" Description="Formamide" SelectorValvePosition="8" />
+ <Reagent Name="LMX1" Description="Linearization Mix" SelectorValvePosition="9" />
+ <Reagent Name="LMX2" Description="R2 Lin Mix" SelectorValvePosition="10" />
+ <Reagent Name="RMF" Description="Resynthesis Mix" SelectorValvePosition="11" />
+ <Reagent Name="HP10" Description="R1 Primer Mix" SelectorValvePosition="12" />
+ <Reagent Name="HP12" Description="Index Primer Mix" SelectorValvePosition="13" />
+ <Reagent Name="HP11" Description="R2 Primer Mix" SelectorValvePosition="14" />
+ <Reagent Name="PW1" Description="Water" SelectorValvePosition="15" />
+ <Reagent Name="PW2" Description="Water" SelectorValvePosition="16" />
+ <Reagent Name="TMP" Description="Template" SelectorValvePosition="17" />
+ <Reagent Name="C1" Description="Custom 1 Primer Mix" SelectorValvePosition="18" />
+ <Reagent Name="C2" Description="Custom 2 Primer Mix" SelectorValvePosition="19" />
+ <Reagent Name="C3" Description="Custom 3 Primer Mix" SelectorValvePosition="20" />
+ <Reagent Name="PW3" Description="Water" SelectorValvePosition="21" />
+</Reagents>
\ No newline at end of file
diff --git a/recipes/Transposon12/Wash/130702_ImplementingCarryoverDecontamWash_v3.docx b/recipes/Transposon12/Wash/130702_ImplementingCarryoverDecontamWash_v3.docx
new file mode 100644
index 0000000..ea4524b
Binary files /dev/null and b/recipes/Transposon12/Wash/130702_ImplementingCarryoverDecontamWash_v3.docx differ
diff --git a/recipes/Transposon12/Wash/LineWash.xml b/recipes/Transposon12/Wash/LineWash.xml
new file mode 100644
index 0000000..ebfa1af
--- /dev/null
+++ b/recipes/Transposon12/Wash/LineWash.xml
@@ -0,0 +1,102 @@
+<?xml version="1.0"?>
+<Recipe xmlns:xsd="http://www.w3.org/2001/XMLSchema" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" Name="LineWash_v0.3">
+
+ <Protocol Version="LineWash">
+ <ChemistryRef ChemistryName="LineWash" Repeat="1" />
+ </Protocol>
+
+ <ChemistryDefinitions Version="LineWash_v0.3">
+ <ChemistryDefinition Name="CleanSyringe">
+ <ChemistryStep Description="CleanSyringe" Repeat="1"> <!--run water through syringe to reduce carryover since about to backflush-->
+ <AspirateFromBypass ReagentName="PW1" AspirationRate="2000" DispenseRate="2500" Volume="1000" />
+ <Wait Duration="10000" />
+ <AspirateFromBypass ReagentName="PW1" AspirationRate="500" DispenseRate="1000" Volume="500" />
+ <Wait Duration="10000" />
+ <AspirateFromBypass ReagentName="PW1" AspirationRate="2000" DispenseRate="2500" Volume="500" />
+ </ChemistryStep>
+ </ChemistryDefinition>
+ <ChemistryDefinition Name="Oscillate">
+ <ChemistryStep Description="Oscillate" Repeat="1">
+ <!--add airbubble, fill syringe, and slowly pump back and forth increasing pressure-->
+ <PumpToFlowcell Solution="23" AspirationRate="1000" DispenseRate="2500" Volume="15" />
+ <AspirateFromBypass ReagentName="PW1" AspirationRate="2000" Volume="250" />
+ </ChemistryStep>
+ <ChemistryStep Description="OscillateSubStep" Repeat="49">
+ <DispenseToFlowcell ReagentName="PW1" DispenseRate="2000" Volume="5"/>
+ <Wait Duration="1000" />
+ <Aspirate ReagentName="PW1" AspirationRate="2000" Volume="5" />
+ <Wait Duration="1000" />
+ <DispenseToFlowcell ReagentName="PW1" DispenseRate="2000" Volume="10"/>
+ <Wait Duration="1000" />
+ <Aspirate ReagentName="PW1" AspirationRate="2000" Volume="5" />
+ <Wait Duration="6000" />
+ </ChemistryStep>
+ </ChemistryDefinition>
+ <ChemistryDefinition Name="Reprime">
+ <ChemistryStep Description="Reprime" Repeat="1"> <!--prime line with 500uL-->
+ <PumpToFlowcell ReagentName="PW1" AspirationRate="2000" DispenseRate="2500" Volume="500" />
+ </ChemistryStep>
+ </ChemistryDefinition>
+ <ChemistryDefinition Name="Flush">
+ <ChemistryStep Description="Flush" Repeat="1"> <!--empty tube and refill from bypass-->
+ <PumpToFlowcell ReagentName="PW1" AspirationRate="5000" DispenseRate="5000" Volume="3000" />
+ <AspirateFromBypass ReagentName="PW1" AspirationRate="2000" Volume="250" />
+ <DispenseToFlowcell ReagentName="PW1" DispenseRate="2000" Volume="250" />
+ <AspirateFromBypass ReagentName="PW1" AspirationRate="2000" Volume="250" />
+ <DispenseToFlowcell ReagentName="PW1" DispenseRate="2000" Volume="250" />
+ <AspirateFromBypass ReagentName="PW1" AspirationRate="2000" Volume="250" />
+ <DispenseToFlowcell ReagentName="PW1" DispenseRate="2000" Volume="250" />
+ <AspirateFromBypass ReagentName="PW1" AspirationRate="2000" Volume="250" />
+ <DispenseToFlowcell ReagentName="PW1" DispenseRate="2000" Volume="250" />
+ <AspirateFromBypass ReagentName="PW1" AspirationRate="2000" Volume="250" />
+ <DispenseToFlowcell ReagentName="PW1" DispenseRate="2000" Volume="250" />
+ <AspirateFromBypass ReagentName="PW1" AspirationRate="2000" Volume="250" />
+ <DispenseToFlowcell ReagentName="PW1" DispenseRate="2000" Volume="250" />
+ <AspirateFromBypass ReagentName="PW1" AspirationRate="2000" Volume="250" />
+ <DispenseToFlowcell ReagentName="PW1" DispenseRate="2000" Volume="250" />
+ <AspirateFromBypass ReagentName="PW1" AspirationRate="2000" Volume="250" />
+ <DispenseToFlowcell ReagentName="PW1" DispenseRate="2000" Volume="250" />
+ <AspirateFromBypass ReagentName="PW1" AspirationRate="2000" Volume="250" />
+ <DispenseToFlowcell ReagentName="PW1" DispenseRate="2000" Volume="250" />
+ <AspirateFromBypass ReagentName="PW1" AspirationRate="2000" Volume="250" />
+ <DispenseToFlowcell ReagentName="PW1" DispenseRate="2000" Volume="250" />
+ <AspirateFromBypass ReagentName="PW1" AspirationRate="2000" Volume="250" />
+ <DispenseToFlowcell ReagentName="PW1" DispenseRate="2000" Volume="250" />
+ <AspirateFromBypass ReagentName="PW1" AspirationRate="2000" Volume="250" />
+ <DispenseToFlowcell ReagentName="PW1" DispenseRate="2000" Volume="250" />
+ </ChemistryStep>
+ </ChemistryDefinition>
+ <ChemistryDefinition Name="Wait180000">
+ <ChemistryStep Description="Wait180000" Repeat="1">
+ <Wait Duration="180000" />
+ </ChemistryStep>
+ </ChemistryDefinition>
+ </ChemistryDefinitions>
+
+ - <Reagents Name="ClogWashReagents" Version="Selector Valve Positions v2.2">
+ <Reagent Name="PW1" Description="Water" SelectorValvePosition="1" />
+ <Reagent Name="PW1" Description="Water" SelectorValvePosition="2" />
+ <Reagent Name="PW1" Description="Water" SelectorValvePosition="3" />
+ <Reagent Name="PW1" Description="Water" SelectorValvePosition="4" />
+ <Reagent Name="PW1" Description="Water" SelectorValvePosition="5" />
+ <Reagent Name="PW1" Description="Water" SelectorValvePosition="6" />
+ <Reagent Name="PW1" Description="Water" SelectorValvePosition="7" />
+ <Reagent Name="PW1" Description="Water" SelectorValvePosition="8" />
+ <Reagent Name="PW1" Description="Water" SelectorValvePosition="9" />
+ <Reagent Name="PW1" Description="Water" SelectorValvePosition="10" />
+ <Reagent Name="PW1" Description="Water" SelectorValvePosition="11" />
+ <Reagent Name="PW1" Description="Water" SelectorValvePosition="12" />
+ <Reagent Name="PW1" Description="Water" SelectorValvePosition="13" />
+ <Reagent Name="PW1" Description="Water" SelectorValvePosition="14" />
+ <Reagent Name="PW1" Description="Water" SelectorValvePosition="15" />
+ <Reagent Name="PW1" Description="Water" SelectorValvePosition="16" />
+ <Reagent Name="PW1" Description="Water" SelectorValvePosition="17" />
+ <Reagent Name="PW1" Description="Water" SelectorValvePosition="18" />
+ <Reagent Name="PW1" Description="Water" SelectorValvePosition="19" />
+ <Reagent Name="PW1" Description="Water" SelectorValvePosition="20" />
+ <Reagent Name="PW1" Description="Water" SelectorValvePosition="21" />
+ <Reagent Name="PW1" Description="Water" SelectorValvePosition="22" />
+ </Reagents>
+
+ <Name>LineWash_v0.3</Name>
+</Recipe>
diff --git a/recipes/Transposon12/Wash/MaintenanceWash.xml b/recipes/Transposon12/Wash/MaintenanceWash.xml
new file mode 100644
index 0000000..52d8301
--- /dev/null
+++ b/recipes/Transposon12/Wash/MaintenanceWash.xml
@@ -0,0 +1,115 @@
+<?xml version="1.0" ?>
+<Recipe xmlns:xsd="http://www.w3.org/2001/XMLSchema" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" Name="Maintenance Wash Recipe">
+ <Protocol>
+ <ChemistryRef Description="PostRun Wash" ChemistryName="Wash" />
+ </Protocol>
+ <ChemistryDefinitions>
+ <ChemistryDefinition Name="Wash">
+ <ChemistryStep Description="Wash">
+ <PumpToFlowcell Solution="4" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="3" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <Dispense DispenseRate="2500" Volume="250" />
+ <AspirateFromBypass ReagentName="PR2" AspirationRate="2000" Volume="250" />
+ <Dispense DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="2" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="1" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="5" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="6" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="7" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="17" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="18" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="19" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="20" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="8" AspirationRate="1000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="9" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="10" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="11" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="12" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="13" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="14" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="17" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="18" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="19" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="20" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="15" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="16" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="21" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="22" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="4" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="3" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <Dispense DispenseRate="2500" Volume="250" />
+ <AspirateFromBypass ReagentName="PR2" AspirationRate="2000" Volume="250" />
+ <Dispense DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="2" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="1" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="5" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="6" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="7" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="17" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="18" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="19" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="20" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="8" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="9" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="10" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="11" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="12" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="13" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="14" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="17" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="18" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="19" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="20" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="4" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="17" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="18" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="19" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="20" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="3" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <Dispense DispenseRate="2500" Volume="250" />
+ <AspirateFromBypass ReagentName="PR2" AspirationRate="2000" Volume="250" />
+ <Dispense DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="17" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="18" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="19" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="20" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="2" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="1" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="3" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <Dispense DispenseRate="2500" Volume="250" />
+ <AspirateFromBypass ReagentName="PR2" AspirationRate="2000" Volume="250" />
+ <Dispense DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="15" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="16" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="21" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="22" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ </ChemistryStep>
+ </ChemistryDefinition>
+ </ChemistryDefinitions>
+ <Reagents>
+ <Reagent Name="PW1" Description="Water" ViciPosition="1" />
+ <Reagent Name="PW1" Description="Water" ViciPosition="2" />
+ <Reagent Name="PW1" Description="Water" ViciPosition="3" />
+ <Reagent Name="PW1" Description="Water" ViciPosition="4" />
+ <Reagent Name="PW1" Description="Water" ViciPosition="5" />
+ <Reagent Name="PW1" Description="Water" ViciPosition="6" />
+ <Reagent Name="PW1" Description="Water" ViciPosition="7" />
+ <Reagent Name="PW1" Description="Water" ViciPosition="8" />
+ <Reagent Name="PW1" Description="Water" ViciPosition="9" />
+ <Reagent Name="PW1" Description="Water" ViciPosition="10" />
+ <Reagent Name="PW1" Description="Water" ViciPosition="11" />
+ <Reagent Name="PW1" Description="Water" ViciPosition="12" />
+ <Reagent Name="PW1" Description="Water" ViciPosition="13" />
+ <Reagent Name="PW1" Description="Water" ViciPosition="14" />
+ <Reagent Name="PW1" Description="Water" ViciPosition="15" />
+ <Reagent Name="PW1" Description="Water" ViciPosition="16" />
+ <Reagent Name="PW1" Description="Water" ViciPosition="17" />
+ <Reagent Name="PW1" Description="Water" ViciPosition="18" />
+ <Reagent Name="PW1" Description="Water" ViciPosition="19" />
+ <Reagent Name="PW1" Description="Water" ViciPosition="20" />
+ <Reagent Name="PW1" Description="Water" ViciPosition="21" />
+ <Reagent Name="PW1" Description="Water" ViciPosition="22" />
+
+ </Reagents>
+ <Name>PostRunWash_v1.0.1</Name>
+</Recipe>
\ No newline at end of file
diff --git a/recipes/Transposon12/Wash/PostRunWash.xml b/recipes/Transposon12/Wash/PostRunWash.xml
new file mode 100644
index 0000000..43bc4d8
--- /dev/null
+++ b/recipes/Transposon12/Wash/PostRunWash.xml
@@ -0,0 +1,180 @@
+<?xml version="1.0"?>
+<Recipe xmlns:xsd="http://www.w3.org/2001/XMLSchema" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" Name="PostRunWash_v1.0.0">
+ <Protocol>
+ <ChemistryRef Description="PostRun Wash" ChemistryName="Wash" />
+ </Protocol>
+
+ <ChemistryDefinitions>
+ <ChemistryDefinition Name="Wash">
+ <ChemistryStep Description="TemplateNaOClAspirate">
+ <PumpToFlowcell Solution="3" AspirationRate="2000" DispenseRate="7500" Volume="1000" />
+ <PumpToFlowcell Solution="17" AspirationRate="2000" DispenseRate="7500" Volume="1250" />
+ </ChemistryStep>
+ <ChemistryStep Description="Prime">
+ <PumpToFlowcell Solution="3" AspirationRate="2000" DispenseRate="7500" Volume="1000" />
+ <Dispense DispenseRate="7500" />
+ </ChemistryStep>
+ <ChemistryStep Description="Wash1" Repeat="8">
+ <Aspirate Solution="3" AspirationRate="2000" Volume="250" />
+ <DispenseToFlowcell Solution="17" DispenseRate="2000" Volume="250" />
+ </ChemistryStep>
+ <ChemistryStep Description="EmptyTube">
+ <PumpToFlowcell Solution="17" AspirationRate="2000" DispenseRate="7500" Volume="2000" />
+ </ChemistryStep>
+ <ChemistryStep Description="Prime">
+ <PumpToFlowcell Solution="3" AspirationRate="2000" DispenseRate="7500" Volume="1000" />
+ <Dispense DispenseRate="7500" />
+ </ChemistryStep>
+ <ChemistryStep Description="Wash2" Repeat="8">
+ <Aspirate Solution="3" AspirationRate="2000" Volume="250" />
+ <DispenseToFlowcell Solution="17" DispenseRate="2000" Volume="250" />
+ </ChemistryStep>
+ <ChemistryStep Description="EmptyTube">
+ <PumpToFlowcell Solution="17" AspirationRate="2000" DispenseRate="7500" Volume="2000" />
+ </ChemistryStep>
+ <ChemistryStep Description="Prime">
+ <PumpToFlowcell Solution="3" AspirationRate="2000" DispenseRate="7500" Volume="1000" />
+ <Dispense DispenseRate="7500" />
+ </ChemistryStep>
+ <ChemistryStep Description="Wash3" Repeat="8">
+ <Aspirate Solution="3" AspirationRate="2000" Volume="250" />
+ <DispenseToFlowcell Solution="17" DispenseRate="2000" Volume="250" />
+ </ChemistryStep>
+ <ChemistryStep Description="Wash">
+ <PumpToFlowcell Solution="4" AspirationRate="2000" DispenseRate="7500" Volume="250" />
+ <PumpToFlowcell Solution="3" AspirationRate="2000" DispenseRate="7500" Volume="250" />
+ <Dispense DispenseRate="7500" Volume="250" />
+ <AspirateFromBypass ReagentName="PR2" AspirationRate="2000" Volume="250" />
+ <Dispense DispenseRate="7500" Volume="250" />
+ <PumpToFlowcell Solution="2" AspirationRate="2000" DispenseRate="7500" Volume="250" />
+ <PumpToFlowcell Solution="1" AspirationRate="2000" DispenseRate="7500" Volume="250" />
+ <Dispense DispenseRate="7500" />
+ <PumpToFlowcell Solution="5" AspirationRate="2000" DispenseRate="7500" Volume="250" />
+ <PumpToFlowcell Solution="6" AspirationRate="2000" DispenseRate="7500" Volume="250" />
+ <Dispense DispenseRate="7500" />
+ <PumpToFlowcell Solution="7" AspirationRate="2000" DispenseRate="7500" Volume="250" />
+ <PumpToFlowcell Solution="17" AspirationRate="2000" DispenseRate="7500" Volume="250" />
+ <Dispense DispenseRate="7500" />
+ <PumpToFlowcell Solution="18" AspirationRate="2000" DispenseRate="7500" Volume="250" />
+ <PumpToFlowcell Solution="19" AspirationRate="2000" DispenseRate="7500" Volume="250" />
+ <Dispense DispenseRate="7500" />
+ <PumpToFlowcell Solution="20" AspirationRate="2000" DispenseRate="7500" Volume="250" />
+ <PumpToFlowcell Solution="8" AspirationRate="1000" DispenseRate="7500" Volume="250" />
+ <Dispense DispenseRate="7500" />
+ <PumpToFlowcell Solution="9" AspirationRate="2000" DispenseRate="7500" Volume="250" />
+ <PumpToFlowcell Solution="10" AspirationRate="2000" DispenseRate="7500" Volume="250" />
+ <Dispense DispenseRate="7500" />
+ <PumpToFlowcell Solution="11" AspirationRate="2000" DispenseRate="7500" Volume="250" />
+ <PumpToFlowcell Solution="12" AspirationRate="2000" DispenseRate="7500" Volume="250" />
+ <Dispense DispenseRate="7500" />
+ <PumpToFlowcell Solution="13" AspirationRate="2000" DispenseRate="7500" Volume="250" />
+ <PumpToFlowcell Solution="14" AspirationRate="2000" DispenseRate="7500" Volume="250" />
+ <Dispense DispenseRate="7500" />
+ <PumpToFlowcell Solution="17" AspirationRate="2000" DispenseRate="7500" Volume="250" />
+ <PumpToFlowcell Solution="18" AspirationRate="2000" DispenseRate="7500" Volume="250" />
+ <Dispense DispenseRate="7500" />
+ <PumpToFlowcell Solution="19" AspirationRate="2000" DispenseRate="7500" Volume="250" />
+ <PumpToFlowcell Solution="20" AspirationRate="2000" DispenseRate="7500" Volume="250" />
+ <Dispense DispenseRate="7500" />
+ <PumpToFlowcell Solution="15" AspirationRate="2000" DispenseRate="7500" Volume="250" />
+ <PumpToFlowcell Solution="16" AspirationRate="2000" DispenseRate="7500" Volume="250" />
+ <Dispense DispenseRate="7500" />
+ <PumpToFlowcell Solution="21" AspirationRate="2000" DispenseRate="7500" Volume="250" />
+ <PumpToFlowcell Solution="22" AspirationRate="2000" DispenseRate="7500" Volume="250" />
+ <Dispense DispenseRate="7500" />
+ <PumpToFlowcell Solution="4" AspirationRate="2000" DispenseRate="7500" Volume="250" />
+ <Dispense DispenseRate="7500" Volume="250" />
+ <PumpToFlowcell Solution="3" AspirationRate="2000" DispenseRate="7500" Volume="250" />
+ <Dispense DispenseRate="7500" Volume="250" />
+ <AspirateFromBypass ReagentName="PR2" AspirationRate="2000" Volume="250" />
+ <Dispense DispenseRate="7500" Volume="250" />
+ <PumpToFlowcell Solution="2" AspirationRate="2000" DispenseRate="7500" Volume="250" />
+ <PumpToFlowcell Solution="1" AspirationRate="2000" DispenseRate="7500" Volume="250" />
+ <Dispense DispenseRate="7500" />
+ <PumpToFlowcell Solution="5" AspirationRate="2000" DispenseRate="7500" Volume="250" />
+ <PumpToFlowcell Solution="6" AspirationRate="2000" DispenseRate="7500" Volume="250" />
+ <Dispense DispenseRate="7500" />
+ <PumpToFlowcell Solution="7" AspirationRate="2000" DispenseRate="7500" Volume="250" />
+ <PumpToFlowcell Solution="17" AspirationRate="2000" DispenseRate="7500" Volume="250" />
+ <Dispense DispenseRate="7500" />
+ <PumpToFlowcell Solution="18" AspirationRate="2000" DispenseRate="7500" Volume="250" />
+ <PumpToFlowcell Solution="19" AspirationRate="2000" DispenseRate="7500" Volume="250" />
+ <Dispense DispenseRate="7500" />
+ <PumpToFlowcell Solution="20" AspirationRate="2000" DispenseRate="7500" Volume="250" />
+ <PumpToFlowcell Solution="8" AspirationRate="2000" DispenseRate="7500" Volume="250" />
+ <Dispense DispenseRate="7500" />
+ <PumpToFlowcell Solution="9" AspirationRate="2000" DispenseRate="7500" Volume="250" />
+ <PumpToFlowcell Solution="10" AspirationRate="2000" DispenseRate="7500" Volume="250" />
+ <Dispense DispenseRate="7500" />
+ <PumpToFlowcell Solution="11" AspirationRate="2000" DispenseRate="7500" Volume="250" />
+ <PumpToFlowcell Solution="12" AspirationRate="2000" DispenseRate="7500" Volume="250" />
+ <Dispense DispenseRate="7500" />
+ <PumpToFlowcell Solution="13" AspirationRate="2000" DispenseRate="7500" Volume="250" />
+ <PumpToFlowcell Solution="14" AspirationRate="2000" DispenseRate="7500" Volume="250" />
+ <Dispense DispenseRate="7500" />
+ <PumpToFlowcell Solution="17" AspirationRate="2000" DispenseRate="7500" Volume="250" />
+ <PumpToFlowcell Solution="18" AspirationRate="2000" DispenseRate="7500" Volume="250" />
+ <Dispense DispenseRate="7500" />
+ <PumpToFlowcell Solution="19" AspirationRate="2000" DispenseRate="7500" Volume="250" />
+ <PumpToFlowcell Solution="20" AspirationRate="2000" DispenseRate="7500" Volume="250" />
+ <Dispense DispenseRate="7500" />
+ <PumpToFlowcell Solution="4" AspirationRate="2000" DispenseRate="7500" Volume="250" />
+ <PumpToFlowcell Solution="17" AspirationRate="2000" DispenseRate="7500" Volume="250" />
+ <Dispense DispenseRate="7500" />
+ <PumpToFlowcell Solution="18" AspirationRate="2000" DispenseRate="7500" Volume="250" />
+ <PumpToFlowcell Solution="19" AspirationRate="2000" DispenseRate="7500" Volume="250" />
+ <Dispense DispenseRate="7500" />
+ <PumpToFlowcell Solution="20" AspirationRate="2000" DispenseRate="7500" Volume="250" />
+ <Dispense DispenseRate="7500" Volume="250" />
+ <PumpToFlowcell Solution="3" AspirationRate="2000" DispenseRate="7500" Volume="250" />
+ <Dispense DispenseRate="7500" Volume="250" />
+ <AspirateFromBypass ReagentName="PR2" AspirationRate="2000" Volume="250" />
+ <Dispense DispenseRate="7500" Volume="250" />
+ <PumpToFlowcell Solution="17" AspirationRate="2000" DispenseRate="7500" Volume="250" />
+ <PumpToFlowcell Solution="18" AspirationRate="2000" DispenseRate="7500" Volume="250" />
+ <Dispense DispenseRate="7500" />
+ <PumpToFlowcell Solution="19" AspirationRate="2000" DispenseRate="7500" Volume="250" />
+ <PumpToFlowcell Solution="20" AspirationRate="2000" DispenseRate="7500" Volume="250" />
+ <Dispense DispenseRate="7500" />
+ <PumpToFlowcell Solution="2" AspirationRate="2000" DispenseRate="7500" Volume="250" />
+ <PumpToFlowcell Solution="1" AspirationRate="2000" DispenseRate="7500" Volume="250" />
+ <Dispense DispenseRate="7500" />
+ <PumpToFlowcell Solution="3" AspirationRate="2000" DispenseRate="7500" Volume="250" />
+ <Dispense DispenseRate="7500" Volume="250" />
+ <AspirateFromBypass ReagentName="PR2" AspirationRate="2000" Volume="250" />
+ <Dispense DispenseRate="7500" Volume="250" />
+ <PumpToFlowcell Solution="15" AspirationRate="2000" DispenseRate="7500" Volume="250" />
+ <PumpToFlowcell Solution="16" AspirationRate="2000" DispenseRate="7500" Volume="250" />
+ <Dispense DispenseRate="7500" />
+ <PumpToFlowcell Solution="21" AspirationRate="2000" DispenseRate="7500" Volume="250" />
+ <PumpToFlowcell Solution="22" AspirationRate="2000" DispenseRate="7500" Volume="250" />
+ </ChemistryStep>
+ </ChemistryDefinition>
+ </ChemistryDefinitions>
+ <Reagents>
+ <Reagent Name="PW1" Description="Water" ViciPosition="1" />
+ <Reagent Name="PW1" Description="Water" ViciPosition="2" />
+ <Reagent Name="PW1" Description="Water" ViciPosition="3" />
+ <Reagent Name="PW1" Description="Water" ViciPosition="4" />
+ <Reagent Name="PW1" Description="Water" ViciPosition="5" />
+ <Reagent Name="PW1" Description="Water" ViciPosition="6" />
+ <Reagent Name="PW1" Description="Water" ViciPosition="7" />
+ <Reagent Name="PW1" Description="Water" ViciPosition="8" />
+ <Reagent Name="PW1" Description="Water" ViciPosition="9" />
+ <Reagent Name="PW1" Description="Water" ViciPosition="10" />
+ <Reagent Name="PW1" Description="Water" ViciPosition="11" />
+ <Reagent Name="PW1" Description="Water" ViciPosition="12" />
+ <Reagent Name="PW1" Description="Water" ViciPosition="13" />
+ <Reagent Name="PW1" Description="Water" ViciPosition="14" />
+ <Reagent Name="PW1" Description="Water" ViciPosition="15" />
+ <Reagent Name="PW1" Description="Water" ViciPosition="16" />
+ <Reagent Name="PW1" Description="DiluteNaOCl" ViciPosition="17" />
+ <Reagent Name="PW1" Description="Water" ViciPosition="18" />
+ <Reagent Name="PW1" Description="Water" ViciPosition="19" />
+ <Reagent Name="PW1" Description="Water" ViciPosition="20" />
+ <Reagent Name="PW1" Description="Water" ViciPosition="21" />
+ <Reagent Name="PW1" Description="Water" ViciPosition="22" />
+
+ </Reagents>
+ <Name>PostRunWash_v1.0.1</Name>
+</Recipe>
\ No newline at end of file
diff --git a/recipes/Transposon12/Wash/PostRunWashOriginal.xml b/recipes/Transposon12/Wash/PostRunWashOriginal.xml
new file mode 100644
index 0000000..fc50905
--- /dev/null
+++ b/recipes/Transposon12/Wash/PostRunWashOriginal.xml
@@ -0,0 +1,115 @@
+<?xml version="1.0"?>
+<Recipe xmlns:xsd="http://www.w3.org/2001/XMLSchema" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" Name="PostRunWash_v1.0.0">
+ <Protocol>
+ <ChemistryRef Description="PostRun Wash" ChemistryName="Wash" />
+ </Protocol>
+ <ChemistryDefinitions>
+ <ChemistryDefinition Name="Wash">
+ <ChemistryStep Description="Wash">
+ <PumpToFlowcell Solution="4" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="3" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <Dispense DispenseRate="2500" Volume="250" />
+ <AspirateFromBypass ReagentName="PR2" AspirationRate="2000" Volume="250" />
+ <Dispense DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="2" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="1" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="5" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="6" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="7" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="17" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="18" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="19" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="20" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="8" AspirationRate="1000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="9" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="10" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="11" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="12" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="13" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="14" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="17" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="18" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="19" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="20" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="15" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="16" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="21" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="22" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="4" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="3" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <Dispense DispenseRate="2500" Volume="250" />
+ <AspirateFromBypass ReagentName="PR2" AspirationRate="2000" Volume="250" />
+ <Dispense DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="2" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="1" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="5" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="6" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="7" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="17" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="18" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="19" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="20" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="8" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="9" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="10" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="11" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="12" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="13" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="14" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="17" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="18" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="19" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="20" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="4" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="17" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="18" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="19" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="20" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="3" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <Dispense DispenseRate="2500" Volume="250" />
+ <AspirateFromBypass ReagentName="PR2" AspirationRate="2000" Volume="250" />
+ <Dispense DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="17" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="18" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="19" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="20" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="2" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="1" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="3" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <Dispense DispenseRate="2500" Volume="250" />
+ <AspirateFromBypass ReagentName="PR2" AspirationRate="2000" Volume="250" />
+ <Dispense DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="15" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="16" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="21" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="22" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ </ChemistryStep>
+ </ChemistryDefinition>
+ </ChemistryDefinitions>
+ <Reagents>
+ <Reagent Name="PW1" Description="Water" ViciPosition="1" />
+ <Reagent Name="PW1" Description="Water" ViciPosition="2" />
+ <Reagent Name="PW1" Description="Water" ViciPosition="3" />
+ <Reagent Name="PW1" Description="Water" ViciPosition="4" />
+ <Reagent Name="PW1" Description="Water" ViciPosition="5" />
+ <Reagent Name="PW1" Description="Water" ViciPosition="6" />
+ <Reagent Name="PW1" Description="Water" ViciPosition="7" />
+ <Reagent Name="PW1" Description="Water" ViciPosition="8" />
+ <Reagent Name="PW1" Description="Water" ViciPosition="9" />
+ <Reagent Name="PW1" Description="Water" ViciPosition="10" />
+ <Reagent Name="PW1" Description="Water" ViciPosition="11" />
+ <Reagent Name="PW1" Description="Water" ViciPosition="12" />
+ <Reagent Name="PW1" Description="Water" ViciPosition="13" />
+ <Reagent Name="PW1" Description="Water" ViciPosition="14" />
+ <Reagent Name="PW1" Description="Water" ViciPosition="15" />
+ <Reagent Name="PW1" Description="Water" ViciPosition="16" />
+ <Reagent Name="PW1" Description="Water" ViciPosition="17" />
+ <Reagent Name="PW1" Description="Water" ViciPosition="18" />
+ <Reagent Name="PW1" Description="Water" ViciPosition="19" />
+ <Reagent Name="PW1" Description="Water" ViciPosition="20" />
+ <Reagent Name="PW1" Description="Water" ViciPosition="21" />
+ <Reagent Name="PW1" Description="Water" ViciPosition="22" />
+
+ </Reagents>
+ <Name>PostRunWash_v1.0.1</Name>
+</Recipe>
\ No newline at end of file
diff --git a/recipes/Transposon12/Wash/StandbyWash.xml b/recipes/Transposon12/Wash/StandbyWash.xml
new file mode 100644
index 0000000..ce83571
--- /dev/null
+++ b/recipes/Transposon12/Wash/StandbyWash.xml
@@ -0,0 +1,70 @@
+<?xml version="1.0"?>
+<Recipe xmlns:xsd="http://www.w3.org/2001/XMLSchema" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" Name="StandbyWash_v1.0.0">
+ <Protocol>
+ <ChemistryRef Description="Standby Wash 1 of 8" ChemistryName="Wash" />
+ <ChemistryRef Description="Standby Wash 2 of 8" ChemistryName="Wash" />
+ <ChemistryRef Description="Standby Wash 3 of 8" ChemistryName="Wash" />
+ <ChemistryRef Description="Standby Wash 4 of 8" ChemistryName="Wash" />
+ <ChemistryRef Description="Standby Wash 5 of 8" ChemistryName="Wash" />
+ <ChemistryRef Description="Standby Wash 6 of 8" ChemistryName="Wash" />
+ <ChemistryRef Description="Standby Wash 7 of 8" ChemistryName="Wash" />
+ <ChemistryRef Description="Standby Wash 8 of 8" ChemistryName="Wash" />
+ </Protocol>
+ <ChemistryDefinitions>
+ <ChemistryDefinition Name="Wash">
+ <ChemistryStep Description="Wash">
+ <PumpToFlowcell Solution="4" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="3" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <Dispense DispenseRate="2500" Volume="250" />
+ <AspirateFromBypass ReagentName="PR2" AspirationRate="2000" Volume="250" />
+ <Dispense DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="2" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="1" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="5" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="6" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="7" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="17" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="18" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="19" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="20" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="8" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="9" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="10" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="11" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="12" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="13" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="14" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="15" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="16" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="21" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ <PumpToFlowcell Solution="22" AspirationRate="2000" DispenseRate="2500" Volume="250" />
+ </ChemistryStep>
+ </ChemistryDefinition>
+ </ChemistryDefinitions>
+ <Reagents>
+ <Reagent Name="PW1" Description="Water" ViciPosition="1" />
+ <Reagent Name="PW1" Description="Water" ViciPosition="2" />
+ <Reagent Name="PW1" Description="Water" ViciPosition="3" />
+ <Reagent Name="PW1" Description="Water" ViciPosition="4" />
+ <Reagent Name="PW1" Description="Water" ViciPosition="5" />
+ <Reagent Name="PW1" Description="Water" ViciPosition="6" />
+ <Reagent Name="PW1" Description="Water" ViciPosition="7" />
+ <Reagent Name="PW1" Description="Water" ViciPosition="8" />
+ <Reagent Name="PW1" Description="Water" ViciPosition="9" />
+ <Reagent Name="PW1" Description="Water" ViciPosition="10" />
+ <Reagent Name="PW1" Description="Water" ViciPosition="11" />
+ <Reagent Name="PW1" Description="Water" ViciPosition="12" />
+ <Reagent Name="PW1" Description="Water" ViciPosition="13" />
+ <Reagent Name="PW1" Description="Water" ViciPosition="14" />
+ <Reagent Name="PW1" Description="Water" ViciPosition="15" />
+ <Reagent Name="PW1" Description="Water" ViciPosition="16" />
+ <Reagent Name="PW1" Description="Water" ViciPosition="17" />
+ <Reagent Name="PW1" Description="Water" ViciPosition="18" />
+ <Reagent Name="PW1" Description="Water" ViciPosition="19" />
+ <Reagent Name="PW1" Description="Water" ViciPosition="20" />
+ <Reagent Name="PW1" Description="Water" ViciPosition="21" />
+ <Reagent Name="PW1" Description="Water" ViciPosition="22" />
+
+ </Reagents>
+ <Name>StandbyWash_v1.0.0</Name>
+</Recipe>
\ No newline at end of file
diff --git a/software_license b/software_license
new file mode 100644
index 0000000..3f03f8b
--- /dev/null
+++ b/software_license
@@ -0,0 +1,680 @@
+This software is Copyright (c) 2013 by Wellcome Trust Sanger Institute.
+
+This is free software, licensed under:
+
+ The GNU General Public License, Version 3, June 2007
+
+ GNU GENERAL PUBLIC LICENSE
+ Version 3, 29 June 2007
+
+ Copyright (C) 2007 Free Software Foundation, Inc. <http://fsf.org/>
+ Everyone is permitted to copy and distribute verbatim copies
+ of this license document, but changing it is not allowed.
+
+ Preamble
+
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+ Nothing in this License shall be construed as excluding or limiting
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+
+ 12. No Surrender of Others' Freedom.
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+
+ 13. Use with the GNU Affero General Public License.
+
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+ 17. Interpretation of Sections 15 and 16.
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+
+ How to Apply These Terms to Your New Programs
+
+ If you develop a new program, and you want it to be of the greatest
+possible use to the public, the best way to achieve this is to make it
+free software which everyone can redistribute and change under these terms.
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+ Copyright (C) <year> <name of author>
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+ This program is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
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+ You should have received a copy of the GNU General Public License
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+
+Also add information on how to contact you by electronic and paper mail.
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+ If the program does terminal interaction, make it output a short
+notice like this when it starts in an interactive mode:
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+ <program> Copyright (C) <year> <name of author>
+ This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'.
+ This is free software, and you are welcome to redistribute it
+ under certain conditions; type `show c' for details.
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+The hypothetical commands `show w' and `show c' should show the appropriate
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+ You should also get your employer (if you work as a programmer) or school,
+if any, to sign a "copyright disclaimer" for the program, if necessary.
+For more information on this, and how to apply and follow the GNU GPL, see
+<http://www.gnu.org/licenses/>.
+
+ The GNU General Public License does not permit incorporating your program
+into proprietary programs. If your program is a subroutine library, you
+may consider it more useful to permit linking proprietary applications with
+the library. If this is what you want to do, use the GNU Lesser General
+Public License instead of this License. But first, please read
+<http://www.gnu.org/philosophy/why-not-lgpl.html>.
diff --git a/t/Bio/Tradis/AddTagsToSeq.t b/t/Bio/Tradis/AddTagsToSeq.t
new file mode 100644
index 0000000..030acc6
--- /dev/null
+++ b/t/Bio/Tradis/AddTagsToSeq.t
@@ -0,0 +1,97 @@
+#!/usr/bin/env perl
+use strict;
+use warnings;
+use File::Temp;
+use File::Slurp;
+
+BEGIN { unshift( @INC, './lib' ) }
+BEGIN { unshift( @INC, '../lib' ) }
+BEGIN {
+ use Test::Most;
+ use_ok('Bio::Tradis::AddTagsToSeq');
+}
+my $samtools_exec = 'samtools';
+
+my $destination_directory_obj = File::Temp->newdir( CLEANUP => 1 );
+my $destination_directory = $destination_directory_obj->dirname();
+
+my ( $bamfile, $obj );
+
+$bamfile = "t/data/AddTags/sample_sm_tr.bam";
+
+ok(
+ $obj = Bio::Tradis::AddTagsToSeq->new(
+ bamfile => $bamfile,
+ script_name => 'name_of_script',
+ outfile => 't/data/output.bam'
+ ),
+ 'creating object'
+);
+
+is($obj->_output_switch, '-b', 'correctly select the bam output switch');
+
+ok( $obj->add_tags_to_seq, 'testing output' );
+ok( -e 't/data/output.bam', 'checking file existence' );
+`$samtools_exec view -h -o t/data/output.sam t/data/output.bam`;
+`$samtools_exec view -h -o t/data/AddTags/expected_tradis.sam t/data/AddTags/expected_tradis.bam`;
+is(
+ read_file('t/data/output.sam'),
+ read_file('t/data/AddTags/expected_tradis.sam'),
+ 'checking file contents'
+);
+
+
+$bamfile = "t/data/AddTags/sample_sm_no_tr.bam";
+ok(
+ $obj = Bio::Tradis::AddTagsToSeq->new(
+ bamfile => $bamfile,
+ script_name => 'name_of_script',
+ outfile => 't/data/output.bam'
+ ),
+ 'creating object'
+);
+ok( -e 't/data/output.bam', 'checking file existence' );
+`$samtools_exec view -h -o t/data/output.sam t/data/output.bam`;
+`$samtools_exec view -h -o t/data/AddTags/sample_sm_no_tr.sam t/data/AddTags/sample_sm_no_tr.bam`;
+is(
+ read_file('t/data/AddTags/sample_sm_no_tr.sam'),
+ read_file('t/data/output.sam'),
+ 'checking file contents'
+);
+
+is(
+ 6,
+ $obj->_number_of_lines_in_bam_file('t/data/AddTags/sample_sm_no_tr.bam'),
+ 'number of reads as expected'
+);
+
+my $cramfile = "t/data/AddTags/sample_sm_tr.cram";
+
+ok(
+ $obj = Bio::Tradis::AddTagsToSeq->new(
+ bamfile => $cramfile,
+ script_name => 'name_of_script',
+ outfile => 't/data/output.cram'
+ ),
+ 'creating object with cram file'
+);
+
+is($obj->_output_switch, '-C', 'correctly select the cram output switch');
+
+ok( $obj->add_tags_to_seq, 'testing output' );
+ok( -e 't/data/output.cram', 'checking file existence' );
+`$samtools_exec view -h -o t/data/output.sam t/data/output.cram`;
+`$samtools_exec view -h -o t/data/AddTags/expected_tradis.sam t/data/AddTags/expected_tradis.cram`;
+is(
+ read_file('t/data/output.sam'),
+ read_file('t/data/AddTags/expected_tradis.sam'),
+ 'checking file contents'
+);
+
+
+unlink('t/data/output.cram');
+unlink('t/data/output.bam');
+unlink('t/data/output.sam');
+unlink('t/data/AddTags/expected_tradis.sam');
+unlink('t/data/AddTags/sample_sm_no_tr.sam');
+done_testing();
diff --git a/t/Bio/Tradis/Analysis/InsertSite.t b/t/Bio/Tradis/Analysis/InsertSite.t
new file mode 100644
index 0000000..ba88fe8
--- /dev/null
+++ b/t/Bio/Tradis/Analysis/InsertSite.t
@@ -0,0 +1,115 @@
+#!/usr/bin/env perl
+use strict;
+use warnings;
+use Data::Dumper;
+
+BEGIN { unshift( @INC, './lib' ) }
+BEGIN { unshift( @INC, '../lib' ) }
+
+BEGIN {
+
+ use Test::Most;
+ use_ok('Bio::Tradis::Analysis::InsertSite');
+}
+
+ok my $insert_site_plots_from_bam = Bio::Tradis::Analysis::InsertSite->new(
+ filename => 't/data/InsertSite/small_multi_sequence.bam',
+ output_base_filename => 't/data/InsertSite/insert_site',
+ mapping_score => 0
+);
+ok $insert_site_plots_from_bam->create_plots();
+
+# parse output files and check they are okay
+ok is_input_string_found_on_given_line( "0 0", 1,
+ 't/data/InsertSite/insert_site.FN543502.insert_site_plot.gz' ),
+ 'check main sequence insert_site values first value';
+ok is_input_string_found_on_given_line( "0 2", 7899,
+ 't/data/InsertSite/insert_site.FN543502.insert_site_plot.gz' ),
+ 'check main sequence insert_site value before site';
+ok is_input_string_found_on_given_line( "0 12", 7915,
+ 't/data/InsertSite/insert_site.FN543502.insert_site_plot.gz' ),
+ 'check main sequence insert_site values for reverse reads only';
+ok is_input_string_found_on_given_line( "0 0", 249,
+ 't/data/InsertSite/insert_site.FN543502.insert_site_plot.gz' ),
+ 'various values';
+ok is_input_string_found_on_given_line( "1 0", 345,
+ 't/data/InsertSite/insert_site.FN543502.insert_site_plot.gz' ),
+ 'various values';
+ok is_input_string_found_on_given_line( "3 0", 354,
+ 't/data/InsertSite/insert_site.FN543502.insert_site_plot.gz' ),
+ 'various values';
+ok is_input_string_found_on_given_line( "1 0", 366,
+ 't/data/InsertSite/insert_site.FN543502.insert_site_plot.gz' ),
+ 'various values';
+ok is_input_string_found_on_given_line( "0 0", 513,
+ 't/data/InsertSite/insert_site.FN543502.insert_site_plot.gz' ),
+ 'various values';
+ok is_input_string_found_on_given_line( "0 0", 1,
+ 't/data/InsertSite/insert_site.pCROD1.insert_site_plot.gz' ),
+ 'check empty plasmid insert_site values first value';
+ok is_input_string_found_on_given_line( "0 0", 59,
+ 't/data/InsertSite/insert_site.pCROD1.insert_site_plot.gz' ),
+ 'check empty plasmid insert_site values last value';
+ok is_input_string_found_on_given_line( "0 0", 1,
+ 't/data/InsertSite/insert_site.pCROD2.insert_site_plot.gz' ),
+ 'check plasmid with 1 read insert_site values first value';
+ok is_input_string_found_on_given_line( "0 1", 143,
+ 't/data/InsertSite/insert_site.pCROD2.insert_site_plot.gz' ),
+ 'check plasmid with 1 read insert_site values first base of read';
+ok is_input_string_found_on_given_line( "0 0", 144,
+ 't/data/InsertSite/insert_site.pCROD2.insert_site_plot.gz' ),
+ 'check plasmid with 1 read insert_site values after last base of read';
+ok is_input_string_found_on_given_line( "0 0", 1000,
+ 't/data/InsertSite/insert_site.pCROD2.insert_site_plot.gz' ),
+ 'check plasmid with 1 read insert_site values last value';
+ok is_input_string_found_on_given_line( "0 0", 1,
+ 't/data/InsertSite/insert_site.pCROD3.insert_site_plot.gz' ),
+ 'check another empty plasmid insert_site values first value';
+ok is_input_string_found_on_given_line( "0 0", 100,
+ 't/data/InsertSite/insert_site.pCROD3.insert_site_plot.gz' ),
+ 'check another empty plasmid insert_site values last value';
+
+unlink("t/data/InsertSite/insert_site.FN543502.insert_site_plot.gz");
+unlink("t/data/InsertSite/insert_site.pCROD1.insert_site_plot.gz");
+unlink("t/data/InsertSite/insert_site.pCROD2.insert_site_plot.gz");
+unlink("t/data/InsertSite/insert_site.pCROD3.insert_site_plot.gz");
+
+
+
+ok $insert_site_plots_from_bam = Bio::Tradis::Analysis::InsertSite->new(
+ filename => 't/data/InsertSite/2_reads.bam',
+ output_base_filename => 't/data/InsertSite/2_reads_output',
+ mapping_score => 0
+);
+ok $insert_site_plots_from_bam->create_plots();
+ok is_input_string_found_on_given_line( "1 0", 100,
+ 't/data/InsertSite/2_reads_output.FN543502.insert_site_plot.gz' ),
+ 'check forward read';
+ ok is_input_string_found_on_given_line( "0 1", 153,
+ 't/data/InsertSite/2_reads_output.FN543502.insert_site_plot.gz' ),
+ 'check reverse read';
+unlink('t/data/InsertSite/2_reads_output.FN543502.insert_site_plot.gz');
+
+done_testing();
+
+sub is_input_string_found_on_given_line {
+ my ( $expected_string, $line_number, $filename ) = @_;
+ my $line_counter = 0;
+ open( IN, '-|', "gzip -dc " . $filename );
+ while (<IN>) {
+ chomp;
+ my $line = $_;
+ $line_counter++;
+ next unless ( $line_counter == $line_number );
+ last if ( $line_counter > $line_number );
+
+ if ( $expected_string eq $line ) { return 1; }
+ else {
+ print STDERR "Expected: "
+ . $expected_string
+ . "\t Got: "
+ . $line . "\n";
+ }
+ }
+ return 0;
+}
diff --git a/t/Bio/Tradis/CombinePlots.t b/t/Bio/Tradis/CombinePlots.t
new file mode 100644
index 0000000..65004be
--- /dev/null
+++ b/t/Bio/Tradis/CombinePlots.t
@@ -0,0 +1,120 @@
+#!/usr/bin/env perl
+use strict;
+use warnings;
+use File::Slurp;
+use Cwd;
+use File::Path qw( remove_tree );
+
+BEGIN { unshift( @INC, './lib' ) }
+BEGIN { unshift( @INC, '../lib' ) }
+BEGIN {
+ use Test::Most;
+ use Test::Files;
+ use_ok('Bio::Tradis::CombinePlots');
+}
+
+my ( $plotfile, $obj );
+
+$plotfile = "t/data/CombinePlots/comb_sample.txt";
+
+ok( $obj = Bio::Tradis::CombinePlots->new( plotfile => $plotfile ),
+ 'creating object' );
+
+ok( $obj->combine, 'combining plots' );
+ok(
+ -e 'combined/first.insert_site_plot.gz',
+ 'checking first combined plot file exists'
+);
+ok(
+ -e 'combined/second.insert_site_plot.gz',
+ 'checking second combined plot file exists'
+);
+ok(
+ -e 'comb_sample.stats',
+ 'checking stats file exists'
+);
+
+system("gunzip -c combined/first.insert_site_plot.gz > first.test.plot");
+is(
+ read_file('first.test.plot'),
+ read_file('t/data/CombinePlots/first.expected.plot'),
+ 'checking first file contents'
+);
+system("gunzip -c combined/second.insert_site_plot.gz > second.test.plot");
+is(
+ read_file('second.test.plot'),
+ read_file('t/data/CombinePlots/second.expected.plot'),
+ 'checking second file contents'
+);
+is(
+ read_file('comb_sample.stats'),
+ read_file('t/data/CombinePlots/comb_expected.stats'),
+ 'checking stats file contents'
+);
+
+#check with gzipped plots
+$plotfile = "t/data/CombinePlots/zip_comb_list.txt";
+
+ok( $obj = Bio::Tradis::CombinePlots->new( plotfile => $plotfile ),
+ 'creating object' );
+
+ok( $obj->combine, 'combining plots' );
+ok(
+ -e 'combined/zip_combined.insert_site_plot.gz',
+ 'checking first combined plot file exists'
+);
+ok(
+ -e 'combined/tabix_sorted.insert_site_plot.gz',
+ 'checking tabix sorted combined plot file exists'
+);
+
+ok(
+ -e 'combined/tabix_sorted.insert_site_plot.gz.tbi',
+ 'checking tabix index file exists'
+);
+
+
+system("gunzip -c combined/zip_combined.insert_site_plot.gz > zip_combined.test.plot");
+is(
+ read_file('zip_combined.test.plot'),
+ read_file('t/data/CombinePlots/zip_comb_exp.plot'),
+ 'checking zipped file contents'
+);
+is(
+ read_file('zip_comb_list.stats'),
+ read_file('t/data/CombinePlots/zip_comb_exp.stats'),
+ 'checking stats file contents'
+);
+
+# check custom directory name
+$plotfile = "t/data/CombinePlots/comb_sample.txt";
+ok( $obj = Bio::Tradis::CombinePlots->new(
+ plotfile => $plotfile,
+ combined_dir => 'comb_test'
+ ),
+ 'creating object'
+);
+
+ok( $obj->combine, 'combining plots' );
+ok( -d 'comb_test', 'checking directory exists' );
+ok(
+ -e 'comb_test/first.insert_site_plot.gz',
+ 'checking first combined plot file exists'
+);
+ok(
+ -e 'comb_test/second.insert_site_plot.gz',
+ 'checking second combined plot file exists'
+);
+
+cleanup_files();
+done_testing();
+
+sub cleanup_files {
+ unlink('first.test.plot');
+ unlink('second.test.plot');
+ unlink('zip_combined.test.plot');
+ unlink('comb_sample.stats');
+ unlink('zip_comb_list.stats');
+ remove_tree('combined');
+ remove_tree('comb_test');
+}
diff --git a/t/Bio/Tradis/CommandLine/TradisAnalysis.t b/t/Bio/Tradis/CommandLine/TradisAnalysis.t
new file mode 100644
index 0000000..fb10610
--- /dev/null
+++ b/t/Bio/Tradis/CommandLine/TradisAnalysis.t
@@ -0,0 +1,92 @@
+#!/usr/bin/env perl
+use strict;
+use warnings;
+use Cwd;
+use File::Path 'rmtree';
+use File::Temp;
+use File::Slurp;
+
+BEGIN { unshift( @INC, './lib' ) }
+BEGIN { unshift( @INC, '../lib' ) }
+
+BEGIN {
+ use Test::Most;
+ use Test::Exception;
+ use_ok('Bio::Tradis::CommandLine::TradisAnalysis');
+}
+
+# Tag which is found in both inputs
+my $output_directory_obj = File::Temp->newdir( 'tmp_TradisAnalysis_tests_XXXXX',
+ CLEANUP => 0,
+ DIR => cwd() );
+my $output_directory = $output_directory_obj->dirname;
+
+ok(
+ my $obj = Bio::Tradis::CommandLine::TradisAnalysis->new(
+ args => ['-f', 't/data/CommandLine/fastq.list', '-t',
+ "TAAGAGTCAG", '-r', "t/data/RunTradis/smallref.fa"],
+ script_name => 'bacteria_tradis_test',
+ _output_directory => $output_directory
+ ),
+ 'creating object'
+);
+
+ok( $obj->run, 'testing run' );
+
+open(STATS, "$output_directory/fastq.stats") or die "Could not open stats file";
+my $line_count = 0;
+while (<STATS>) { $line_count++; }
+is( $line_count, 3, "both files have reads with tag");
+rmtree($output_directory);
+
+# Only one file has a read with the given tag
+$output_directory_obj = File::Temp->newdir( 'tmp_TradisAnalysis_tests_XXXXX',
+ CLEANUP => 0,
+ DIR => cwd() );
+$output_directory = $output_directory_obj->dirname;
+
+$obj = Bio::Tradis::CommandLine::TradisAnalysis->new(
+ args => ['-f', 't/data/CommandLine/fastq.list', '-t',
+ "CGCACAGCCG", '-r', "t/data/RunTradis/smallref.fa"],
+ script_name => 'bacteria_tradis_test',
+ _output_directory => $output_directory
+);
+
+{
+ my $warning_counter = 0;
+ local $SIG{'__WARN__'} = sub { $warning_counter++; };
+ ok( $obj->run, 'testing run with tag only found in one fastq' );
+ is( $warning_counter, 1, "one warning raised" );
+}
+open(STATS, "$output_directory/fastq.stats") or die "Could not open stats file";
+$line_count = 0;
+while (<STATS>) { $line_count++; }
+is( $line_count, 2, "only one input fastq has reads with tag");
+rmtree($output_directory);
+
+# Neither fastq input has a read with the given tag
+$output_directory_obj = File::Temp->newdir( 'tmp_TradisAnalysis_tests_XXXXX',
+ CLEANUP => 0,
+ DIR => cwd() );
+$output_directory = $output_directory_obj->dirname;
+
+$obj = Bio::Tradis::CommandLine::TradisAnalysis->new(
+ args => ['-f', 't/data/CommandLine/fastq.list', '-t',
+ "AAAAAAAAAA", '-r', "t/data/RunTradis/smallref.fa"],
+ script_name => 'bacteria_tradis_test',
+ _output_directory => $output_directory
+);
+
+{
+ my $warning_counter = 0;
+ local $SIG{'__WARN__'} = sub { $warning_counter++; };
+ throws_ok {$obj->run} 'Bio::Tradis::Exception::TagFilterError', 'testing run without tag in either fastq';
+ is( $warning_counter, 2, "two warnings raised" );
+}
+open(STATS, "$output_directory/fastq.stats") or die "Could not open stats file";
+$line_count = 0;
+while (<STATS>) { $line_count++; }
+is( $line_count, 0, "neither input fastq has reads with tag");
+rmtree($output_directory);
+
+done_testing();
diff --git a/t/Bio/Tradis/DetectTags.t b/t/Bio/Tradis/DetectTags.t
new file mode 100644
index 0000000..fec94b8
--- /dev/null
+++ b/t/Bio/Tradis/DetectTags.t
@@ -0,0 +1,55 @@
+#!/usr/bin/env perl
+use strict;
+use warnings;
+use File::Temp;
+
+BEGIN { unshift( @INC, './lib' ) }
+BEGIN { unshift( @INC, '../lib' ) }
+
+BEGIN {
+ use Test::Most;
+ use_ok('Bio::Tradis::DetectTags');
+}
+
+my $destination_directory_obj = File::Temp->newdir( CLEANUP => 1 );
+my $destination_directory = $destination_directory_obj->dirname();
+
+my ( $bamfile, $obj );
+
+$bamfile = "t/data/DetectTags/sample_sm_tr.bam";
+
+ok(
+ $obj = Bio::Tradis::DetectTags->new(
+ bamfile => $bamfile,
+ script_name => 'name_of_script'
+ ),
+ 'testing tag checker - tradis'
+);
+is( $obj->tags_present, 1, 'testing output' );
+
+
+my $cramfile = "t/data/DetectTags/sample_sm_tr.cram";
+
+ok(
+ $obj = Bio::Tradis::DetectTags->new(
+ bamfile => $cramfile,
+ script_name => 'name_of_script'
+ ),
+ 'testing tag checker for cram- tradis'
+);
+is( $obj->tags_present, 1, 'testing output cram' );
+
+
+
+$bamfile = "t/data/DetectTags/sample_sm_no_tr.bam";
+
+ok(
+ $obj = Bio::Tradis::DetectTags->new(
+ bamfile => $bamfile,
+ script_name => 'name_of_script'
+ ),
+ 'testing tag checker - no tradis'
+);
+is( $obj->tags_present, 0, 'testing output' );
+
+done_testing();
diff --git a/t/Bio/Tradis/FilterTags.t b/t/Bio/Tradis/FilterTags.t
new file mode 100644
index 0000000..3441ce0
--- /dev/null
+++ b/t/Bio/Tradis/FilterTags.t
@@ -0,0 +1,101 @@
+#!/usr/bin/env perl
+use strict;
+use warnings;
+use File::Temp;
+use File::Slurp;
+
+BEGIN { unshift( @INC, './lib' ) }
+BEGIN { unshift( @INC, '../lib' ) }
+BEGIN {
+ use Test::Most;
+ use_ok('Bio::Tradis::FilterTags');
+}
+
+my $destination_directory_obj = File::Temp->newdir( CLEANUP => 1 );
+my $destination_directory = $destination_directory_obj->dirname();
+
+my ( $fastqfile, $tag, $obj );
+
+$fastqfile = "t/data/FilterTags/sample.fastq";
+$tag = "CAACGTTTT";
+
+ok(
+ $obj = Bio::Tradis::FilterTags->new(
+ fastqfile => $fastqfile,
+ tag => $tag,
+ mismatch => 0,
+ outfile => 'output.fastq'
+ ),
+ 'creating object'
+);
+ok( $obj->filter_tags, 'testing output' );
+ok( -e 'output.fastq', 'checking file existence' );
+is(
+ read_file('output.fastq'),
+ read_file('t/data/FilterTags/expected.caa.fastq'),
+ 'checking file contents'
+);
+
+# Test tag mismatch option
+ok(
+ $obj = Bio::Tradis::FilterTags->new(
+ fastqfile => $fastqfile,
+ tag => $tag,
+ mismatch => 1,
+ outfile => 'output.fastq'
+ ),
+ 'creating object'
+);
+ok( $obj->filter_tags, 'testing output' );
+ok( -e 'output.fastq', 'checking file existence' );
+is(
+ read_file('output.fastq'),
+ read_file('t/data/FilterTags/expected.1mm.caa.fastq'),
+ 'checking file contents'
+);
+
+# Different tag
+$tag = "TNAGAGACAG";
+
+ok(
+ $obj = Bio::Tradis::FilterTags->new(
+ fastqfile => $fastqfile,
+ tag => $tag,
+ mismatch => 0,
+ outfile => 'output.fastq'
+ ),
+ 'creating object'
+);
+ok( $obj->filter_tags, 'testing output' );
+ok( -e 'output.fastq', 'checking file existence' );
+is(
+ read_file('output.fastq'),
+ read_file('t/data/FilterTags/expected.tna.fastq'),
+ 'checking file contents'
+);
+
+# Gzipped input
+$fastqfile = "t/data/FilterTags/sample.fastq.gz";
+$tag = "CAACGTTTT";
+
+ok(
+ $obj = Bio::Tradis::FilterTags->new(
+ fastqfile => $fastqfile,
+ tag => $tag,
+ mismatch => 0,
+ outfile => 'output.fastq'
+ ),
+ 'creating object'
+);
+ok( $obj->filter_tags, 'testing output' );
+ok( -e 'output.fastq', 'checking file existence' );
+is(
+ read_file('output.fastq'),
+ read_file('t/data/FilterTags/expected.caa.fastq'),
+ 'checking file contents'
+);
+
+unlink('t/data/output.fastq');
+unlink('t/data/FilterTags/expected.caa.fastq');
+unlink('t/data/FilterTags/expected.tna.fastq');
+done_testing();
diff --git a/t/Bio/Tradis/Map.t b/t/Bio/Tradis/Map.t
new file mode 100644
index 0000000..c58161d
--- /dev/null
+++ b/t/Bio/Tradis/Map.t
@@ -0,0 +1,77 @@
+#!/usr/bin/env perl
+use strict;
+use warnings;
+use File::Temp;
+use File::Slurp;
+
+BEGIN {
+ unshift( @INC, '../lib' );
+ unshift( @INC, './lib' );
+}
+
+BEGIN {
+ use Test::Most;
+ use_ok('Bio::Tradis::Map');
+}
+
+my $destination_directory_obj = File::Temp->newdir( CLEANUP => 1 );
+my $destination_directory = $destination_directory_obj->dirname();
+
+my ( $fastqfile, $ref, $obj, $refname, $outfile );
+
+$fastqfile = "t/data/Map/test.fastq";
+$ref = "t/data/Map/smallref.fa";
+$refname = "t/data/Map/test.ref";
+$outfile = "t/data/Map/mapped.out";
+
+ok(
+ $obj = Bio::Tradis::Map->new(
+ fastqfile => $fastqfile,
+ reference => $ref,
+ refname => $refname,
+ outfile => $outfile
+ ),
+ 'creating object'
+);
+ok( $obj->index_ref, 'testing reference indexing' );
+ok( -e 't/data/Map/test.ref.sma', 'checking index file existence' );
+ok( -e 't/data/Map/test.ref.smi', 'checking index file existence' );
+
+ok( $obj->do_mapping, 'testing reference indexing' );
+ok( -e 't/data/Map/mapped.out', 'checking index file existence' );
+system("grep -v ^\@ t/data/Map/mapped.out > mapped.nohead.out");
+system("grep -v ^\@ t/data/Map/expected.mapped > expected.nohead.mapped");
+is(
+ read_file('mapped.nohead.out'),
+ read_file('expected.nohead.mapped'),
+ 'checking file contents'
+);
+
+# test optional smalt parameters
+ok(
+ $obj = Bio::Tradis::Map->new(
+ fastqfile => $fastqfile,
+ reference => $ref,
+ refname => $refname,
+ outfile => $outfile,
+ smalt_k => 10,
+ smalt_s => 10,
+ smalt_y => 0.9
+ ),
+ 'creating object'
+);
+
+my $index_cmd = $obj->index_ref;
+my $index_exp = "smalt index -k 10 -s 10 $refname $ref > /dev/null 2>&1";
+is( $index_cmd, $index_exp, "indexing args correct" );
+
+my $map_cmd = $obj->do_mapping;
+my $map_exp = "smalt map -n 1 -x -r -1 -y 0.9 $refname $fastqfile 1> $outfile 2> smalt.stderr";
+is( $map_cmd, $map_exp, "mapping args correct" );
+
+
+
+unlink('t/data/Map/test.ref.sma');
+unlink('t/data/Map/test.ref.smi');
+unlink('t/data/Map/mapped.out');
+done_testing();
diff --git a/t/Bio/Tradis/Parser/Bam.t b/t/Bio/Tradis/Parser/Bam.t
new file mode 100644
index 0000000..ce9f743
--- /dev/null
+++ b/t/Bio/Tradis/Parser/Bam.t
@@ -0,0 +1,105 @@
+#!/usr/bin/env perl
+use strict;
+use warnings;
+use File::Temp;
+use File::Slurp;
+
+BEGIN { unshift( @INC, './lib' ) }
+BEGIN { unshift( @INC, '../lib' ) }
+
+BEGIN {
+ use Test::Most;
+ use_ok('Bio::Tradis::Parser::Bam');
+}
+
+my ( $obj, $bamfile );
+
+$bamfile = "t/data/Parsers/test.bam";
+
+ok(
+ $obj = Bio::Tradis::Parser::Bam->new(
+ file => $bamfile,
+ ),
+ 'creating object'
+);
+isa_ok $obj, 'Bio::Tradis::Parser::Bam';
+
+# Test sequence info
+my %si = $obj->seq_info;
+is ref( \%si ), 'HASH', 'seq_info returns a hash';
+
+# Test reading first result
+is $obj->next_read, 1, 'first result detected';
+my $read_info = $obj->read_info;
+is_deeply $read_info,
+ {
+ QNAME => 'MS5_9521:1:1101:10072:14269#14',
+ FLAG => '16',
+ BINARY_FLAG => '10000',
+ RNAME => 'ENA|AE004091|AE004091.2',
+ POS => '5',
+ MAPQ => '37',
+ CIGAR => '50M',
+ RNEXT => '*',
+ PNEXT => '0',
+ TLEN => '0',
+ SEQ => 'AAGAGACCGGCGATTCTAGTGAAATCGAACGGGCAGGTCAATTTCCAACC',
+ QUAL => 'HHHGGGGGGGHHHHHHHHHHHGHHHGHHGGGGGGGGGGFFFBFFCBAABA',
+ X0 => '1',
+ X1 => '0',
+ BC => 'TCTCGGTT',
+ MD => '50',
+ RG => '1#14',
+ XG => '0',
+ NM => '0',
+ XM => '0',
+ XO => '0',
+ QT => 'BBCDECBC',
+ XT => 'U',
+ tq => 'CCCBBFFFFF',
+ tr => 'TAAGAGTCAG',
+ READ => 'MS5_9521:1:1101:10072:14269#14 16 ENA|AE004091|AE004091.2 5 37 50M * 0 0 AAGAGACCGGCGATTCTAGTGAAATCGAACGGGCAGGTCAATTTCCAACC HHHGGGGGGGHHHHHHHHHHHGHHHGHHGGGGGGGGGGFFFBFFCBAABA X0:i:1 X1:i:0 BC:Z:TCTCGGTT MD:Z:50 RG:Z:1#14 XG:i:0 NM:i:0 XM:i:0 XO:i:0 QT:Z:BBCDECBC XT:A:U tq:Z:CCCBBFFFFF tr:Z:TAAGAGTCAG'
+ },
+ 'read_info contains correct info for first line';
+
+is $obj->is_mapped, 1, 'testing flag parsing - mapped';
+is $obj->is_reverse, 1, 'testing flag parsing - reverse complement';
+
+# Test reading second/last result
+is $obj->next_read, 1, 'last result detected';
+$read_info = $obj->read_info;
+is_deeply $read_info,
+ {
+ QNAME => 'MS5_9521:1:1103:26809:18585#14',
+ FLAG => '1040',
+ BINARY_FLAG => '10000010000',
+ RNAME => 'ENA|AE004091|AE004091.2',
+ POS => '23',
+ MAPQ => '37',
+ CIGAR => '50M',
+ RNEXT => '*',
+ PNEXT => '0',
+ TLEN => '0',
+ SEQ => 'GTGAAATCGAACGGGCAGGTCAATTTCCAACCAGCGATGACGTAATAGAT',
+ QUAL => '5FGGHHGEGHFEHHHHHGFHHGHGGHGFGGFCGEGBBAFC?DFFFBBBB3',
+ X0 => '1',
+ X1 => '0',
+ BC => 'TCTCGGTT',
+ MD => '50',
+ RG => '1#14',
+ XG => '0',
+ NM => '0',
+ XM => '0',
+ XO => '0',
+ QT => 'CCCCCCCC',
+ XT => 'U',
+ tq => 'BCCCCFFFFF',
+ tr => 'TAAGAGTCAG',
+ READ => 'MS5_9521:1:1103:26809:18585#14 1040 ENA|AE004091|AE004091.2 23 37 50M * 0 0 GTGAAATCGAACGGGCAGGTCAATTTCCAACCAGCGATGACGTAATAGAT 5FGGHHGEGHFEHHHHHGFHHGHGGHGFGGFCGEGBBAFC?DFFFBBBB3 X0:i:1 X1:i:0 BC:Z:TCTCGGTT MD:Z:50 RG:Z:1#14 XG:i:0 NM:i:0 XM:i:0 XO:i:0 QT:Z:CCCCCCCC XT:A:U tq:Z:BCCCCFFFFF tr:Z:TAAGAGTCAG'
+ },
+ 'read_info contains correct info for last line';
+
+# Ensure end of file is detected
+is $obj->next_read, 0, 'EOF detected';
+
+done_testing();
diff --git a/t/Bio/Tradis/Parser/Cigar.t b/t/Bio/Tradis/Parser/Cigar.t
new file mode 100755
index 0000000..f6a4d78
--- /dev/null
+++ b/t/Bio/Tradis/Parser/Cigar.t
@@ -0,0 +1,84 @@
+#!/usr/bin/env perl
+use strict;
+use warnings;
+use File::Temp;
+use File::Slurp;
+
+BEGIN { unshift( @INC, './lib' ) }
+BEGIN { unshift( @INC, '../lib' ) }
+
+BEGIN {
+ use Test::Most;
+ use_ok('Bio::Tradis::Parser::Cigar');
+}
+
+my ( $obj, $fastqfile );
+
+my @cigar_tests = (
+ {
+ name => 'all matching',
+ cigar => '100M',
+ coord => 100,
+ start => 100,
+ end => 199,
+ },
+ {
+ name => 'nothing matching',
+ cigar => '*',
+ coord => 1000,
+ start => 0,
+ end => 0,
+ },
+ {
+ name => 'soft clipping at start',
+ cigar => '10S90M',
+ coord => 100,
+ start => 110,
+ end => 199,
+ },
+ {
+ name => 'soft clipping at end',
+ cigar => '90M10S',
+ coord => 100,
+ start => 100,
+ end => 189,
+ },
+ {
+ name => 'soft clipping at both ends',
+ cigar => '10S80M10S',
+ coord => 100,
+ start => 110,
+ end => 189,
+ },
+ {
+ name => 'deletion in middle',
+ 'cigar' => '20M1D80M',
+ 'coord' => 20,
+ 'end' => 120,
+ 'start' => 20
+ },
+ {
+ name => 'insertions and deletions',
+ 'cigar' => '27M1I6M1D66M',
+ 'coord' => 46,
+ 'end' => 145,
+ 'start' => 46
+ },
+ {
+ name => 'insertions in the middle',
+ 'cigar' => '90M1I9M',
+ 'coord' => 80,
+ 'end' => 178,
+ 'start' => 80
+ }
+
+);
+
+for my $cigar_test (@cigar_tests) {
+ ok( $obj = Bio::Tradis::Parser::Cigar->new( coordinate => $cigar_test->{coord}, cigar => $cigar_test->{cigar} ),
+ 'initialise obj -' . $cigar_test->{name} );
+ is( $obj->start, $cigar_test->{start}, 'read start -' . $cigar_test->{name} );
+ is( $obj->end, $cigar_test->{end}, 'read end -' . $cigar_test->{name} );
+}
+
+done_testing();
diff --git a/t/Bio/Tradis/Parser/Fastq.t b/t/Bio/Tradis/Parser/Fastq.t
new file mode 100644
index 0000000..5452d25
--- /dev/null
+++ b/t/Bio/Tradis/Parser/Fastq.t
@@ -0,0 +1,52 @@
+#!/usr/bin/env perl
+use strict;
+use warnings;
+use File::Temp;
+use File::Slurp;
+
+BEGIN { unshift( @INC, './lib' ) }
+BEGIN { unshift( @INC, '../lib' ) }
+
+BEGIN {
+ use Test::Most;
+ use_ok('Bio::Tradis::Parser::Fastq');
+}
+
+my ( $obj, $fastqfile );
+
+$fastqfile = "t/data/Parsers/test.fastq";
+
+ok(
+ $obj = Bio::Tradis::Parser::Fastq->new(
+ file => $fastqfile,
+ ),
+ 'creating object'
+);
+isa_ok $obj, 'Bio::Tradis::Parser::Fastq';
+
+# Test reading first result
+is $obj->next_read, 1, 'first result detected';
+my @read_info = $obj->read_info;
+is_deeply \@read_info,
+ [
+ 'HS21_09876:1:1105:9650:48712#83',
+ 'TAAGAGTCAGGGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG',
+ 'CCCFFFFFHHHHCEE8EEFGFFGFIFGGFGEEHFFFGGGFGFGEGEEEFGFGFF'
+ ],
+ 'read_info contains correct info for first line';
+
+# Test reading second/last result
+is $obj->next_read, 1, 'last result detected';
+ at read_info = $obj->read_info;
+is_deeply \@read_info,
+ [
+ 'HS21_09876:1:1106:8638:38957#83',
+ 'TAAGAGTCAGGGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG',
+ 'B at CFFFFFHHHHCEF7FHFFFFGFEGEFFEHEGEGFGGGEGFGFGGFEHGFEFD'
+ ],
+ 'read_info contains correct info for last line';
+
+# Ensure end of file is detected
+is $obj->next_read, 0, 'EOF detected';
+
+done_testing();
diff --git a/t/Bio/Tradis/RemoveTags.t b/t/Bio/Tradis/RemoveTags.t
new file mode 100644
index 0000000..f2289c9
--- /dev/null
+++ b/t/Bio/Tradis/RemoveTags.t
@@ -0,0 +1,82 @@
+#!/usr/bin/env perl
+use strict;
+use warnings;
+use File::Temp;
+use File::Slurp;
+
+BEGIN { unshift( @INC, './lib' ) }
+BEGIN { unshift( @INC, '../lib' ) }
+
+BEGIN {
+ use Test::Most;
+ use_ok('Bio::Tradis::RemoveTags');
+}
+
+my $destination_directory_obj = File::Temp->newdir( CLEANUP => 1 );
+my $destination_directory = $destination_directory_obj->dirname();
+
+my ( $fastqfile, $tag, $obj );
+
+$fastqfile = "t/data/RemoveTags/sample.caa.fastq";
+$tag = "CAACGTTTT";
+
+# Test without mismatch option
+ok(
+ $obj = Bio::Tradis::RemoveTags->new(
+ fastqfile => $fastqfile,
+ tag => $tag,
+ mismatch => 0,
+ outfile => 't/data/output.fastq'
+ ),
+ 'creating object'
+);
+ok( $obj->remove_tags, 'testing output' );
+ok( -e 't/data/output.fastq', 'checking file existence' );
+is(
+ read_file('t/data/output.fastq'),
+ read_file('t/data/RemoveTags/expected.rm.caa.fastq'),
+ 'checking file contents'
+);
+
+# Test with 1 mismatch allowed
+ok(
+ $obj = Bio::Tradis::RemoveTags->new(
+ fastqfile => $fastqfile,
+ tag => $tag,
+ mismatch => 1,
+ outfile => 't/data/output.fastq'
+ ),
+ 'creating object'
+);
+ok( $obj->remove_tags, 'testing output' );
+ok( -e 't/data/output.fastq', 'checking file existence' );
+is(
+ read_file('t/data/output.fastq'),
+ read_file('t/data/RemoveTags/expected.rm.1mm.caa.fastq'),
+ 'checking file contents'
+);
+
+$fastqfile = "t/data/RemoveTags/sample.tna.fastq";
+$tag = "TNAGAGACAG";
+
+ok(
+ $obj = Bio::Tradis::RemoveTags->new(
+ fastqfile => $fastqfile,
+ tag => $tag,
+ mismatch => 0,
+ outfile => 't/data/output.fastq'
+ ),
+ 'creating object'
+);
+ok( $obj->remove_tags, 'testing output' );
+ok( -e 't/data/output.fastq', 'checking file existence' );
+is(
+ read_file('t/data/output.fastq'),
+ read_file('t/data/RemoveTags/expected.rm.tna.fastq'),
+ 'checking file contents'
+);
+
+unlink('t/data/output.fastq');
+unlink('t/data/RemoveTags/expected.rm.caa.fastq');
+unlink('t/data/RemoveTags/expected.rm.tna.fastq');
+done_testing();
diff --git a/t/Bio/Tradis/RunTradis.t b/t/Bio/Tradis/RunTradis.t
new file mode 100644
index 0000000..3e78f03
--- /dev/null
+++ b/t/Bio/Tradis/RunTradis.t
@@ -0,0 +1,261 @@
+#!/usr/bin/env perl
+use strict;
+use warnings;
+use Cwd;
+use File::Path 'rmtree';
+use File::Temp;
+use File::Slurp;
+
+BEGIN { unshift( @INC, './lib' ) }
+BEGIN { unshift( @INC, '../lib' ) }
+
+BEGIN {
+ use Test::Most;
+ use Test::Exception;
+ use_ok('Bio::Tradis::RunTradis');
+}
+
+my $output_directory_obj = File::Temp->newdir( 'tmp_run_tradis_tests_XXXXX',
+ CLEANUP => 0,
+ DIR => cwd() );
+my $output_directory = $output_directory_obj->dirname;
+my $temp_directory_obj = File::Temp->newdir( CLEANUP => 0,
+ DIR => $output_directory );
+my $temp_directory = $temp_directory_obj->dirname();
+
+my ( $obj, $fastqfile, $stats_handle, $ref, $tag, $outfile );
+
+# First, test all parts and complete pipeline without mismatch
+
+$fastqfile = "t/data/RunTradis/test.tagged.fastq";
+$ref = "t/data/RunTradis/smallref.fa";
+$tag = "TAAGAGTCAG";
+$outfile = "test.plot";
+open( $stats_handle, '>', "$output_directory/test.stats" );
+
+ok(
+ $obj = Bio::Tradis::RunTradis->new(
+ fastqfile => $fastqfile,
+ reference => $ref,
+ tag => $tag,
+ outfile => $outfile,
+ output_directory => $output_directory,
+ _temp_directory => $temp_directory,
+ _stats_handle => $stats_handle
+ ),
+ 'creating object - Normal files, no mismatch'
+);
+
+# Filtering step
+ok( $obj->_filter, 'testing filtering step' );
+ok(
+ -e "$temp_directory/filter.fastq",
+ 'checking filtered file existence - Normal files, no mismatch'
+);
+is(
+ read_file("$temp_directory/filter.fastq"),
+ read_file('t/data/RunTradis/filtered.fastq'),
+ 'checking filtered file contents - Normal files, no mismatch'
+);
+
+# Check filtering step
+ok( $obj->_check_filter, 'testing check filtering step' );
+system("mv $temp_directory/filter.fastq $temp_directory/filter.fastq.bak");
+throws_ok {$obj->_check_filter} 'Bio::Tradis::Exception::TagFilterError', 'complain if no filtered reads';
+system("touch $temp_directory/filter.fastq");
+throws_ok {$obj->_check_filter} 'Bio::Tradis::Exception::TagFilterError', 'complain if filtered reads are empty';
+system("echo foo > $temp_directory/filter.fastq");
+throws_ok {$obj->_check_filter} 'Bio::Tradis::Exception::TagFilterError', 'complain if filtered reads has less than 4 lines';
+system("echo 'foo\nbar\nbaz\nquux' > $temp_directory/filter.fastq");
+throws_ok {$obj->_check_filter} 'Bio::Tradis::Exception::TagFilterError', 'complain if filtered reads do not look like a fastq';
+system("echo 'foo\nbar\n+' > $temp_directory/filter.fastq");
+throws_ok {$obj->_check_filter} 'Bio::Tradis::Exception::TagFilterError', 'complain if filtered reads are too short';
+system("echo 'foo\nbar\n+\nquux' > $temp_directory/filter.fastq");
+ok( $obj->_check_filter, 'check very basic filtered reads validation');
+system("mv $temp_directory/filter.fastq.bak $temp_directory/filter.fastq");
+
+# Tag removal
+ok( $obj->_remove, 'testing tag removal' );
+ok( -e "$temp_directory/tags_removed.fastq",
+ 'checking de-tagged file existence - Normal files, no mismatch' );
+is(
+ read_file("$temp_directory/tags_removed.fastq"),
+ read_file('t/data/RunTradis/notags.fastq'),
+ 'checking de-tagged file contents - Normal files, no mismatch'
+);
+
+# Mapping
+ok( $obj->_map, 'testing mapping' );
+ok( -e "$temp_directory/mapped.sam", 'checking SAM existence' );
+`grep -v "\@PG" $temp_directory/mapped.sam > $output_directory/tmp1.sam`;
+`grep -v "\@PG" t/data/RunTradis/mapped.sam > $output_directory/tmp2.sam`;
+is( read_file("$output_directory/tmp1.sam"), read_file("$output_directory/tmp2.sam"),
+ 'checking mapped file contents' );
+
+# Conversion
+ok( $obj->_sam2bam, 'testing SAM/BAM conversion' );
+ok( -e "$temp_directory/mapped.bam", 'checking BAM existence' );
+
+# Sorting
+ok( $obj->_sort_bam, 'testing BAM sorting' );
+ok( -e "$temp_directory/mapped.sort.bam",
+ 'checking sorted BAM existence - Normal files, no mismatch' );
+ok( -e "$temp_directory/mapped.sort.bam.bai",
+ 'checking indexed BAM existence - Normal files, no mismatch' );
+
+#Bamcheck
+ok( $obj->_bamcheck, 'testing bamcheck' );
+ok( -e "$temp_directory/mapped.bamcheck",
+ 'checking bamcheck file existence - Normal files, no mismatch' );
+
+# Plot
+ok( $obj->_make_plot, 'testing plotting' );
+ok( -e "$temp_directory/test.plot.AE004091.insert_site_plot.gz",
+ 'checking plot file existence - Normal files, no mismatch' );
+system(
+"gunzip -c $temp_directory/test.plot.AE004091.insert_site_plot.gz > $output_directory/test.plot.unzipped"
+);
+system("gunzip -c t/data/RunTradis/expected.plot.gz > $output_directory/expected.plot.unzipped");
+is(
+ read_file("$output_directory/test.plot.unzipped"),
+ read_file("$output_directory/expected.plot.unzipped"),
+ 'checking plot file contents - Normal files, no mismatch'
+);
+
+
+# Complete pipeline
+ok( $obj->run_tradis, 'testing complete analysis - Normal files, no mismatch' );
+ok( -e "$output_directory/test.plot.AE004091.insert_site_plot.gz",
+ 'checking plot file existence - Normal files, no mismatch' );
+system("gunzip -c $output_directory/test.plot.AE004091.insert_site_plot.gz > $output_directory/test.plot.unzipped");
+system("gunzip -c t/data/RunTradis/expected.plot.gz > $output_directory/expected.plot.unzipped");
+is(
+ read_file("$output_directory/test.plot.unzipped"),
+ read_file("$output_directory/expected.plot.unzipped"),
+ 'checking completed pipeline file contents - Normal files, no mismatch'
+);
+
+unlink("$temp_directory/filter.fastq");
+unlink("$temp_directory/tags_removed.fastq");
+
+unlink("$output_directory/test.plot.AE004091.insert_site_plot.gz");
+unlink("$output_directory/expected.plot.unzipped");
+unlink("$output_directory/test.plot.unzipped");
+
+# Test complete pipeline with 1 mismatch allowed
+
+$temp_directory_obj = File::Temp->newdir( CLEANUP => 0,
+ DIR => $output_directory );
+$temp_directory = $temp_directory_obj->dirname();
+
+ok(
+ $obj = Bio::Tradis::RunTradis->new(
+ fastqfile => $fastqfile,
+ reference => $ref,
+ tag => $tag,
+ outfile => $outfile,
+ mismatch => 1,
+ output_directory => $output_directory,
+ _temp_directory => $temp_directory,
+ _stats_handle => $stats_handle
+ ),
+ 'creating object - Normal files one mismatch'
+);
+
+ok( $obj->run_tradis, 'testing complete analysis with mismatch' );
+ok( -e "$output_directory/test.plot.AE004091.insert_site_plot.gz",
+ 'checking plot file existence - Normal files one mismatch' );
+system("gunzip -c $output_directory/test.plot.AE004091.insert_site_plot.gz > $output_directory/test.plot.unzipped");
+system(
+ "gunzip -c t/data/RunTradis/expected.1mm.plot.gz > $output_directory/expected.plot.unzipped");
+is(
+ read_file("$output_directory/test.plot.unzipped"),
+ read_file("$output_directory/expected.plot.unzipped"),
+ 'checking completed pipeline with mismatch file contents - Normal files one mismatch'
+);
+
+unlink("$output_directory/tmp1.sam");
+unlink("$output_directory/tmp2.sam");
+unlink("$output_directory/test.plot.AE004091.insert_site_plot.gz");
+unlink("$output_directory/expected.plot.unzipped");
+unlink("$output_directory/test.plot.unzipped");
+
+# Test pipeline with gzipped input
+$temp_directory_obj = File::Temp->newdir( CLEANUP => 0,
+ DIR => $output_directory );
+$temp_directory = $temp_directory_obj->dirname();
+$fastqfile = "t/data/RunTradis/test.tagged.fastq.gz";
+ok(
+ $obj = Bio::Tradis::RunTradis->new(
+ fastqfile => $fastqfile,
+ reference => $ref,
+ tag => $tag,
+ outfile => $outfile,
+ output_directory => $output_directory,
+ _temp_directory => $temp_directory,
+ _stats_handle => $stats_handle
+ ),
+ 'creating object with gzipped data - Normal files one mismatch'
+);
+
+ok( $obj->run_tradis, 'testing complete analysis with gzipped data' );
+ok(
+ -e "$output_directory/test.plot.AE004091.insert_site_plot.gz",
+ 'checking plot file existence (gzipped data) - Normal files one mismatch'
+);
+ok( -e "$output_directory/test.plot.mapped.bam", 'checking mapped bam existence - Normal files one mismatch');
+ok( -e "$output_directory/test.plot.mapped.bam.bai", 'checking indexed bam file - Normal files one mismatch');
+
+system("gunzip -c $output_directory/test.plot.AE004091.insert_site_plot.gz > $output_directory/test.plot.unzipped");
+system("gunzip -c t/data/RunTradis/expected.plot.gz > $output_directory/expected.plot.unzipped");
+is(
+ read_file("$output_directory/test.plot.unzipped"),
+ read_file("$output_directory/expected.plot.unzipped"),
+ 'checking completed pipeline with gzipped data file contents - Normal files one mismatch'
+);
+
+# Test mapping stage with custom smalt parameters
+$temp_directory_obj = File::Temp->newdir( CLEANUP => 0,
+ DIR => $output_directory );
+$temp_directory = $temp_directory_obj->dirname();
+ok(
+ $obj = Bio::Tradis::RunTradis->new(
+ fastqfile => $fastqfile,
+ reference => $ref,
+ tag => $tag,
+ outfile => $outfile,
+ output_directory => $output_directory,
+ _temp_directory => $temp_directory,
+ _stats_handle => $stats_handle,
+ smalt_k => 10,
+ smalt_s => 2
+ ),
+ 'creating object with custom smalt parameters'
+);
+# Filtering step
+$obj->_filter;
+$obj->_remove;
+ok( $obj->_map, 'mapping with custom parameters fine' );
+
+# Check die if ref is not found
+$temp_directory_obj = File::Temp->newdir( CLEANUP => 0,
+ DIR => $output_directory );
+$temp_directory = $temp_directory_obj->dirname();
+ok(
+ $obj = Bio::Tradis::RunTradis->new(
+ fastqfile => $fastqfile,
+ reference => "not_really_a_ref.fa",
+ tag => $tag,
+ outfile => $outfile,
+ output_directory => $output_directory,
+ _temp_directory => $temp_directory,
+ _stats_handle => $stats_handle,
+ smalt_k => 10,
+ smalt_s => 2
+ ),
+ 'creating object with custom smalt parameters'
+);
+throws_ok {$obj->run_tradis} 'Bio::Tradis::Exception::RefNotFound', 'correct error thrown';
+
+rmtree($output_directory);
+done_testing();
diff --git a/t/Bio/Tradis/TradisPlot.t b/t/Bio/Tradis/TradisPlot.t
new file mode 100644
index 0000000..6efe43a
--- /dev/null
+++ b/t/Bio/Tradis/TradisPlot.t
@@ -0,0 +1,43 @@
+#!/usr/bin/env perl
+use strict;
+use warnings;
+use File::Temp;
+use File::Slurp;
+use Test::Files;
+
+BEGIN { unshift( @INC, './lib' ) }
+BEGIN { unshift( @INC, '../lib' ) }
+
+BEGIN {
+ use Test::Most;
+ use_ok('Bio::Tradis::TradisPlot');
+}
+
+my $destination_directory_obj = File::Temp->newdir( CLEANUP => 1 );
+my $destination_directory = $destination_directory_obj->dirname();
+
+my ( $mappedfile, $obj, $outfile );
+
+$mappedfile = "t/data/TradisPlot/test.mapped.bam";
+$outfile = "test.plot";
+
+ok(
+ $obj = Bio::Tradis::TradisPlot->new(
+ mappedfile => $mappedfile,
+ outfile => $outfile,
+ mapping_score => 30
+ ),
+ 'creating object'
+);
+
+ok( $obj->plot, 'testing plotting' );
+ok( -e 'test.plot.AE004091.insert_site_plot.gz',
+ 'checking plot file existence' );
+
+system("gunzip -c test.plot.AE004091.insert_site_plot.gz > test.plot.unzipped");
+system("gunzip -c t/data/TradisPlot/expected.plot.gz > expected.plot.unzipped");
+compare_ok('test.plot.unzipped','expected.plot.unzipped','checking file contents');
+
+unlink('test.plot.AE004091.insert_site_plot.gz');
+unlink('expected.plot.unzipped');
+done_testing();
diff --git a/t/data/AddTags/expected_tradis.bam b/t/data/AddTags/expected_tradis.bam
new file mode 100644
index 0000000..b51b1b8
Binary files /dev/null and b/t/data/AddTags/expected_tradis.bam differ
diff --git a/t/data/AddTags/expected_tradis.cram b/t/data/AddTags/expected_tradis.cram
new file mode 100644
index 0000000..4d3f44d
Binary files /dev/null and b/t/data/AddTags/expected_tradis.cram differ
diff --git a/t/data/AddTags/sample_sm_no_tr.bam b/t/data/AddTags/sample_sm_no_tr.bam
new file mode 100644
index 0000000..b51b1b8
Binary files /dev/null and b/t/data/AddTags/sample_sm_no_tr.bam differ
diff --git a/t/data/AddTags/sample_sm_tr.bam b/t/data/AddTags/sample_sm_tr.bam
new file mode 100644
index 0000000..1904961
Binary files /dev/null and b/t/data/AddTags/sample_sm_tr.bam differ
diff --git a/t/data/AddTags/sample_sm_tr.cram b/t/data/AddTags/sample_sm_tr.cram
new file mode 100644
index 0000000..a47880b
Binary files /dev/null and b/t/data/AddTags/sample_sm_tr.cram differ
diff --git a/t/data/CombinePlots/comb_expected.stats b/t/data/CombinePlots/comb_expected.stats
new file mode 100644
index 0000000..22b1b25
--- /dev/null
+++ b/t/data/CombinePlots/comb_expected.stats
@@ -0,0 +1,3 @@
+ID,Sequence Length,Unique Insertion Sites,Seq Len/UIS
+first,20,10,2
+second,25,5,5
diff --git a/t/data/CombinePlots/comb_sample.txt b/t/data/CombinePlots/comb_sample.txt
new file mode 100644
index 0000000..b798920
--- /dev/null
+++ b/t/data/CombinePlots/comb_sample.txt
@@ -0,0 +1,2 @@
+first test1.plot test2.plot
+second test3.plot test4.plot
\ No newline at end of file
diff --git a/t/data/CombinePlots/first.expected.plot b/t/data/CombinePlots/first.expected.plot
new file mode 100644
index 0000000..48fe1ef
--- /dev/null
+++ b/t/data/CombinePlots/first.expected.plot
@@ -0,0 +1,20 @@
+0 1
+3 0
+0 0
+0 0
+0 4
+1 0
+0 0
+0 6
+0 0
+3 0
+0 0
+0 0
+2 0
+1 0
+0 0
+0 7
+0 0
+0 0
+0 0
+10 1
\ No newline at end of file
diff --git a/t/data/CombinePlots/sample1.sm.plot.gz b/t/data/CombinePlots/sample1.sm.plot.gz
new file mode 100644
index 0000000..b2fa361
Binary files /dev/null and b/t/data/CombinePlots/sample1.sm.plot.gz differ
diff --git a/t/data/CombinePlots/sample2.sm.plot.gz b/t/data/CombinePlots/sample2.sm.plot.gz
new file mode 100644
index 0000000..c9ac95a
Binary files /dev/null and b/t/data/CombinePlots/sample2.sm.plot.gz differ
diff --git a/t/data/CombinePlots/second.expected.plot b/t/data/CombinePlots/second.expected.plot
new file mode 100644
index 0000000..0429a13
--- /dev/null
+++ b/t/data/CombinePlots/second.expected.plot
@@ -0,0 +1,25 @@
+0 0
+0 0
+0 0
+2 0
+0 0
+0 0
+0 1
+0 0
+0 0
+0 0
+0 0
+0 0
+0 7
+1 0
+0 0
+0 0
+0 0
+0 0
+0 0
+0 0
+0 0
+9 0
+0 0
+0 0
+0 0
\ No newline at end of file
diff --git a/t/data/CombinePlots/tabix_sorted.insert_site_plot.gz b/t/data/CombinePlots/tabix_sorted.insert_site_plot.gz
new file mode 100644
index 0000000..247fd41
Binary files /dev/null and b/t/data/CombinePlots/tabix_sorted.insert_site_plot.gz differ
diff --git a/t/data/CombinePlots/tabix_sorted.insert_site_plot.gz.tbi b/t/data/CombinePlots/tabix_sorted.insert_site_plot.gz.tbi
new file mode 100644
index 0000000..d03f7b7
Binary files /dev/null and b/t/data/CombinePlots/tabix_sorted.insert_site_plot.gz.tbi differ
diff --git a/t/data/CombinePlots/test1.plot b/t/data/CombinePlots/test1.plot
new file mode 100644
index 0000000..1272c23
--- /dev/null
+++ b/t/data/CombinePlots/test1.plot
@@ -0,0 +1,20 @@
+0 0
+1 0
+0 0
+0 0
+0 2
+0 0
+0 0
+0 0
+0 0
+3 0
+0 0
+0 0
+1 0
+1 0
+0 0
+0 7
+0 0
+0 0
+0 0
+10 0
\ No newline at end of file
diff --git a/t/data/CombinePlots/test2.plot b/t/data/CombinePlots/test2.plot
new file mode 100644
index 0000000..d7fdc26
--- /dev/null
+++ b/t/data/CombinePlots/test2.plot
@@ -0,0 +1,20 @@
+0 1
+2 0
+0 0
+0 0
+0 2
+1 0
+0 0
+0 6
+0 0
+0 0
+0 0
+0 0
+1 0
+0 0
+0 0
+0 0
+0 0
+0 0
+0 0
+0 1
\ No newline at end of file
diff --git a/t/data/CombinePlots/test3.plot b/t/data/CombinePlots/test3.plot
new file mode 100644
index 0000000..db4ef1e
--- /dev/null
+++ b/t/data/CombinePlots/test3.plot
@@ -0,0 +1,25 @@
+0 0
+0 0
+0 0
+1 0
+0 0
+0 0
+0 1
+0 0
+0 0
+0 0
+0 0
+0 0
+0 2
+1 0
+0 0
+0 0
+0 0
+0 0
+0 0
+0 0
+0 0
+0 0
+0 0
+0 0
+0 0
\ No newline at end of file
diff --git a/t/data/CombinePlots/test4.plot b/t/data/CombinePlots/test4.plot
new file mode 100644
index 0000000..280a058
--- /dev/null
+++ b/t/data/CombinePlots/test4.plot
@@ -0,0 +1,25 @@
+0 0
+0 0
+0 0
+1 0
+0 0
+0 0
+0 0
+0 0
+0 0
+0 0
+0 0
+0 0
+0 5
+0 0
+0 0
+0 0
+0 0
+0 0
+0 0
+0 0
+0 0
+9 0
+0 0
+0 0
+0 0
\ No newline at end of file
diff --git a/t/data/CombinePlots/zip_comb_exp.plot b/t/data/CombinePlots/zip_comb_exp.plot
new file mode 100644
index 0000000..25ca72d
--- /dev/null
+++ b/t/data/CombinePlots/zip_comb_exp.plot
@@ -0,0 +1,100 @@
+0 0
+0 0
+0 0
+4 0
+0 0
+0 0
+0 0
+0 0
+0 0
+0 0
+0 0
+0 0
+0 0
+0 0
+0 0
+0 5
+0 0
+0 0
+0 0
+0 0
+0 0
+0 0
+0 0
+0 0
+0 0
+0 0
+0 0
+0 0
+0 0
+0 0
+0 0
+4 0
+0 0
+0 0
+0 0
+0 0
+0 0
+0 0
+0 0
+0 0
+0 0
+0 0
+0 0
+0 0
+0 0
+0 0
+0 0
+0 0
+0 0
+0 0
+0 0
+0 0
+0 0
+0 0
+0 0
+0 0
+0 0
+0 0
+0 0
+0 0
+0 0
+0 0
+0 0
+1 5
+0 0
+0 0
+0 0
+0 0
+0 0
+0 0
+0 0
+0 0
+0 0
+0 0
+0 0
+0 0
+0 0
+0 0
+0 0
+0 0
+0 0
+0 0
+0 0
+0 0
+0 0
+0 0
+0 0
+0 0
+0 0
+0 0
+0 0
+0 0
+0 0
+0 0
+0 0
+0 0
+0 0
+0 0
+0 0
+0 0
\ No newline at end of file
diff --git a/t/data/CombinePlots/zip_comb_exp.stats b/t/data/CombinePlots/zip_comb_exp.stats
new file mode 100644
index 0000000..2559142
--- /dev/null
+++ b/t/data/CombinePlots/zip_comb_exp.stats
@@ -0,0 +1,2 @@
+ID,Sequence Length,Unique Insertion Sites,Seq Len/UIS
+zip_combined,100,4,25
diff --git a/t/data/CombinePlots/zip_comb_list.txt b/t/data/CombinePlots/zip_comb_list.txt
new file mode 100644
index 0000000..f87cee1
--- /dev/null
+++ b/t/data/CombinePlots/zip_comb_list.txt
@@ -0,0 +1 @@
+zip_combined sample1.sm.plot.gz sample2.sm.plot.gz
diff --git a/t/data/CommandLine/fastq.list b/t/data/CommandLine/fastq.list
new file mode 100644
index 0000000..8f04cd2
--- /dev/null
+++ b/t/data/CommandLine/fastq.list
@@ -0,0 +1,2 @@
+test_1.fastq
+test_2.fastq
diff --git a/t/data/CommandLine/test_1.fastq b/t/data/CommandLine/test_1.fastq
new file mode 100644
index 0000000..94d01f9
--- /dev/null
+++ b/t/data/CommandLine/test_1.fastq
@@ -0,0 +1,56 @@
+ at HS21_09876:1:1105:9650:48712#84
+TAAGATTCAGGGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG
++
+CCCFFFFFHHHHCEE8EEFGFFGFIFGGFGEEHFFFGGGFGFGEGEEEFGFGFF
+ at HS21_09876:1:1106:8638:38957#84
+TGAGAGTCAGGGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG
++
+B at CFFFFFHHHHCEF7FHFFFFGFEGEFFEHEGEGFGGGEGFGFGGFEHGFEFD
+ at HS21_09876:1:1105:9650:48712#83
+TAAGAGTCAGGGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG
++
+CCCFFFFFHHHHCEE8EEFGFFGFIFGGFGEEHFFFGGGFGFGEGEEEFGFGFF
+ at HS21_09876:1:1106:8638:38957#83
+TAAGAGTCAGGGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG
++
+B at CFFFFFHHHHCEF7FHFFFFGFEGEFFEHEGEGFGGGEGFGFGGFEHGFEFD
+ at HS21_09876:1:1204:19746:42237#83
+TAAGAGTCAGGGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG
++
+CCCFFFFFHHHHCBF2GGFFEFGEEFFFEEHEEHFFFFGFGFFFGGGGHGFEFF
+ at HS21_09876:1:2210:2408:11148#83
+TAAGAGTCAGGGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG
++
+BBCFFFFFHHHHCBF,GGFF<FEHFFEGFGFEEEGFGGGFGFFFGGGFHGFEFF
+ at HS21_09876:1:2210:16541:84795#83
+TAAGAGTCAGGGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG
++
+BCCFFFFFHHFDB at F%GEFDCFGHE<FD>GEEEGFFGGFFGFFBG8FGFGFEEE
+ at HS21_09876:1:1201:6607:66324#83
+TAAGAGTCAGCCCACCGACGGCTCCGGATGGCTGACCCGCTGCTGGATGGGGCT
++
+BCCDFBDEHHHHCDF8EHFEGFAGIFEDEGFEFFGFEGFEGFGFGEGGHGFEFD
+ at HS21_09876:1:2102:12312:75235#83
+TAAGAGTCAGCCCACCGACGGCTCCGGATGGCTGACCCGCTGCTGGATGGGGCT
++
+BCCDFFFFHHHHCDH8EHFFGFAGDFIEEEGEFFGFFGFFGFFEGEFFFGFEFE
+ at HS21_09876:1:1106:16061:54950#83
+TAAGAGTCAGGGGATGGGGCTGATCTCGGCCATGGTCTCGCTGACCCAGGCTTC
++
+BBBDFFFFHHFHCBD4GHFFGFEEC<FCGEFEGHGFFEGFGFFFGDFGDGFDFF
+ at HS21_09876:1:2101:14032:85058#83
+TAAGAGTCAGGAATCGAGCGCGCGCTGCCCAAGGACACCTGGGGACCGGCGCGG
++
+BCCDFFFFHHHHCEH5GHFFFFGEDC;GHFFEHGGFFGFEGFFJGDGFHGFGFF
+ at HS21_09876:1:2111:11125:6617#83
+TAAGAGTCAGGAATCGAGCGCGCGCTGCCCAAGGACACCCGGGGACCGGCGCGG
++
+BCCDDDDDFHHG2BH8HEFGFFGH;EFGHFGEGGGFEGGFGFFGGDGEHGFEFF
+ at HS21_09876:1:2202:3163:76297#83
+TAAGAGTCAGGAATCGAGCGCGCGCTGCCCAAGGACACCTGGGGACCGGCGCGG
++
+BCCDFDDDHHHHCEH8EGFEGFGEIFDGHFGEHECFFGGFGFFDGEGGHGFEFF
+ at HS21_09876:1:2205:20175:3703#83
+TAAGAGTCAGGAATCGAGCGCGCGCTGCCCAAGGACACCTGGGGACCGGCGCGG
++
+BCCDFFFEHHH>8BI2A<FEFFGCE<EDFDDEHH?F=GFFGF3FGEGGHGDDFE
diff --git a/t/data/CommandLine/test_2.fastq b/t/data/CommandLine/test_2.fastq
new file mode 100644
index 0000000..058e801
--- /dev/null
+++ b/t/data/CommandLine/test_2.fastq
@@ -0,0 +1,56 @@
+ at HS21_09876:1:2205:6527:34286#83
+TAAGAGTCAGGAATCGAGCGCGCGCTGCCCAAGGACACCTGGGGACCGGCGCGG
++
+BCCDFFFFHHHGBDH4HHFGFFGFDFDGHEGEHGGFEGFJGFGGGEGFHGFFFF
+ at HS21_09876:1:1201:10071:48582#83
+TAAGAGTCAGGCCCCAAGGACACCTGGGGACCGGCGCGGCTGGACGCGGTATCG
++
+CCCDFFFFHHHHCDI8EHFGFFGEFFFGGFGEFGGFFGGFGFG8G8ECFGFFAE
+ at HS21_09876:1:2107:20205:78513#83
+TAAGAGTCAGGCCCCGAGGACACCTGGGGACCGGCGCGGCTGGACGCGGTATCG
++
+BCCFFFFFHHHHCEI%EGFFEFEGIFGDGFE>GDGFFGFEBFGDGEGEH;EFDD
+ at HS21_09876:1:2207:12005:97464#83
+TAAGAGTCAGGCCCCAAGGACACCTGGGGACCGGCGCGGCTGGACGCGGTATCG
++
+BCCDFFFFHHHGBBH0EG?<FFEHCBGEE>DEDF?FFGFE1FE89EEGD;;@?D
+ at HS21_09876:1:1208:12319:4648#83
+TAAGAGTCAGCAACCTGGGGACCGGCGCGGCTGGACGCGGTATCGATGATCTTC
++
+B=BDFFFDH>AA>EF8EIFFGFGEC<F;FEEEG3?FFG/E=F?DG89C=GAD?E
+ at HS21_09876:1:2209:14024:59451#83
+TAAGAGTCAGCCCGGTGCGCTACCCGTTCCTGTGGAACGCGGCGCGGCAGAACA
++
+BCCDFFFFHHFHCBF.E<FEFFGHHGE;H>GEFHFFFGFFGFFFGEFGFGFGFF
+ at HS21_09876:2:1211:5990:82312#83
+TAAGAGTCAGTTTTCGGTCACCGCGGTGCGCAACCTGCACCCGGTGACCCTCTC
++
+BCCFFFFFHHHGFEH0FFDDDGCF7GFD1GCFGFGGFGFFGHEFF?FFFEEDEE
+ at HS21_09876:2:2103:19946:55809#83
+TAAGAGTCAGGGGTCATAACGCCGCGGAGATTCTCTCGCGCGGTCAGCAGAAGC
++
+BBCFDEFFHHHHEAE'EFFEGGGFHEFAHGFHG at GEFHFEGFGFFF<FGEEDCE
+ at HS21_09876:2:1104:10740:37072#83
+TAAGAGTCAGCCCACCGACGGCTCCGGATGGCTGACCCGCTGCTGGATGGGGCT
++
+BBBDDFFFHHHHFAE,FIGDEG;FHFFHH>FAGGFFF;><GHA9<F<FGE=F at C
+ at HS21_09876:2:2201:4547:41892#83
+TAAGAGTCAGCCCACCGACGGCTCCGGATGGCTGACCCGCTGCTGGATGGGGCT
++
+BCCDFFFFHHGGEEE7EFGEDGEDHGGAHFGHGFDGFCFEGFAFFFDFBEEEDE
+ at HS21_09876:2:2213:12056:100809#83
+TAAGAGTCAGGGGATGGGGCTGATCTCGGCCATGGTCTCGCTGACCCAGGCTTC
++
+BBCDDDDDHDBFEE?,B>DFG=EDF:GHHEG6GGDGFFFFGGF6FFEFGC1BFF
+ at HS21_09876:1:1115:10349:43433#83
+TTTTCGACAACCTTTTGCCTGCCGGAGAAACACGCAGTTGCTACCNNACNCTNN
++
+8,(,*A<A2;DGE4B>HGFEDDCFG8CE=FF8BB7ED?FEEE522!!<2!:0!!
+ at HS21_09876:1:1211:4356:84410#83
+TTCTCGACAACCTTTTGCCTGCCGGAGAAACACGCAGTTGCTACCTGACTCTTA
++
+>E52EHFGFFGGFFFGHGHEEEGFGEGFGFGFGCGGFGFGFDHHHHFFFFFCCC
+ at HS21_09876:1:1101:19209:27276#83
+CGCACAGCCGTGTGGAAAAAACCGCTGTGGATAACCATCTCGGCCTGACTCTTA
++
+CEF4GHFDFFEEIFECHFGEFFGFEFGFGFFFGDHGHGFEFFHHHHFFFFFCCC
diff --git a/t/data/DetectTags/sample_sm_no_tr.bam b/t/data/DetectTags/sample_sm_no_tr.bam
new file mode 100644
index 0000000..5578ab7
Binary files /dev/null and b/t/data/DetectTags/sample_sm_no_tr.bam differ
diff --git a/t/data/DetectTags/sample_sm_tr.bam b/t/data/DetectTags/sample_sm_tr.bam
new file mode 100644
index 0000000..1904961
Binary files /dev/null and b/t/data/DetectTags/sample_sm_tr.bam differ
diff --git a/t/data/DetectTags/sample_sm_tr.cram b/t/data/DetectTags/sample_sm_tr.cram
new file mode 100644
index 0000000..a5212b0
Binary files /dev/null and b/t/data/DetectTags/sample_sm_tr.cram differ
diff --git a/t/data/FilterTags/expected.1mm.caa.fastq b/t/data/FilterTags/expected.1mm.caa.fastq
new file mode 100644
index 0000000..2781abe
--- /dev/null
+++ b/t/data/FilterTags/expected.1mm.caa.fastq
@@ -0,0 +1,40 @@
+ at IL2_4334:7:5:6843:6843
+CGACGTTTTCTGCGTGTTGCCGATATTCTGGAAAGCA
++
+=8>;A<@>=B;FF8>CCF:=CC-7(C>/22C:4;<=;
+ at IL2_4334:7:5:18259:13400
+CACCGTTTTCTGCGTGTTGCCGATATTCTGGAAAGCA
++
+<8:=B>=B(B88A?C@@A;;B at +21AA/38><8=C;>
+ at IL2_4334:7:15:5608:3756
+CAACGTTTTCTGCGTGTTGCCGATATTTTGGAAAGCA
++
+9AA9:17<988@=@AB6=:?;:-08C=&,6C@:8A4=
+ at IL2_4334:7:18:16351:15714
+CAACGTTTTCTGCGTGTTGCCGATATTCTGGAAAGCA
++
+<===?;=@<<>FCBFF=:B7?A+4/A>(22@?64?5@
+ at IL2_4334:7:39:12877:7020
+CAACGTTTTCTGCGTGTTGCCGATATTCTGGAAAGCA
++
+=B?=<>ACB=@;FFF=FFA<AC071??/84C=;3?75
+ at IL2_4334:7:42:14437:19550
+CAACGTTTTCTGCGTGTTGCCGATATTCTGGAAAGCA
++
+<7=B8 at B=;8;DF;CF;F;8A?2<6;:18;81;<;8C
+ at IL2_4334:7:53:4426:3757
+CAACGTTTTCTGCGTGTTGCCGATATTCTGGAAAGCA
++
+=B<7<:9B@:@AF at A>?F@<F=47. at A,11D<45D9<
+ at IL2_4334:7:79:9021:16833
+CAACGTTTTCTGCGTGTTGCCGATATTCTGGAAAGCA
++
+;A:7A;CBFBFA?ABCC>86 at B:C?A>6=:6<CB:>C
+ at IL2_4334:7:82:17494:18362
+CAACGTTTTCTGCGTGTTGCCGATATTCTGGAAAGCA
++
+<79:<9;7<>8=CB@:C:AB=7410=C-46;,75>>F
+ at IL2_4334:7:84:7230:17356
+CAACGTTTTCTGCGTGTTGCCGATATTCTGGAAAGCA
++
+DADFDFFDDD>8:=>=?@48 at 87A4@F6>??BF??B@
diff --git a/t/data/FilterTags/expected.caa.fastq b/t/data/FilterTags/expected.caa.fastq
new file mode 100644
index 0000000..f36ff76
--- /dev/null
+++ b/t/data/FilterTags/expected.caa.fastq
@@ -0,0 +1,32 @@
+ at IL2_4334:7:15:5608:3756
+CAACGTTTTCTGCGTGTTGCCGATATTTTGGAAAGCA
++
+9AA9:17<988@=@AB6=:?;:-08C=&,6C@:8A4=
+ at IL2_4334:7:18:16351:15714
+CAACGTTTTCTGCGTGTTGCCGATATTCTGGAAAGCA
++
+<===?;=@<<>FCBFF=:B7?A+4/A>(22@?64?5@
+ at IL2_4334:7:39:12877:7020
+CAACGTTTTCTGCGTGTTGCCGATATTCTGGAAAGCA
++
+=B?=<>ACB=@;FFF=FFA<AC071??/84C=;3?75
+ at IL2_4334:7:42:14437:19550
+CAACGTTTTCTGCGTGTTGCCGATATTCTGGAAAGCA
++
+<7=B8 at B=;8;DF;CF;F;8A?2<6;:18;81;<;8C
+ at IL2_4334:7:53:4426:3757
+CAACGTTTTCTGCGTGTTGCCGATATTCTGGAAAGCA
++
+=B<7<:9B@:@AF at A>?F@<F=47. at A,11D<45D9<
+ at IL2_4334:7:79:9021:16833
+CAACGTTTTCTGCGTGTTGCCGATATTCTGGAAAGCA
++
+;A:7A;CBFBFA?ABCC>86 at B:C?A>6=:6<CB:>C
+ at IL2_4334:7:82:17494:18362
+CAACGTTTTCTGCGTGTTGCCGATATTCTGGAAAGCA
++
+<79:<9;7<>8=CB@:C:AB=7410=C-46;,75>>F
+ at IL2_4334:7:84:7230:17356
+CAACGTTTTCTGCGTGTTGCCGATATTCTGGAAAGCA
++
+DADFDFFDDD>8:=>=?@48 at 87A4@F6>??BF??B@
diff --git a/t/data/FilterTags/expected.tna.fastq b/t/data/FilterTags/expected.tna.fastq
new file mode 100644
index 0000000..e410d63
--- /dev/null
+++ b/t/data/FilterTags/expected.tna.fastq
@@ -0,0 +1,12 @@
+ at IL2_4334:6:120:19845:10197
+TNAGAGACAGGTATTACTCTGCATCANTNAANNGAGA
++
+:)::9:9;BA;1CB7F:BCC==7 at 5A)=%76%%0B67
+ at IL2_4334:6:120:19846:21043
+TNAGAGACAGTGTCTAGGGCATCACTNANGGNNGAGG
++
+<)72:19:?>:A>C?@@??CC@?:6;)5%>9%%;;;<
+ at IL2_4334:6:120:19846:19594
+TNAGAGACAGATCCTATGGGGCTGAANTNTNNNGTGA
++
+:)7:782?=AC<;@=5444@:B;>?*%)%4%%%?161
diff --git a/t/data/FilterTags/sample.fastq b/t/data/FilterTags/sample.fastq
new file mode 100644
index 0000000..8136d33
--- /dev/null
+++ b/t/data/FilterTags/sample.fastq
@@ -0,0 +1,52 @@
+ at IL2_4334:7:5:6843:6843
+CGACGTTTTCTGCGTGTTGCCGATATTCTGGAAAGCA
++
+=8>;A<@>=B;FF8>CCF:=CC-7(C>/22C:4;<=;
+ at IL2_4334:7:5:18259:13400
+CACCGTTTTCTGCGTGTTGCCGATATTCTGGAAAGCA
++
+<8:=B>=B(B88A?C@@A;;B at +21AA/38><8=C;>
+ at IL2_4334:7:15:5608:3756
+CAACGTTTTCTGCGTGTTGCCGATATTTTGGAAAGCA
++
+9AA9:17<988@=@AB6=:?;:-08C=&,6C@:8A4=
+ at IL2_4334:7:18:16351:15714
+CAACGTTTTCTGCGTGTTGCCGATATTCTGGAAAGCA
++
+<===?;=@<<>FCBFF=:B7?A+4/A>(22@?64?5@
+ at IL2_4334:7:39:12877:7020
+CAACGTTTTCTGCGTGTTGCCGATATTCTGGAAAGCA
++
+=B?=<>ACB=@;FFF=FFA<AC071??/84C=;3?75
+ at IL2_4334:7:42:14437:19550
+CAACGTTTTCTGCGTGTTGCCGATATTCTGGAAAGCA
++
+<7=B8 at B=;8;DF;CF;F;8A?2<6;:18;81;<;8C
+ at IL2_4334:7:53:4426:3757
+CAACGTTTTCTGCGTGTTGCCGATATTCTGGAAAGCA
++
+=B<7<:9B@:@AF at A>?F@<F=47. at A,11D<45D9<
+ at IL2_4334:7:79:9021:16833
+CAACGTTTTCTGCGTGTTGCCGATATTCTGGAAAGCA
++
+;A:7A;CBFBFA?ABCC>86 at B:C?A>6=:6<CB:>C
+ at IL2_4334:6:120:19845:10197
+TNAGAGACAGGTATTACTCTGCATCANTNAANNGAGA
++
+:)::9:9;BA;1CB7F:BCC==7 at 5A)=%76%%0B67
+ at IL2_4334:7:82:17494:18362
+CAACGTTTTCTGCGTGTTGCCGATATTCTGGAAAGCA
++
+<79:<9;7<>8=CB@:C:AB=7410=C-46;,75>>F
+ at IL2_4334:7:84:7230:17356
+CAACGTTTTCTGCGTGTTGCCGATATTCTGGAAAGCA
++
+DADFDFFDDD>8:=>=?@48 at 87A4@F6>??BF??B@
+ at IL2_4334:6:120:19846:21043
+TNAGAGACAGTGTCTAGGGCATCACTNANGGNNGAGG
++
+<)72:19:?>:A>C?@@??CC@?:6;)5%>9%%;;;<
+ at IL2_4334:6:120:19846:19594
+TNAGAGACAGATCCTATGGGGCTGAANTNTNNNGTGA
++
+:)7:782?=AC<;@=5444@:B;>?*%)%4%%%?161
\ No newline at end of file
diff --git a/t/data/FilterTags/sample.fastq.gz b/t/data/FilterTags/sample.fastq.gz
new file mode 100644
index 0000000..41b9c6e
Binary files /dev/null and b/t/data/FilterTags/sample.fastq.gz differ
diff --git a/t/data/InsertSite/2_reads.bam b/t/data/InsertSite/2_reads.bam
new file mode 100644
index 0000000..29f929a
Binary files /dev/null and b/t/data/InsertSite/2_reads.bam differ
diff --git a/t/data/InsertSite/small_multi_sequence.bam b/t/data/InsertSite/small_multi_sequence.bam
new file mode 100644
index 0000000..4337614
Binary files /dev/null and b/t/data/InsertSite/small_multi_sequence.bam differ
diff --git a/t/data/Map/expected.mapped b/t/data/Map/expected.mapped
new file mode 100644
index 0000000..cbcca9e
--- /dev/null
+++ b/t/data/Map/expected.mapped
@@ -0,0 +1,26 @@
+ at HD VN:1.3 SO:unknown
+ at SQ SN:AE004091 LN:9840
+ at PG ID:smalt PN:smalt VN:0.7.4 CL:smalt map -x -r -1 -y 0.96 test.ref.index /Users/cc21/Development/repos/Bio-Tradis/t/data/Map/test.fastq
+HS21_09876:1:1105:9650:48712#83 0 AE004091 6698 54 1S43M * 0 0 GGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG HHCEE8EEFGFFGFIFGGFGEEHFFFGGGFGFGEGEEEFGFGFF NM:i:0 AS:i:43
+HS21_09876:1:1106:8638:38957#83 0 AE004091 6698 54 1S43M * 0 0 GGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG HHCEF7FHFFFFGFEGEFFEHEGEGFGGGEGFGFGGFEHGFEFD NM:i:0 AS:i:43
+HS21_09876:1:1204:19746:42237#83 0 AE004091 6698 54 1S43M * 0 0 GGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG HHCBF2GGFFEFGEEFFFEEHEEHFFFFGFGFFFGGGGHGFEFF NM:i:0 AS:i:43
+HS21_09876:1:2210:2408:11148#83 0 AE004091 6698 54 1S43M * 0 0 GGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG HHCBF,GGFF<FEHFFEGFGFEEEGFGGGFGFFFGGGFHGFEFF NM:i:0 AS:i:43
+HS21_09876:1:2210:16541:84795#83 0 AE004091 6698 54 1S43M * 0 0 GGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG FDB at F%GEFDCFGHE<FD>GEEEGFFGGFFGFFBG8FGFGFEEE NM:i:0 AS:i:43
+HS21_09876:1:1201:6607:66324#83 0 AE004091 7026 54 1S43M * 0 0 CCCACCGACGGCTCCGGATGGCTGACCCGCTGCTGGATGGGGCT HHCDF8EHFEGFAGIFEDEGFEFFGFEGFEGFGFGEGGHGFEFD NM:i:0 AS:i:43
+HS21_09876:1:2102:12312:75235#83 0 AE004091 7026 54 1S43M * 0 0 CCCACCGACGGCTCCGGATGGCTGACCCGCTGCTGGATGGGGCT HHCDH8EHFFGFAGDFIEEEGEFFGFFGFFGFFEGEFFFGFEFE NM:i:0 AS:i:43
+HS21_09876:1:1106:16061:54950#83 0 AE004091 7059 54 1S43M * 0 0 GGGATGGGGCTGATCTCGGCCATGGTCTCGCTGACCCAGGCTTC FHCBD4GHFFGFEEC<FCGEFEGHGFFEGFGFFFGDFGDGFDFF NM:i:0 AS:i:43
+HS21_09876:1:2101:14032:85058#83 0 AE004091 9250 54 2S42M * 0 0 GAATCGAGCGCGCGCTGCCCAAGGACACCTGGGGACCGGCGCGG HHCEH5GHFFFFGEDC;GHFFEHGGFFGFEGFFJGDGFHGFGFF NM:i:0 AS:i:42
+HS21_09876:1:2111:11125:6617#83 4 * 0 0 * * 0 0 GAATCGAGCGCGCGCTGCCCAAGGACACCCGGGGACCGGCGCGG HG2BH8HEFGFFGH;EFGHFGEGGGFEGGFGFFGGDGEHGFEFF NM:i:0 AS:i:0
+HS21_09876:1:2202:3163:76297#83 0 AE004091 9250 54 2S42M * 0 0 GAATCGAGCGCGCGCTGCCCAAGGACACCTGGGGACCGGCGCGG HHCEH8EGFEGFGEIFDGHFGEHECFFGGFGFFDGEGGHGFEFF NM:i:0 AS:i:42
+HS21_09876:1:2205:20175:3703#83 0 AE004091 9250 54 2S42M * 0 0 GAATCGAGCGCGCGCTGCCCAAGGACACCTGGGGACCGGCGCGG H>8BI2A<FEFFGCE<EDFDDEHH?F=GFFGF3FGEGGHGDDFE NM:i:0 AS:i:42
+HS21_09876:1:2205:6527:34286#83 0 AE004091 9250 54 2S42M * 0 0 GAATCGAGCGCGCGCTGCCCAAGGACACCTGGGGACCGGCGCGG HGBDH4HHFGFFGFDFDGHEGEHGGFEGFJGFGGGEGFHGFFFF NM:i:0 AS:i:42
+HS21_09876:1:1201:10071:48582#83 0 AE004091 9265 54 2S42M * 0 0 GCCCCAAGGACACCTGGGGACCGGCGCGGCTGGACGCGGTATCG HHCDI8EHFGFFGEFFFGGFGEFGGFFGGFGFG8G8ECFGFFAE NM:i:0 AS:i:42
+HS21_09876:1:2107:20205:78513#83 4 * 0 0 * * 0 0 GCCCCGAGGACACCTGGGGACCGGCGCGGCTGGACGCGGTATCG HHCEI%EGFFEFEGIFGDGFE>GDGFFGFEBFGDGEGEH;EFDD NM:i:0 AS:i:0
+HS21_09876:1:2207:12005:97464#83 0 AE004091 9265 54 2S42M * 0 0 GCCCCAAGGACACCTGGGGACCGGCGCGGCTGGACGCGGTATCG HGBBH0EG?<FFEHCBGEE>DEDF?FFGFE1FE89EEGD;;@?D NM:i:0 AS:i:42
+HS21_09876:1:1208:12319:4648#83 0 AE004091 9274 54 2S42M * 0 0 CAACCTGGGGACCGGCGCGGCTGGACGCGGTATCGATGATCTTC AA>EF8EIFFGFGEC<F;FEEEG3?FFG/E=F?DG89C=GAD?E NM:i:0 AS:i:42
+HS21_09876:1:2209:14024:59451#83 0 AE004091 9391 54 1S43M * 0 0 CCCGGTGCGCTACCCGTTCCTGTGGAACGCGGCGCGGCAGAACA FHCBF.E<FEFFGHHGE;H>GEFHFFFGFFGFFFGEFGFGFGFF NM:i:1 AS:i:40
+HS21_09876:2:1211:5990:82312#83 0 AE004091 3185 54 1S43M * 0 0 TTTTCGGTCACCGCGGTGCGCAACCTGCACCCGGTGACCCTCTC HGFEH0FFDDDGCF7GFD1GCFGFGGFGFFGHEFF?FFFEEDEE NM:i:0 AS:i:43
+HS21_09876:2:2103:19946:55809#83 0 AE004091 3958 54 1S43M * 0 0 GGGTCATAACGCCGCGGAGATTCTCTCGCGCGGTCAGCAGAAGC HHEAE'EFFEGGGFHEFAHGFHG at GEFHFEGFGFFF<FGEEDCE NM:i:0 AS:i:43
+HS21_09876:2:1104:10740:37072#83 0 AE004091 7026 54 1S43M * 0 0 CCCACCGACGGCTCCGGATGGCTGACCCGCTGCTGGATGGGGCT HHFAE,FIGDEG;FHFFHH>FAGGFFF;><GHA9<F<FGE=F at C NM:i:0 AS:i:43
+HS21_09876:2:2201:4547:41892#83 0 AE004091 7026 54 1S43M * 0 0 CCCACCGACGGCTCCGGATGGCTGACCCGCTGCTGGATGGGGCT GGEEE7EFGEDGEDHGGAHFGHGFDGFCFEGFAFFFDFBEEEDE NM:i:0 AS:i:43
+HS21_09876:2:2213:12056:100809#83 0 AE004091 7059 54 1S43M * 0 0 GGGATGGGGCTGATCTCGGCCATGGTCTCGCTGACCCAGGCTTC BFEE?,B>DFG=EDF:GHHEG6GGDGFFFFGGF6FFEFGC1BFF NM:i:0 AS:i:43
diff --git a/t/data/Map/smallref.fa b/t/data/Map/smallref.fa
new file mode 100644
index 0000000..58dcfe9
--- /dev/null
+++ b/t/data/Map/smallref.fa
@@ -0,0 +1,165 @@
+>AE004091 AE004091.2 Pseudomonas aeruginosa PAO1, complete genome.
+tttaaagagaccggcgattctagtgaaatcgaacgggcaggtcaatttccaaccagcgat
+gacgtaatagatagatacaaggaagtcatttttcttttaaaggatagaaacggttaatgc
+tcttgggacggcgcttttctgtgcataactcgatgaagcccagcaattgcgtgtttctcc
+ggcaggcaaaaggttgtcgagaaccggtgtcgaggctgtttccttcctgagcgaagcctg
+gggatgaacgagatggttatccacagcggttttttccacacggctgtgcgcagggatgta
+cccccttcaaagcaagggttatccacaaagtccaggacgaccgtccgtcggcctgcctgc
+ttttattaaggtcttgatttgcttggggcctcagcgcatcggcatgtggataagtccggc
+ccgtccggctacaataggcgcttatttcgttgtgccgcctttccaatctttgggggatat
+ccgtgtccgtggaactttggcagcagtgcgtggatcttctccgcgatgagctgccgtccc
+aacaattcaacacctggatccgtcccttgcaggtcgaagccgaaggcgacgaattgcgtg
+tgtatgcacccaaccgtttcgtcctcgattgggtgaacgagaaatacctcggtcggcttc
+tggaactgctcggtgaacgcggcgagggtcagttgcccgcgctttccttattaataggca
+gcaagcgtagccgtacgccgcgcgccgccatcgtcccatcgcagacccacgtggctcccc
+cgcctccggttgctccgccgccggcgccagtgcagccggtatcggccgcgcccgtggtag
+tgccacgtgaagagctgccgccagtgacgacggctcccagcgtgtcgagcgatccctacg
+agccggaagaacccagcatcgatccgctggccgccgccatgccggctggagcagcgcctg
+cggtgcgcaccgagcgcaacgtccaggtcgaaggtgcgctgaagcacaccagctatctca
+accgtaccttcaccttcgagaacttcgtcgagggcaagtccaaccagttggcccgcgccg
+ccgcctggcaggtggcggacaacctcaagcacggctacaacccgctgttcctctacggtg
+gcgtcggtctgggcaagacccacctgatgcatgcggtgggcaaccacctgctgaagaaga
+acccgaacgccaaggtggtctacctgcattcggaacgtttcgtcgcggacatggtgaagg
+ccttgcagctcaacgccatcaacgaattcaagcgcttctaccgctcggtggacgcactgt
+tgatcgacgacatccagttcttcgcccgtaaggagcgctcccaggaggagttcttccaca
+ccttcaatgcccttctcgaaggcggccagcaggtgatcctcaccagcgaccgctatccga
+aggaaatcgaaggcctggaagagcggctgaaatcccgcttcggctggggcctgacggtgg
+ccgtcgagccgccggaactggaaacccgggtggcgatcctgatgaagaaggccgagcagg
+cgaagatcgagctgccgcacgatgcggccttcttcatcgcccagcgcatccgttccaacg
+tgcgtgaactggaaggtgcgctgaagcgggtgatcgcccactcgcacttcatgggccggc
+cgatcaccatcgagctgattcgcgagtcgctgaaggacctgttggcccttcaggacaagc
+tggtcagcatcgacaacatccagcgcaccgtcgccgagtactacaagatcaagatatccg
+atctgttgtccaagcggcgttcgcgctcggtggcgcgcccgcgccaggtggccatggcgc
+tctccaaggagctgaccaaccacagcctgccggagatcggcgtggccttcggcggtcggg
+atcacaccacggtgttgcacgcctgtcgtaagatcgctcaacttagggaatccgacgcgg
+atatccgcgaggactacaagaacctgctgcgtaccctgacaacctgacgcagcccacgag
+gcaagggactagaccatgcatttcaccattcaacgcgaagccctgttgaaaccgctgcaa
+ctggtcgccggcgtcgtggaacgccgccagacattgccggttctctccaacgtcctgctg
+gtggtcgaaggccagcaactgtcgctgaccggcaccgacctcgaagtcgagctggttggt
+cgcgtggtactggaagatgccgccgaacccggcgagatcaccgtaccggcgcgcaagctg
+atggacatctgcaagagcctgccgaacgacgtgctgatcgacatccgtgtcgaagagcag
+aaacttctggtgaaggccgggcgtagccgcttcaccctgtccaccctgccggccaacgat
+ttccccaccgtagaggaaggtcccggctcgctgaacttcagcattgcccagagcaagctg
+cgtcgcctgatcgaccgcaccagcttcgccatggcccagcaggacgtgcgttactacctc
+aacggcatgctgctggaagtgaacggcggcaccctgcgctccgtcgccaccgacggccac
+cgactggccatgtgctcgctggatgcgcagatcccgtcgcaggaccgccaccaggtgatc
+gtgccgcgcaaaggcatcctcgaactggctcgtctgctcaccgagcaggacggcgaagtc
+ggcatcgtcctgggccagcaccatatccgtgccaccactggcgaattcaccttcacttcg
+aagctggtggacggcaagttcccggactacgagcgtgtactgccgcgcggtggcgacaag
+ctggtggtcggtgaccgccagcaactgcgcgaagccttcagccgtaccgcgatcctctcc
+aacgagaagtaccgcggcattcgcctgcagctttccaacggtttgctgaaaatccaggcg
+aacaacccggagcaggaagaggccgaggaagaagtgcaggtcgagtacaacggcggcaac
+ctggagataggcttcaacgtcagttacctgctcgacgtgctgggtgtgatcggtaccgag
+caggtccgcttcatcctttccgattccaacagcagcgccctggtccacgaggccgacaat
+gacgattctgcctatgtcgtcatgccgatgcgcctctaaacatactgaatgtccctgacc
+cgcgtttcggtcaccgcggtgcgcaacctgcacccggtgaccctctccccctccccccgc
+atcaacatcctctacggcgacaacggcagcggcaagaccagcgtgctcgaagccatccac
+ctgctgggcctggcgcgttcattccgcagtgcgcgcttgcagccggtgatccagtatgag
+gaagcggcctgcaccgtattcggccaggtgatgttggccaacggcatcgccagcaacctg
+gggatttcccgtgagcgccagggcgagttcaccatccgcatcgatgggcagaacgcccgg
+agtgcggctcaattggcggaaactctcccactgcaactgatcaacccggacagctttcgg
+ttgctcgagggagcgccgaagatccggcgacagttcctcgattggggagtgttccacgtg
+gaacctcggtttctgcccgtctggcagcgcctgcagaaggcgctgcgccagcggaactcc
+tggctccggcatggtaaactggaccccgcgtcgcaagcggcctgggaccgggaattgagc
+ctggccagcgatgagatcgatgcctaccgcagaagctatatccaggcgttgaaaccggta
+ttcgaggaaacactcgccgaattggtttcactggatgacctgacccttagctactaccga
+ggctgggacaaggaccgggacctcctggaggttctggcttccagcctgttgcgcgaccag
+cagatgggccacacccaggcgggaccgcagcgtgcggatcttcgcatacggttggcaggt
+cataacgccgcggagattctctcgcgcggtcagcagaagctggtggtatgcgccctgcgc
+atcgcccaaggccatctgatcaatcgcgccaagcgcggacagtgcgtctacctggtggac
+gacctgccctcggaactggatgagcagcatcgaatggctctttgccgcttgcttgaagat
+ttgggttgccaggtattcatcacctgcgtggacccgcaactattgaaagacggctggcgc
+acggatacgccggtatccatgttccacgtggaacatggaaaagtctctcagaccacgacc
+atcgggagtgaagcatgagcgagaacaacacgtacgactcttccagcatcaaggtgctga
+aggggctggatgccgtacgcaagcgccccggcatgtacatcggcgacaccgacgatggca
+ccggtctgcaccacatggtgttcgaggtggtggataactccatcgacgaagcgctggccg
+gttactgcagcgaaatcagcatcaccatccatacggatgagtcgatcactgtccgcgaca
+atggacgcggtattccggtggatatccacaaggaagaaggggtttctgcggcggaagtga
+tcatgaccgtcctccacgccggcggcaagttcgacgacaacacctacaaggtgtccggcg
+gcttgcacggtgtgggcgtctcggtggtgaacgcgctgtcccatgaactacgcctgacca
+tccgtcgccacaacaaggtctgggaacaggtctaccaccacggcgttccgcagttcccac
+tgcgcgaagtgggcgagaccgatggctccggcaccgaagttcacttcaagccgtccccgg
+agaccttcagcaacatccacttcagttgggacatcctggccaagcgcatccgcgagctgt
+ccttcctcaactccggcgtcggcatcctgctgcgcgacgagcgtaccggcaaggaggagc
+tgttcaagtacgaaggcggtctgaaggccttcgtcgagtacctgaacaccaacaagaccg
+cggtgaacgaggtattccacttcaacgtccagcgtgaagaggacggcgtgggtgtggaag
+tcgccttgcagtggaacgacagcttcaacgagaacctgctctgcttcaccaacaacatcc
+cgcagcgtgacggcggcacccacctggccggtttccgttcggcgctgacgcgtaacctga
+acaactacatcgaggccgaaggcctggcgaagaagttcaagatcgccaccaccggcgacg
+atgcccgcgaaggcctcaccgcgatcatctcggtgaaggtaccggacccgaagttcagct
+cgcagaccaaggacaagctggtctcctccgaggtgaagactgcggtggaacaggagatgg
+gcaagtacttcgccgacttcctgctggagaatcccaacgaagccaaggccgtggtcggca
+agatgatcgacgccgcccgtgcccgcgaggccgcgcgcaaggcgcgcgagatgacccgcc
+gcaagggcgcgctggacatcgccggcctgcccggcaaactggccgattgccaggaaaagg
+acccggcgctctccgaactgtacatcgtggagggtgactccgcgggcggttccgccaagc
+agggccgcaatcgccggacccaggcgatcctgccgctcaagggcaagatcctcaacgtcg
+aaaaggcgcgcttcgacaagatgctctcctcccaggaggtcggtacgctgatcaccgccc
+tgggctgtggcatcggccgcgaggaatacaacatcgacaagctgcgctaccacaacatca
+tcatcatgaccgatgctgacgtcgacggttcgcacatccgcaccctgctgttgaccttct
+tcttccgccagatgcccgagctgatcgagcgtggctacatctacatcgcccagcccccgt
+tgtacaaggtcaagcgcggcaagcaggagcagtacatcaaggacgaccaggccatggaag
+agtacatgacccagtcggccctggaagacgccagcctgcacgtcaacgagcacgctccgg
+gcctgtccggggcggcgctggagaaactggtcaacgagtatcgcggggtgatcgccaccc
+tcaagcgcctgtcgcgcctgtacccccaggagctgaccgagcacttcatctacctgccta
+ccgtgtcggtggacgacctggctaacgagtcggccatgcagggctggttggagaagttcc
+aggcgcgcctgaccgccgccgagaagtccggcctgacctacaaggccagcctgcgcgaag
+accgcgagcgccacctgtggctgcccgaggtggaactggtggcccacggcctgtccagct
+acgtcaccttcaaccgtgacttcttcgccagcaatgactaccgctcggtgtcgctgctcg
+gcgaccagctgaacagcctgctggaagacggcgcctacgtgcagaagggtgagcgcaagc
+gcccgatcagcgccttcaaggacggcctggactggctgatggccgaaggtaccaagcgcc
+acagcatccagcgatacaaggggctgggcgagatgaaccctgagcagctgtgggaaacca
+ccatggatccgaacgtccggcgcatgctcaaggtgaccatcgaggatgccatcgccgccg
+accagatcttcaacaccctgatgggcgatgccgtggagccgcgccgcgacttcatcgaaa
+gcaacgcgctggcggtgtcgaacctggacgtgtgacaggtcggcagaccgaccctcatgg
+aaaccccggcctggcgccggggttttctttttgcgccaggtagcctggatacgggcgcca
+ggggtgccttgccaaggtgtggccgagccccggttactcgccggcattggcaccctggac
+ccgggcctcctggcggcgtggcaccgcttctgtgggcagcggtcgccggtcggttcggtc
+gatcgttgccagccggccttgctttgcgcctcgcgtgaaaacaagaagccccgctatggc
+ggggcttcttttatcgaatcggcgcacagtacgccttgcagggggctttgcggcccttca
+cgagaccaccgacggctccggatggctgacccgctgctggatggggctgatctcggccat
+ggtctcgctgacccaggcttcggcgcgctggtttagctcggcgatggcgcgcgggccttc
+gccttcggcgtgcatggccgggccgatcaccacctggatggtgcccgggtacttggccca
+gccggccttgggccaatactgcccggcgttgtgggcgatcggcagtaccggtagcccggc
+gttgaccgccagggcggtgccgccgcgggagaacttgcccatctgccccaccggaatacg
+cgtgccttccgggaagatcagcacccaggcgcctttcttcaggcactcgtcgccctgctt
+ggccagttgcttgagggccagcttgggctggctgcggtcgatggcgatgggcttgagcag
+ggccagggcccagccgaagaacggcacgtagagcagctcgcgcttgagtacctggctgag
+tggctcgaagaagccggagaggaagaaggtttcccaggtgctctggtgcttggagaggat
+cacgcagggcttttccgggatgttctccagtccgcgcacctcgtagcggatgccggcgac
+cacgcgggtcagccagatcgcgaagcggcaccagttctgtaccacgaagcggtagcgggc
+gcggaacggcaggatcggcgcgatgaagaagctgagggtgccccagacgaacgcgctggc
+ggacagcagcaggtaaaagaggacggttctgatggcctgcactgtcgacatgtattctga
+ccttactgaagtaatgcgctggcgactgccgccagatcgtcgaatatcagggtgccctct
+ggcaagggcttgcccagcgtacgtacaccttttccggtctttaccaataccggctgacaa
+tcgacggcccgcgccgcctccaggtcaccgatgctgtcgccgacgaaccagatacccgac
+agatcgaccccgtagtgctcgccgatctgccgcagcatacccggcttcggcttgcggcag
+tcgcaaccgtcgtccggtccatgcggacaatagacgatgaggccgacctcgccgccctgc
+tccgcgaccagttcgcgcaagcgcgcatgcatggcctcgagcactgccaggtcgtaatag
+ccacgggcgatgccggactggttggtagccaccgcgacggtccagccggcctggctcagg
+cgggcgatggcctcgatcgagctggggatggggatccactcgtcgagggtcttgatgtaa
+tcgtcggagtcgaggttgatgactccatcgcggtcgagaatcagcagggaacgggacatc
+gatgcgcagttggccatgaacggaaaggatcgattctacctcagccagccggagcatcgc
+ggatggatcgacgagccccctacgctggacaatctgtactagattcaataatggcaatgg
+aatggcaatcccaggccagggagtcatttggcacgcagcagtgggtgtctcggagtacgt
+gcgaaccccttggcgggtggatcaccggagtaacgcagtaagcgcctatcgcatgccagc
+acggccgaccggccgtgtttccaccacaggtggagcgggcgtgacgacggggagttccgg
+ggcgtctgcccgttcccaaggacggtaaccgtgaaacgcctgaaaaagacactgcacctt
+tcaagcttgtccctcgcttccctggctctttcttccgccgccctggcggccgctccggtc
+atgctcgaccagggcaaggaatggaccgaaagccaccgccaggacttctacagccgcgac
+cagggctcgcaggtgatgcccctgccctggctcaaggcgttgcgacagccggatggaacg
+cctttcctcgccgacagcctggcccgctacggctatttgcccaaccccaaggcgcccgcg
+gaaggcctgccggtgggcttcaccgtagccggcacgggcgcccggcagatggtcggcatg
+acctgttcggcctgccatacccggcagatcgaggtgaagggcactgcctatcggatcgac
+ggcggtccggcgatcgtcgacttccaggcattcctcgccgacctcgatcgggccgtggga
+ccgctgaccagcgatgacgccgccttcgacgccttcgccaagccgatcctcggggccaat
+ccgcctcccggtgcgcgcgacgctctgctcgcggcggtgaaggaatggtacgagccctat
+cacacgctgatcgagcgcgcgctgcccaaggacacctggggaccggcgcggctggacgcg
+gtatcgatgatcttcaaccgccttaccgggctggatatcggcaccgcgccgccctacctg
+attcccgacaacatcaaggcggccgatgcgccggtgcgctatccgttcctgtggaacgcg
+gcgcggcagaacaagacccagtggcccggcttcgccgccaacggcaacgacctgctcggc
+ctggcgcgcaatgtcggcgaggtctacggggtgttcgccaccttccacccgcagaagagc
+aagttccacctgctgggcatggactacctgaagatcaactcggccaacttccacgggctg
+ggcaagctggaagacctgatcaagaagatcggcccgccgaagtggccctgggcggtggac
+aagcacctggccaggaaaggcgcgctgatcttcgcccgcaagaccgacgaaggtggctgc
+gtggagtgccacggcatccggatcaaggacctggtgctttgggacactccgctgagggac
+gtcggcagcgacagccgccagcacgccatcctcgatggccaggtgcagaccggcgtgatg
diff --git a/t/data/Map/test.fastq b/t/data/Map/test.fastq
new file mode 100644
index 0000000..ed95c28
--- /dev/null
+++ b/t/data/Map/test.fastq
@@ -0,0 +1,92 @@
+ at HS21_09876:1:1105:9650:48712#83
+GGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG
++
+HHCEE8EEFGFFGFIFGGFGEEHFFFGGGFGFGEGEEEFGFGFF
+ at HS21_09876:1:1106:8638:38957#83
+GGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG
++
+HHCEF7FHFFFFGFEGEFFEHEGEGFGGGEGFGFGGFEHGFEFD
+ at HS21_09876:1:1204:19746:42237#83
+GGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG
++
+HHCBF2GGFFEFGEEFFFEEHEEHFFFFGFGFFFGGGGHGFEFF
+ at HS21_09876:1:2210:2408:11148#83
+GGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG
++
+HHCBF,GGFF<FEHFFEGFGFEEEGFGGGFGFFFGGGFHGFEFF
+ at HS21_09876:1:2210:16541:84795#83
+GGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG
++
+FDB at F%GEFDCFGHE<FD>GEEEGFFGGFFGFFBG8FGFGFEEE
+ at HS21_09876:1:1201:6607:66324#83
+CCCACCGACGGCTCCGGATGGCTGACCCGCTGCTGGATGGGGCT
++
+HHCDF8EHFEGFAGIFEDEGFEFFGFEGFEGFGFGEGGHGFEFD
+ at HS21_09876:1:2102:12312:75235#83
+CCCACCGACGGCTCCGGATGGCTGACCCGCTGCTGGATGGGGCT
++
+HHCDH8EHFFGFAGDFIEEEGEFFGFFGFFGFFEGEFFFGFEFE
+ at HS21_09876:1:1106:16061:54950#83
+GGGATGGGGCTGATCTCGGCCATGGTCTCGCTGACCCAGGCTTC
++
+FHCBD4GHFFGFEEC<FCGEFEGHGFFEGFGFFFGDFGDGFDFF
+ at HS21_09876:1:2101:14032:85058#83
+GAATCGAGCGCGCGCTGCCCAAGGACACCTGGGGACCGGCGCGG
++
+HHCEH5GHFFFFGEDC;GHFFEHGGFFGFEGFFJGDGFHGFGFF
+ at HS21_09876:1:2111:11125:6617#83
+GAATCGAGCGCGCGCTGCCCAAGGACACCCGGGGACCGGCGCGG
++
+HG2BH8HEFGFFGH;EFGHFGEGGGFEGGFGFFGGDGEHGFEFF
+ at HS21_09876:1:2202:3163:76297#83
+GAATCGAGCGCGCGCTGCCCAAGGACACCTGGGGACCGGCGCGG
++
+HHCEH8EGFEGFGEIFDGHFGEHECFFGGFGFFDGEGGHGFEFF
+ at HS21_09876:1:2205:20175:3703#83
+GAATCGAGCGCGCGCTGCCCAAGGACACCTGGGGACCGGCGCGG
++
+H>8BI2A<FEFFGCE<EDFDDEHH?F=GFFGF3FGEGGHGDDFE
+ at HS21_09876:1:2205:6527:34286#83
+GAATCGAGCGCGCGCTGCCCAAGGACACCTGGGGACCGGCGCGG
++
+HGBDH4HHFGFFGFDFDGHEGEHGGFEGFJGFGGGEGFHGFFFF
+ at HS21_09876:1:1201:10071:48582#83
+GCCCCAAGGACACCTGGGGACCGGCGCGGCTGGACGCGGTATCG
++
+HHCDI8EHFGFFGEFFFGGFGEFGGFFGGFGFG8G8ECFGFFAE
+ at HS21_09876:1:2107:20205:78513#83
+GCCCCGAGGACACCTGGGGACCGGCGCGGCTGGACGCGGTATCG
++
+HHCEI%EGFFEFEGIFGDGFE>GDGFFGFEBFGDGEGEH;EFDD
+ at HS21_09876:1:2207:12005:97464#83
+GCCCCAAGGACACCTGGGGACCGGCGCGGCTGGACGCGGTATCG
++
+HGBBH0EG?<FFEHCBGEE>DEDF?FFGFE1FE89EEGD;;@?D
+ at HS21_09876:1:1208:12319:4648#83
+CAACCTGGGGACCGGCGCGGCTGGACGCGGTATCGATGATCTTC
++
+AA>EF8EIFFGFGEC<F;FEEEG3?FFG/E=F?DG89C=GAD?E
+ at HS21_09876:1:2209:14024:59451#83
+CCCGGTGCGCTACCCGTTCCTGTGGAACGCGGCGCGGCAGAACA
++
+FHCBF.E<FEFFGHHGE;H>GEFHFFFGFFGFFFGEFGFGFGFF
+ at HS21_09876:2:1211:5990:82312#83
+TTTTCGGTCACCGCGGTGCGCAACCTGCACCCGGTGACCCTCTC
++
+HGFEH0FFDDDGCF7GFD1GCFGFGGFGFFGHEFF?FFFEEDEE
+ at HS21_09876:2:2103:19946:55809#83
+GGGTCATAACGCCGCGGAGATTCTCTCGCGCGGTCAGCAGAAGC
++
+HHEAE'EFFEGGGFHEFAHGFHG at GEFHFEGFGFFF<FGEEDCE
+ at HS21_09876:2:1104:10740:37072#83
+CCCACCGACGGCTCCGGATGGCTGACCCGCTGCTGGATGGGGCT
++
+HHFAE,FIGDEG;FHFFHH>FAGGFFF;><GHA9<F<FGE=F at C
+ at HS21_09876:2:2201:4547:41892#83
+CCCACCGACGGCTCCGGATGGCTGACCCGCTGCTGGATGGGGCT
++
+GGEEE7EFGEDGEDHGGAHFGHGFDGFCFEGFAFFFDFBEEEDE
+ at HS21_09876:2:2213:12056:100809#83
+GGGATGGGGCTGATCTCGGCCATGGTCTCGCTGACCCAGGCTTC
++
+BFEE?,B>DFG=EDF:GHHEG6GGDGFFFFGGF6FFEFGC1BFF
diff --git a/t/data/Parsers/test.bam b/t/data/Parsers/test.bam
new file mode 100644
index 0000000..6ee5bbd
Binary files /dev/null and b/t/data/Parsers/test.bam differ
diff --git a/t/data/Parsers/test.fastq b/t/data/Parsers/test.fastq
new file mode 100644
index 0000000..1953324
--- /dev/null
+++ b/t/data/Parsers/test.fastq
@@ -0,0 +1,8 @@
+ at HS21_09876:1:1105:9650:48712#83
+TAAGAGTCAGGGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG
++
+CCCFFFFFHHHHCEE8EEFGFFGFIFGGFGEEHFFFGGGFGFGEGEEEFGFGFF
+ at HS21_09876:1:1106:8638:38957#83
+TAAGAGTCAGGGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG
++
+B at CFFFFFHHHHCEF7FHFFFFGFEGEFFEHEGEGFGGGEGFGFGGFEHGFEFD
diff --git a/t/data/RemoveTags/expected.rm.1mm.caa.fastq b/t/data/RemoveTags/expected.rm.1mm.caa.fastq
new file mode 100644
index 0000000..283f502
--- /dev/null
+++ b/t/data/RemoveTags/expected.rm.1mm.caa.fastq
@@ -0,0 +1,40 @@
+ at IL2_4334:7:5:6843:6843
+CTGCGTGTTGCCGATATTCTGGAAAGCA
++
+B;FF8>CCF:=CC-7(C>/22C:4;<=;
+ at IL2_4334:7:5:18259:13400
+CTGCGTGTTGCCGATATTCTGGAAAGCA
++
+B88A?C@@A;;B at +21AA/38><8=C;>
+ at IL2_4334:7:15:5608:3756
+CTGCGTGTTGCCGATATTTTGGAAAGCA
++
+88@=@AB6=:?;:-08C=&,6C@:8A4=
+ at IL2_4334:7:18:16351:15714
+CTGCGTGTTGCCGATATTCTGGAAAGCA
++
+<>FCBFF=:B7?A+4/A>(22@?64?5@
+ at IL2_4334:7:39:12877:7020
+CTGCGTGTTGCCGATATTCTGGAAAGCA
++
+=@;FFF=FFA<AC071??/84C=;3?75
+ at IL2_4334:7:42:14437:19550
+CTGCGTGTTGCCGATATTCTGGAAAGCA
++
+8;DF;CF;F;8A?2<6;:18;81;<;8C
+ at IL2_4334:7:53:4426:3757
+CTGCGTGTTGCCGATATTCTGGAAAGCA
++
+:@AF at A>?F@<F=47. at A,11D<45D9<
+ at IL2_4334:7:79:9021:16833
+CTGCGTGTTGCCGATATTCTGGAAAGCA
++
+BFA?ABCC>86 at B:C?A>6=:6<CB:>C
+ at IL2_4334:7:82:17494:18362
+CTGCGTGTTGCCGATATTCTGGAAAGCA
++
+>8=CB@:C:AB=7410=C-46;,75>>F
+ at IL2_4334:7:84:7230:17356
+CTGCGTGTTGCCGATATTCTGGAAAGCA
++
+D>8:=>=?@48 at 87A4@F6>??BF??B@
diff --git a/t/data/RemoveTags/expected.rm.caa.fastq b/t/data/RemoveTags/expected.rm.caa.fastq
new file mode 100644
index 0000000..14adee6
--- /dev/null
+++ b/t/data/RemoveTags/expected.rm.caa.fastq
@@ -0,0 +1,40 @@
+ at IL2_4334:7:5:6843:6843
+CGACGTTTTCTGCGTGTTGCCGATATTCTGGAAAGCA
++
+=8>;A<@>=B;FF8>CCF:=CC-7(C>/22C:4;<=;
+ at IL2_4334:7:5:18259:13400
+CACCGTTTTCTGCGTGTTGCCGATATTCTGGAAAGCA
++
+<8:=B>=B(B88A?C@@A;;B at +21AA/38><8=C;>
+ at IL2_4334:7:15:5608:3756
+CTGCGTGTTGCCGATATTTTGGAAAGCA
++
+88@=@AB6=:?;:-08C=&,6C@:8A4=
+ at IL2_4334:7:18:16351:15714
+CTGCGTGTTGCCGATATTCTGGAAAGCA
++
+<>FCBFF=:B7?A+4/A>(22@?64?5@
+ at IL2_4334:7:39:12877:7020
+CTGCGTGTTGCCGATATTCTGGAAAGCA
++
+=@;FFF=FFA<AC071??/84C=;3?75
+ at IL2_4334:7:42:14437:19550
+CTGCGTGTTGCCGATATTCTGGAAAGCA
++
+8;DF;CF;F;8A?2<6;:18;81;<;8C
+ at IL2_4334:7:53:4426:3757
+CTGCGTGTTGCCGATATTCTGGAAAGCA
++
+:@AF at A>?F@<F=47. at A,11D<45D9<
+ at IL2_4334:7:79:9021:16833
+CTGCGTGTTGCCGATATTCTGGAAAGCA
++
+BFA?ABCC>86 at B:C?A>6=:6<CB:>C
+ at IL2_4334:7:82:17494:18362
+CTGCGTGTTGCCGATATTCTGGAAAGCA
++
+>8=CB@:C:AB=7410=C-46;,75>>F
+ at IL2_4334:7:84:7230:17356
+CTGCGTGTTGCCGATATTCTGGAAAGCA
++
+D>8:=>=?@48 at 87A4@F6>??BF??B@
diff --git a/t/data/RemoveTags/expected.rm.tna.fastq b/t/data/RemoveTags/expected.rm.tna.fastq
new file mode 100644
index 0000000..7219671
--- /dev/null
+++ b/t/data/RemoveTags/expected.rm.tna.fastq
@@ -0,0 +1,12 @@
+ at IL2_4334:6:120:19845:10197
+GTATTACTCTGCATCANTNAANNGAGA
++
+;1CB7F:BCC==7 at 5A)=%76%%0B67
+ at IL2_4334:6:120:19846:21043
+TGTCTAGGGCATCACTNANGGNNGAGG
++
+:A>C?@@??CC@?:6;)5%>9%%;;;<
+ at IL2_4334:6:120:19846:19594
+ATCCTATGGGGCTGAANTNTNNNGTGA
++
+C<;@=5444@:B;>?*%)%4%%%?161
diff --git a/t/data/RemoveTags/sample.caa.fastq b/t/data/RemoveTags/sample.caa.fastq
new file mode 100644
index 0000000..2781abe
--- /dev/null
+++ b/t/data/RemoveTags/sample.caa.fastq
@@ -0,0 +1,40 @@
+ at IL2_4334:7:5:6843:6843
+CGACGTTTTCTGCGTGTTGCCGATATTCTGGAAAGCA
++
+=8>;A<@>=B;FF8>CCF:=CC-7(C>/22C:4;<=;
+ at IL2_4334:7:5:18259:13400
+CACCGTTTTCTGCGTGTTGCCGATATTCTGGAAAGCA
++
+<8:=B>=B(B88A?C@@A;;B at +21AA/38><8=C;>
+ at IL2_4334:7:15:5608:3756
+CAACGTTTTCTGCGTGTTGCCGATATTTTGGAAAGCA
++
+9AA9:17<988@=@AB6=:?;:-08C=&,6C@:8A4=
+ at IL2_4334:7:18:16351:15714
+CAACGTTTTCTGCGTGTTGCCGATATTCTGGAAAGCA
++
+<===?;=@<<>FCBFF=:B7?A+4/A>(22@?64?5@
+ at IL2_4334:7:39:12877:7020
+CAACGTTTTCTGCGTGTTGCCGATATTCTGGAAAGCA
++
+=B?=<>ACB=@;FFF=FFA<AC071??/84C=;3?75
+ at IL2_4334:7:42:14437:19550
+CAACGTTTTCTGCGTGTTGCCGATATTCTGGAAAGCA
++
+<7=B8 at B=;8;DF;CF;F;8A?2<6;:18;81;<;8C
+ at IL2_4334:7:53:4426:3757
+CAACGTTTTCTGCGTGTTGCCGATATTCTGGAAAGCA
++
+=B<7<:9B@:@AF at A>?F@<F=47. at A,11D<45D9<
+ at IL2_4334:7:79:9021:16833
+CAACGTTTTCTGCGTGTTGCCGATATTCTGGAAAGCA
++
+;A:7A;CBFBFA?ABCC>86 at B:C?A>6=:6<CB:>C
+ at IL2_4334:7:82:17494:18362
+CAACGTTTTCTGCGTGTTGCCGATATTCTGGAAAGCA
++
+<79:<9;7<>8=CB@:C:AB=7410=C-46;,75>>F
+ at IL2_4334:7:84:7230:17356
+CAACGTTTTCTGCGTGTTGCCGATATTCTGGAAAGCA
++
+DADFDFFDDD>8:=>=?@48 at 87A4@F6>??BF??B@
diff --git a/t/data/RemoveTags/sample.tna.fastq b/t/data/RemoveTags/sample.tna.fastq
new file mode 100644
index 0000000..e410d63
--- /dev/null
+++ b/t/data/RemoveTags/sample.tna.fastq
@@ -0,0 +1,12 @@
+ at IL2_4334:6:120:19845:10197
+TNAGAGACAGGTATTACTCTGCATCANTNAANNGAGA
++
+:)::9:9;BA;1CB7F:BCC==7 at 5A)=%76%%0B67
+ at IL2_4334:6:120:19846:21043
+TNAGAGACAGTGTCTAGGGCATCACTNANGGNNGAGG
++
+<)72:19:?>:A>C?@@??CC@?:6;)5%>9%%;;;<
+ at IL2_4334:6:120:19846:19594
+TNAGAGACAGATCCTATGGGGCTGAANTNTNNNGTGA
++
+:)7:782?=AC<;@=5444@:B;>?*%)%4%%%?161
diff --git a/t/data/RunTradis/expected.1mm.plot.gz b/t/data/RunTradis/expected.1mm.plot.gz
new file mode 100644
index 0000000..d340513
Binary files /dev/null and b/t/data/RunTradis/expected.1mm.plot.gz differ
diff --git a/t/data/RunTradis/expected.plot.gz b/t/data/RunTradis/expected.plot.gz
new file mode 100644
index 0000000..ca5111c
Binary files /dev/null and b/t/data/RunTradis/expected.plot.gz differ
diff --git a/t/data/RunTradis/filelist.txt b/t/data/RunTradis/filelist.txt
new file mode 100644
index 0000000..cc9c0cc
--- /dev/null
+++ b/t/data/RunTradis/filelist.txt
@@ -0,0 +1,2 @@
+test.tagged.fastq
+test2.tagged.fastq
diff --git a/t/data/RunTradis/filtered.fastq b/t/data/RunTradis/filtered.fastq
new file mode 100644
index 0000000..5fbeb3f
--- /dev/null
+++ b/t/data/RunTradis/filtered.fastq
@@ -0,0 +1,92 @@
+ at HS21_09876:1:1105:9650:48712#83
+TAAGAGTCAGGGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG
++
+CCCFFFFFHHHHCEE8EEFGFFGFIFGGFGEEHFFFGGGFGFGEGEEEFGFGFF
+ at HS21_09876:1:1106:8638:38957#83
+TAAGAGTCAGGGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG
++
+B at CFFFFFHHHHCEF7FHFFFFGFEGEFFEHEGEGFGGGEGFGFGGFEHGFEFD
+ at HS21_09876:1:1204:19746:42237#83
+TAAGAGTCAGGGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG
++
+CCCFFFFFHHHHCBF2GGFFEFGEEFFFEEHEEHFFFFGFGFFFGGGGHGFEFF
+ at HS21_09876:1:2210:2408:11148#83
+TAAGAGTCAGGGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG
++
+BBCFFFFFHHHHCBF,GGFF<FEHFFEGFGFEEEGFGGGFGFFFGGGFHGFEFF
+ at HS21_09876:1:2210:16541:84795#83
+TAAGAGTCAGGGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG
++
+BCCFFFFFHHFDB at F%GEFDCFGHE<FD>GEEEGFFGGFFGFFBG8FGFGFEEE
+ at HS21_09876:1:1201:6607:66324#83
+TAAGAGTCAGCCCACCGACGGCTCCGGATGGCTGACCCGCTGCTGGATGGGGCT
++
+BCCDFBDEHHHHCDF8EHFEGFAGIFEDEGFEFFGFEGFEGFGFGEGGHGFEFD
+ at HS21_09876:1:2102:12312:75235#83
+TAAGAGTCAGCCCACCGACGGCTCCGGATGGCTGACCCGCTGCTGGATGGGGCT
++
+BCCDFFFFHHHHCDH8EHFFGFAGDFIEEEGEFFGFFGFFGFFEGEFFFGFEFE
+ at HS21_09876:1:1106:16061:54950#83
+TAAGAGTCAGGGGATGGGGCTGATCTCGGCCATGGTCTCGCTGACCCAGGCTTC
++
+BBBDFFFFHHFHCBD4GHFFGFEEC<FCGEFEGHGFFEGFGFFFGDFGDGFDFF
+ at HS21_09876:1:2101:14032:85058#83
+TAAGAGTCAGGAATCGAGCGCGCGCTGCCCAAGGACACCTGGGGACCGGCGCGG
++
+BCCDFFFFHHHHCEH5GHFFFFGEDC;GHFFEHGGFFGFEGFFJGDGFHGFGFF
+ at HS21_09876:1:2111:11125:6617#83
+TAAGAGTCAGGAATCGAGCGCGCGCTGCCCAAGGACACCCGGGGACCGGCGCGG
++
+BCCDDDDDFHHG2BH8HEFGFFGH;EFGHFGEGGGFEGGFGFFGGDGEHGFEFF
+ at HS21_09876:1:2202:3163:76297#83
+TAAGAGTCAGGAATCGAGCGCGCGCTGCCCAAGGACACCTGGGGACCGGCGCGG
++
+BCCDFDDDHHHHCEH8EGFEGFGEIFDGHFGEHECFFGGFGFFDGEGGHGFEFF
+ at HS21_09876:1:2205:20175:3703#83
+TAAGAGTCAGGAATCGAGCGCGCGCTGCCCAAGGACACCTGGGGACCGGCGCGG
++
+BCCDFFFEHHH>8BI2A<FEFFGCE<EDFDDEHH?F=GFFGF3FGEGGHGDDFE
+ at HS21_09876:1:2205:6527:34286#83
+TAAGAGTCAGGAATCGAGCGCGCGCTGCCCAAGGACACCTGGGGACCGGCGCGG
++
+BCCDFFFFHHHGBDH4HHFGFFGFDFDGHEGEHGGFEGFJGFGGGEGFHGFFFF
+ at HS21_09876:1:1201:10071:48582#83
+TAAGAGTCAGGCCCCAAGGACACCTGGGGACCGGCGCGGCTGGACGCGGTATCG
++
+CCCDFFFFHHHHCDI8EHFGFFGEFFFGGFGEFGGFFGGFGFG8G8ECFGFFAE
+ at HS21_09876:1:2107:20205:78513#83
+TAAGAGTCAGGCCCCGAGGACACCTGGGGACCGGCGCGGCTGGACGCGGTATCG
++
+BCCFFFFFHHHHCEI%EGFFEFEGIFGDGFE>GDGFFGFEBFGDGEGEH;EFDD
+ at HS21_09876:1:2207:12005:97464#83
+TAAGAGTCAGGCCCCAAGGACACCTGGGGACCGGCGCGGCTGGACGCGGTATCG
++
+BCCDFFFFHHHGBBH0EG?<FFEHCBGEE>DEDF?FFGFE1FE89EEGD;;@?D
+ at HS21_09876:1:1208:12319:4648#83
+TAAGAGTCAGCAACCTGGGGACCGGCGCGGCTGGACGCGGTATCGATGATCTTC
++
+B=BDFFFDH>AA>EF8EIFFGFGEC<F;FEEEG3?FFG/E=F?DG89C=GAD?E
+ at HS21_09876:1:2209:14024:59451#83
+TAAGAGTCAGCCCGGTGCGCTACCCGTTCCTGTGGAACGCGGCGCGGCAGAACA
++
+BCCDFFFFHHFHCBF.E<FEFFGHHGE;H>GEFHFFFGFFGFFFGEFGFGFGFF
+ at HS21_09876:2:1211:5990:82312#83
+TAAGAGTCAGTTTTCGGTCACCGCGGTGCGCAACCTGCACCCGGTGACCCTCTC
++
+BCCFFFFFHHHGFEH0FFDDDGCF7GFD1GCFGFGGFGFFGHEFF?FFFEEDEE
+ at HS21_09876:2:2103:19946:55809#83
+TAAGAGTCAGGGGTCATAACGCCGCGGAGATTCTCTCGCGCGGTCAGCAGAAGC
++
+BBCFDEFFHHHHEAE'EFFEGGGFHEFAHGFHG at GEFHFEGFGFFF<FGEEDCE
+ at HS21_09876:2:1104:10740:37072#83
+TAAGAGTCAGCCCACCGACGGCTCCGGATGGCTGACCCGCTGCTGGATGGGGCT
++
+BBBDDFFFHHHHFAE,FIGDEG;FHFFHH>FAGGFFF;><GHA9<F<FGE=F at C
+ at HS21_09876:2:2201:4547:41892#83
+TAAGAGTCAGCCCACCGACGGCTCCGGATGGCTGACCCGCTGCTGGATGGGGCT
++
+BCCDFFFFHHGGEEE7EFGEDGEDHGGAHFGHGFDGFCFEGFAFFFDFBEEEDE
+ at HS21_09876:2:2213:12056:100809#83
+TAAGAGTCAGGGGATGGGGCTGATCTCGGCCATGGTCTCGCTGACCCAGGCTTC
++
+BBCDDDDDHDBFEE?,B>DFG=EDF:GHHEG6GGDGFFFFGGF6FFEFGC1BFF
diff --git a/t/data/RunTradis/mapped.sam b/t/data/RunTradis/mapped.sam
new file mode 100644
index 0000000..527cc1f
--- /dev/null
+++ b/t/data/RunTradis/mapped.sam
@@ -0,0 +1,26 @@
+ at HD VN:1.3 SO:unknown
+ at SQ SN:AE004091 LN:9840
+ at PG ID:smalt PN:smalt VN:0.7.4 CL:smalt map -x -r -1 -y 0.96 ref.index /Users/cc21/Development/repos/Bio-Tradis/t/data/RunTradis/notags.fastq
+HS21_09876:1:1105:9650:48712#83 0 AE004091 6698 54 1S43M * 0 0 GGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG HHCEE8EEFGFFGFIFGGFGEEHFFFGGGFGFGEGEEEFGFGFF NM:i:0 AS:i:43
+HS21_09876:1:1106:8638:38957#83 0 AE004091 6698 54 1S43M * 0 0 GGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG HHCEF7FHFFFFGFEGEFFEHEGEGFGGGEGFGFGGFEHGFEFD NM:i:0 AS:i:43
+HS21_09876:1:1204:19746:42237#83 0 AE004091 6698 54 1S43M * 0 0 GGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG HHCBF2GGFFEFGEEFFFEEHEEHFFFFGFGFFFGGGGHGFEFF NM:i:0 AS:i:43
+HS21_09876:1:2210:2408:11148#83 0 AE004091 6698 54 1S43M * 0 0 GGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG HHCBF,GGFF<FEHFFEGFGFEEEGFGGGFGFFFGGGFHGFEFF NM:i:0 AS:i:43
+HS21_09876:1:2210:16541:84795#83 0 AE004091 6698 54 1S43M * 0 0 GGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG FDB at F%GEFDCFGHE<FD>GEEEGFFGGFFGFFBG8FGFGFEEE NM:i:0 AS:i:43
+HS21_09876:1:1201:6607:66324#83 0 AE004091 7026 54 1S43M * 0 0 CCCACCGACGGCTCCGGATGGCTGACCCGCTGCTGGATGGGGCT HHCDF8EHFEGFAGIFEDEGFEFFGFEGFEGFGFGEGGHGFEFD NM:i:0 AS:i:43
+HS21_09876:1:2102:12312:75235#83 0 AE004091 7026 54 1S43M * 0 0 CCCACCGACGGCTCCGGATGGCTGACCCGCTGCTGGATGGGGCT HHCDH8EHFFGFAGDFIEEEGEFFGFFGFFGFFEGEFFFGFEFE NM:i:0 AS:i:43
+HS21_09876:1:1106:16061:54950#83 0 AE004091 7059 54 1S43M * 0 0 GGGATGGGGCTGATCTCGGCCATGGTCTCGCTGACCCAGGCTTC FHCBD4GHFFGFEEC<FCGEFEGHGFFEGFGFFFGDFGDGFDFF NM:i:0 AS:i:43
+HS21_09876:1:2101:14032:85058#83 0 AE004091 9250 54 2S42M * 0 0 GAATCGAGCGCGCGCTGCCCAAGGACACCTGGGGACCGGCGCGG HHCEH5GHFFFFGEDC;GHFFEHGGFFGFEGFFJGDGFHGFGFF NM:i:0 AS:i:42
+HS21_09876:1:2111:11125:6617#83 4 * 0 0 * * 0 0 GAATCGAGCGCGCGCTGCCCAAGGACACCCGGGGACCGGCGCGG HG2BH8HEFGFFGH;EFGHFGEGGGFEGGFGFFGGDGEHGFEFF NM:i:0 AS:i:0
+HS21_09876:1:2202:3163:76297#83 0 AE004091 9250 54 2S42M * 0 0 GAATCGAGCGCGCGCTGCCCAAGGACACCTGGGGACCGGCGCGG HHCEH8EGFEGFGEIFDGHFGEHECFFGGFGFFDGEGGHGFEFF NM:i:0 AS:i:42
+HS21_09876:1:2205:20175:3703#83 0 AE004091 9250 54 2S42M * 0 0 GAATCGAGCGCGCGCTGCCCAAGGACACCTGGGGACCGGCGCGG H>8BI2A<FEFFGCE<EDFDDEHH?F=GFFGF3FGEGGHGDDFE NM:i:0 AS:i:42
+HS21_09876:1:2205:6527:34286#83 0 AE004091 9250 54 2S42M * 0 0 GAATCGAGCGCGCGCTGCCCAAGGACACCTGGGGACCGGCGCGG HGBDH4HHFGFFGFDFDGHEGEHGGFEGFJGFGGGEGFHGFFFF NM:i:0 AS:i:42
+HS21_09876:1:1201:10071:48582#83 0 AE004091 9265 54 2S42M * 0 0 GCCCCAAGGACACCTGGGGACCGGCGCGGCTGGACGCGGTATCG HHCDI8EHFGFFGEFFFGGFGEFGGFFGGFGFG8G8ECFGFFAE NM:i:0 AS:i:42
+HS21_09876:1:2107:20205:78513#83 4 * 0 0 * * 0 0 GCCCCGAGGACACCTGGGGACCGGCGCGGCTGGACGCGGTATCG HHCEI%EGFFEFEGIFGDGFE>GDGFFGFEBFGDGEGEH;EFDD NM:i:0 AS:i:0
+HS21_09876:1:2207:12005:97464#83 0 AE004091 9265 54 2S42M * 0 0 GCCCCAAGGACACCTGGGGACCGGCGCGGCTGGACGCGGTATCG HGBBH0EG?<FFEHCBGEE>DEDF?FFGFE1FE89EEGD;;@?D NM:i:0 AS:i:42
+HS21_09876:1:1208:12319:4648#83 0 AE004091 9274 54 2S42M * 0 0 CAACCTGGGGACCGGCGCGGCTGGACGCGGTATCGATGATCTTC AA>EF8EIFFGFGEC<F;FEEEG3?FFG/E=F?DG89C=GAD?E NM:i:0 AS:i:42
+HS21_09876:1:2209:14024:59451#83 0 AE004091 9391 54 1S43M * 0 0 CCCGGTGCGCTACCCGTTCCTGTGGAACGCGGCGCGGCAGAACA FHCBF.E<FEFFGHHGE;H>GEFHFFFGFFGFFFGEFGFGFGFF NM:i:1 AS:i:40
+HS21_09876:2:1211:5990:82312#83 0 AE004091 3185 54 1S43M * 0 0 TTTTCGGTCACCGCGGTGCGCAACCTGCACCCGGTGACCCTCTC HGFEH0FFDDDGCF7GFD1GCFGFGGFGFFGHEFF?FFFEEDEE NM:i:0 AS:i:43
+HS21_09876:2:2103:19946:55809#83 0 AE004091 3958 54 1S43M * 0 0 GGGTCATAACGCCGCGGAGATTCTCTCGCGCGGTCAGCAGAAGC HHEAE'EFFEGGGFHEFAHGFHG at GEFHFEGFGFFF<FGEEDCE NM:i:0 AS:i:43
+HS21_09876:2:1104:10740:37072#83 0 AE004091 7026 54 1S43M * 0 0 CCCACCGACGGCTCCGGATGGCTGACCCGCTGCTGGATGGGGCT HHFAE,FIGDEG;FHFFHH>FAGGFFF;><GHA9<F<FGE=F at C NM:i:0 AS:i:43
+HS21_09876:2:2201:4547:41892#83 0 AE004091 7026 54 1S43M * 0 0 CCCACCGACGGCTCCGGATGGCTGACCCGCTGCTGGATGGGGCT GGEEE7EFGEDGEDHGGAHFGHGFDGFCFEGFAFFFDFBEEEDE NM:i:0 AS:i:43
+HS21_09876:2:2213:12056:100809#83 0 AE004091 7059 54 1S43M * 0 0 GGGATGGGGCTGATCTCGGCCATGGTCTCGCTGACCCAGGCTTC BFEE?,B>DFG=EDF:GHHEG6GGDGFFFFGGF6FFEFGC1BFF NM:i:0 AS:i:43
diff --git a/t/data/RunTradis/notags.fastq b/t/data/RunTradis/notags.fastq
new file mode 100644
index 0000000..ed95c28
--- /dev/null
+++ b/t/data/RunTradis/notags.fastq
@@ -0,0 +1,92 @@
+ at HS21_09876:1:1105:9650:48712#83
+GGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG
++
+HHCEE8EEFGFFGFIFGGFGEEHFFFGGGFGFGEGEEEFGFGFF
+ at HS21_09876:1:1106:8638:38957#83
+GGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG
++
+HHCEF7FHFFFFGFEGEFFEHEGEGFGGGEGFGFGGFEHGFEFD
+ at HS21_09876:1:1204:19746:42237#83
+GGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG
++
+HHCBF2GGFFEFGEEFFFEEHEEHFFFFGFGFFFGGGGHGFEFF
+ at HS21_09876:1:2210:2408:11148#83
+GGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG
++
+HHCBF,GGFF<FEHFFEGFGFEEEGFGGGFGFFFGGGFHGFEFF
+ at HS21_09876:1:2210:16541:84795#83
+GGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG
++
+FDB at F%GEFDCFGHE<FD>GEEEGFFGGFFGFFBG8FGFGFEEE
+ at HS21_09876:1:1201:6607:66324#83
+CCCACCGACGGCTCCGGATGGCTGACCCGCTGCTGGATGGGGCT
++
+HHCDF8EHFEGFAGIFEDEGFEFFGFEGFEGFGFGEGGHGFEFD
+ at HS21_09876:1:2102:12312:75235#83
+CCCACCGACGGCTCCGGATGGCTGACCCGCTGCTGGATGGGGCT
++
+HHCDH8EHFFGFAGDFIEEEGEFFGFFGFFGFFEGEFFFGFEFE
+ at HS21_09876:1:1106:16061:54950#83
+GGGATGGGGCTGATCTCGGCCATGGTCTCGCTGACCCAGGCTTC
++
+FHCBD4GHFFGFEEC<FCGEFEGHGFFEGFGFFFGDFGDGFDFF
+ at HS21_09876:1:2101:14032:85058#83
+GAATCGAGCGCGCGCTGCCCAAGGACACCTGGGGACCGGCGCGG
++
+HHCEH5GHFFFFGEDC;GHFFEHGGFFGFEGFFJGDGFHGFGFF
+ at HS21_09876:1:2111:11125:6617#83
+GAATCGAGCGCGCGCTGCCCAAGGACACCCGGGGACCGGCGCGG
++
+HG2BH8HEFGFFGH;EFGHFGEGGGFEGGFGFFGGDGEHGFEFF
+ at HS21_09876:1:2202:3163:76297#83
+GAATCGAGCGCGCGCTGCCCAAGGACACCTGGGGACCGGCGCGG
++
+HHCEH8EGFEGFGEIFDGHFGEHECFFGGFGFFDGEGGHGFEFF
+ at HS21_09876:1:2205:20175:3703#83
+GAATCGAGCGCGCGCTGCCCAAGGACACCTGGGGACCGGCGCGG
++
+H>8BI2A<FEFFGCE<EDFDDEHH?F=GFFGF3FGEGGHGDDFE
+ at HS21_09876:1:2205:6527:34286#83
+GAATCGAGCGCGCGCTGCCCAAGGACACCTGGGGACCGGCGCGG
++
+HGBDH4HHFGFFGFDFDGHEGEHGGFEGFJGFGGGEGFHGFFFF
+ at HS21_09876:1:1201:10071:48582#83
+GCCCCAAGGACACCTGGGGACCGGCGCGGCTGGACGCGGTATCG
++
+HHCDI8EHFGFFGEFFFGGFGEFGGFFGGFGFG8G8ECFGFFAE
+ at HS21_09876:1:2107:20205:78513#83
+GCCCCGAGGACACCTGGGGACCGGCGCGGCTGGACGCGGTATCG
++
+HHCEI%EGFFEFEGIFGDGFE>GDGFFGFEBFGDGEGEH;EFDD
+ at HS21_09876:1:2207:12005:97464#83
+GCCCCAAGGACACCTGGGGACCGGCGCGGCTGGACGCGGTATCG
++
+HGBBH0EG?<FFEHCBGEE>DEDF?FFGFE1FE89EEGD;;@?D
+ at HS21_09876:1:1208:12319:4648#83
+CAACCTGGGGACCGGCGCGGCTGGACGCGGTATCGATGATCTTC
++
+AA>EF8EIFFGFGEC<F;FEEEG3?FFG/E=F?DG89C=GAD?E
+ at HS21_09876:1:2209:14024:59451#83
+CCCGGTGCGCTACCCGTTCCTGTGGAACGCGGCGCGGCAGAACA
++
+FHCBF.E<FEFFGHHGE;H>GEFHFFFGFFGFFFGEFGFGFGFF
+ at HS21_09876:2:1211:5990:82312#83
+TTTTCGGTCACCGCGGTGCGCAACCTGCACCCGGTGACCCTCTC
++
+HGFEH0FFDDDGCF7GFD1GCFGFGGFGFFGHEFF?FFFEEDEE
+ at HS21_09876:2:2103:19946:55809#83
+GGGTCATAACGCCGCGGAGATTCTCTCGCGCGGTCAGCAGAAGC
++
+HHEAE'EFFEGGGFHEFAHGFHG at GEFHFEGFGFFF<FGEEDCE
+ at HS21_09876:2:1104:10740:37072#83
+CCCACCGACGGCTCCGGATGGCTGACCCGCTGCTGGATGGGGCT
++
+HHFAE,FIGDEG;FHFFHH>FAGGFFF;><GHA9<F<FGE=F at C
+ at HS21_09876:2:2201:4547:41892#83
+CCCACCGACGGCTCCGGATGGCTGACCCGCTGCTGGATGGGGCT
++
+GGEEE7EFGEDGEDHGGAHFGHGFDGFCFEGFAFFFDFBEEEDE
+ at HS21_09876:2:2213:12056:100809#83
+GGGATGGGGCTGATCTCGGCCATGGTCTCGCTGACCCAGGCTTC
++
+BFEE?,B>DFG=EDF:GHHEG6GGDGFFFFGGF6FFEFGC1BFF
diff --git a/t/data/RunTradis/smallref.fa b/t/data/RunTradis/smallref.fa
new file mode 100644
index 0000000..58dcfe9
--- /dev/null
+++ b/t/data/RunTradis/smallref.fa
@@ -0,0 +1,165 @@
+>AE004091 AE004091.2 Pseudomonas aeruginosa PAO1, complete genome.
+tttaaagagaccggcgattctagtgaaatcgaacgggcaggtcaatttccaaccagcgat
+gacgtaatagatagatacaaggaagtcatttttcttttaaaggatagaaacggttaatgc
+tcttgggacggcgcttttctgtgcataactcgatgaagcccagcaattgcgtgtttctcc
+ggcaggcaaaaggttgtcgagaaccggtgtcgaggctgtttccttcctgagcgaagcctg
+gggatgaacgagatggttatccacagcggttttttccacacggctgtgcgcagggatgta
+cccccttcaaagcaagggttatccacaaagtccaggacgaccgtccgtcggcctgcctgc
+ttttattaaggtcttgatttgcttggggcctcagcgcatcggcatgtggataagtccggc
+ccgtccggctacaataggcgcttatttcgttgtgccgcctttccaatctttgggggatat
+ccgtgtccgtggaactttggcagcagtgcgtggatcttctccgcgatgagctgccgtccc
+aacaattcaacacctggatccgtcccttgcaggtcgaagccgaaggcgacgaattgcgtg
+tgtatgcacccaaccgtttcgtcctcgattgggtgaacgagaaatacctcggtcggcttc
+tggaactgctcggtgaacgcggcgagggtcagttgcccgcgctttccttattaataggca
+gcaagcgtagccgtacgccgcgcgccgccatcgtcccatcgcagacccacgtggctcccc
+cgcctccggttgctccgccgccggcgccagtgcagccggtatcggccgcgcccgtggtag
+tgccacgtgaagagctgccgccagtgacgacggctcccagcgtgtcgagcgatccctacg
+agccggaagaacccagcatcgatccgctggccgccgccatgccggctggagcagcgcctg
+cggtgcgcaccgagcgcaacgtccaggtcgaaggtgcgctgaagcacaccagctatctca
+accgtaccttcaccttcgagaacttcgtcgagggcaagtccaaccagttggcccgcgccg
+ccgcctggcaggtggcggacaacctcaagcacggctacaacccgctgttcctctacggtg
+gcgtcggtctgggcaagacccacctgatgcatgcggtgggcaaccacctgctgaagaaga
+acccgaacgccaaggtggtctacctgcattcggaacgtttcgtcgcggacatggtgaagg
+ccttgcagctcaacgccatcaacgaattcaagcgcttctaccgctcggtggacgcactgt
+tgatcgacgacatccagttcttcgcccgtaaggagcgctcccaggaggagttcttccaca
+ccttcaatgcccttctcgaaggcggccagcaggtgatcctcaccagcgaccgctatccga
+aggaaatcgaaggcctggaagagcggctgaaatcccgcttcggctggggcctgacggtgg
+ccgtcgagccgccggaactggaaacccgggtggcgatcctgatgaagaaggccgagcagg
+cgaagatcgagctgccgcacgatgcggccttcttcatcgcccagcgcatccgttccaacg
+tgcgtgaactggaaggtgcgctgaagcgggtgatcgcccactcgcacttcatgggccggc
+cgatcaccatcgagctgattcgcgagtcgctgaaggacctgttggcccttcaggacaagc
+tggtcagcatcgacaacatccagcgcaccgtcgccgagtactacaagatcaagatatccg
+atctgttgtccaagcggcgttcgcgctcggtggcgcgcccgcgccaggtggccatggcgc
+tctccaaggagctgaccaaccacagcctgccggagatcggcgtggccttcggcggtcggg
+atcacaccacggtgttgcacgcctgtcgtaagatcgctcaacttagggaatccgacgcgg
+atatccgcgaggactacaagaacctgctgcgtaccctgacaacctgacgcagcccacgag
+gcaagggactagaccatgcatttcaccattcaacgcgaagccctgttgaaaccgctgcaa
+ctggtcgccggcgtcgtggaacgccgccagacattgccggttctctccaacgtcctgctg
+gtggtcgaaggccagcaactgtcgctgaccggcaccgacctcgaagtcgagctggttggt
+cgcgtggtactggaagatgccgccgaacccggcgagatcaccgtaccggcgcgcaagctg
+atggacatctgcaagagcctgccgaacgacgtgctgatcgacatccgtgtcgaagagcag
+aaacttctggtgaaggccgggcgtagccgcttcaccctgtccaccctgccggccaacgat
+ttccccaccgtagaggaaggtcccggctcgctgaacttcagcattgcccagagcaagctg
+cgtcgcctgatcgaccgcaccagcttcgccatggcccagcaggacgtgcgttactacctc
+aacggcatgctgctggaagtgaacggcggcaccctgcgctccgtcgccaccgacggccac
+cgactggccatgtgctcgctggatgcgcagatcccgtcgcaggaccgccaccaggtgatc
+gtgccgcgcaaaggcatcctcgaactggctcgtctgctcaccgagcaggacggcgaagtc
+ggcatcgtcctgggccagcaccatatccgtgccaccactggcgaattcaccttcacttcg
+aagctggtggacggcaagttcccggactacgagcgtgtactgccgcgcggtggcgacaag
+ctggtggtcggtgaccgccagcaactgcgcgaagccttcagccgtaccgcgatcctctcc
+aacgagaagtaccgcggcattcgcctgcagctttccaacggtttgctgaaaatccaggcg
+aacaacccggagcaggaagaggccgaggaagaagtgcaggtcgagtacaacggcggcaac
+ctggagataggcttcaacgtcagttacctgctcgacgtgctgggtgtgatcggtaccgag
+caggtccgcttcatcctttccgattccaacagcagcgccctggtccacgaggccgacaat
+gacgattctgcctatgtcgtcatgccgatgcgcctctaaacatactgaatgtccctgacc
+cgcgtttcggtcaccgcggtgcgcaacctgcacccggtgaccctctccccctccccccgc
+atcaacatcctctacggcgacaacggcagcggcaagaccagcgtgctcgaagccatccac
+ctgctgggcctggcgcgttcattccgcagtgcgcgcttgcagccggtgatccagtatgag
+gaagcggcctgcaccgtattcggccaggtgatgttggccaacggcatcgccagcaacctg
+gggatttcccgtgagcgccagggcgagttcaccatccgcatcgatgggcagaacgcccgg
+agtgcggctcaattggcggaaactctcccactgcaactgatcaacccggacagctttcgg
+ttgctcgagggagcgccgaagatccggcgacagttcctcgattggggagtgttccacgtg
+gaacctcggtttctgcccgtctggcagcgcctgcagaaggcgctgcgccagcggaactcc
+tggctccggcatggtaaactggaccccgcgtcgcaagcggcctgggaccgggaattgagc
+ctggccagcgatgagatcgatgcctaccgcagaagctatatccaggcgttgaaaccggta
+ttcgaggaaacactcgccgaattggtttcactggatgacctgacccttagctactaccga
+ggctgggacaaggaccgggacctcctggaggttctggcttccagcctgttgcgcgaccag
+cagatgggccacacccaggcgggaccgcagcgtgcggatcttcgcatacggttggcaggt
+cataacgccgcggagattctctcgcgcggtcagcagaagctggtggtatgcgccctgcgc
+atcgcccaaggccatctgatcaatcgcgccaagcgcggacagtgcgtctacctggtggac
+gacctgccctcggaactggatgagcagcatcgaatggctctttgccgcttgcttgaagat
+ttgggttgccaggtattcatcacctgcgtggacccgcaactattgaaagacggctggcgc
+acggatacgccggtatccatgttccacgtggaacatggaaaagtctctcagaccacgacc
+atcgggagtgaagcatgagcgagaacaacacgtacgactcttccagcatcaaggtgctga
+aggggctggatgccgtacgcaagcgccccggcatgtacatcggcgacaccgacgatggca
+ccggtctgcaccacatggtgttcgaggtggtggataactccatcgacgaagcgctggccg
+gttactgcagcgaaatcagcatcaccatccatacggatgagtcgatcactgtccgcgaca
+atggacgcggtattccggtggatatccacaaggaagaaggggtttctgcggcggaagtga
+tcatgaccgtcctccacgccggcggcaagttcgacgacaacacctacaaggtgtccggcg
+gcttgcacggtgtgggcgtctcggtggtgaacgcgctgtcccatgaactacgcctgacca
+tccgtcgccacaacaaggtctgggaacaggtctaccaccacggcgttccgcagttcccac
+tgcgcgaagtgggcgagaccgatggctccggcaccgaagttcacttcaagccgtccccgg
+agaccttcagcaacatccacttcagttgggacatcctggccaagcgcatccgcgagctgt
+ccttcctcaactccggcgtcggcatcctgctgcgcgacgagcgtaccggcaaggaggagc
+tgttcaagtacgaaggcggtctgaaggccttcgtcgagtacctgaacaccaacaagaccg
+cggtgaacgaggtattccacttcaacgtccagcgtgaagaggacggcgtgggtgtggaag
+tcgccttgcagtggaacgacagcttcaacgagaacctgctctgcttcaccaacaacatcc
+cgcagcgtgacggcggcacccacctggccggtttccgttcggcgctgacgcgtaacctga
+acaactacatcgaggccgaaggcctggcgaagaagttcaagatcgccaccaccggcgacg
+atgcccgcgaaggcctcaccgcgatcatctcggtgaaggtaccggacccgaagttcagct
+cgcagaccaaggacaagctggtctcctccgaggtgaagactgcggtggaacaggagatgg
+gcaagtacttcgccgacttcctgctggagaatcccaacgaagccaaggccgtggtcggca
+agatgatcgacgccgcccgtgcccgcgaggccgcgcgcaaggcgcgcgagatgacccgcc
+gcaagggcgcgctggacatcgccggcctgcccggcaaactggccgattgccaggaaaagg
+acccggcgctctccgaactgtacatcgtggagggtgactccgcgggcggttccgccaagc
+agggccgcaatcgccggacccaggcgatcctgccgctcaagggcaagatcctcaacgtcg
+aaaaggcgcgcttcgacaagatgctctcctcccaggaggtcggtacgctgatcaccgccc
+tgggctgtggcatcggccgcgaggaatacaacatcgacaagctgcgctaccacaacatca
+tcatcatgaccgatgctgacgtcgacggttcgcacatccgcaccctgctgttgaccttct
+tcttccgccagatgcccgagctgatcgagcgtggctacatctacatcgcccagcccccgt
+tgtacaaggtcaagcgcggcaagcaggagcagtacatcaaggacgaccaggccatggaag
+agtacatgacccagtcggccctggaagacgccagcctgcacgtcaacgagcacgctccgg
+gcctgtccggggcggcgctggagaaactggtcaacgagtatcgcggggtgatcgccaccc
+tcaagcgcctgtcgcgcctgtacccccaggagctgaccgagcacttcatctacctgccta
+ccgtgtcggtggacgacctggctaacgagtcggccatgcagggctggttggagaagttcc
+aggcgcgcctgaccgccgccgagaagtccggcctgacctacaaggccagcctgcgcgaag
+accgcgagcgccacctgtggctgcccgaggtggaactggtggcccacggcctgtccagct
+acgtcaccttcaaccgtgacttcttcgccagcaatgactaccgctcggtgtcgctgctcg
+gcgaccagctgaacagcctgctggaagacggcgcctacgtgcagaagggtgagcgcaagc
+gcccgatcagcgccttcaaggacggcctggactggctgatggccgaaggtaccaagcgcc
+acagcatccagcgatacaaggggctgggcgagatgaaccctgagcagctgtgggaaacca
+ccatggatccgaacgtccggcgcatgctcaaggtgaccatcgaggatgccatcgccgccg
+accagatcttcaacaccctgatgggcgatgccgtggagccgcgccgcgacttcatcgaaa
+gcaacgcgctggcggtgtcgaacctggacgtgtgacaggtcggcagaccgaccctcatgg
+aaaccccggcctggcgccggggttttctttttgcgccaggtagcctggatacgggcgcca
+ggggtgccttgccaaggtgtggccgagccccggttactcgccggcattggcaccctggac
+ccgggcctcctggcggcgtggcaccgcttctgtgggcagcggtcgccggtcggttcggtc
+gatcgttgccagccggccttgctttgcgcctcgcgtgaaaacaagaagccccgctatggc
+ggggcttcttttatcgaatcggcgcacagtacgccttgcagggggctttgcggcccttca
+cgagaccaccgacggctccggatggctgacccgctgctggatggggctgatctcggccat
+ggtctcgctgacccaggcttcggcgcgctggtttagctcggcgatggcgcgcgggccttc
+gccttcggcgtgcatggccgggccgatcaccacctggatggtgcccgggtacttggccca
+gccggccttgggccaatactgcccggcgttgtgggcgatcggcagtaccggtagcccggc
+gttgaccgccagggcggtgccgccgcgggagaacttgcccatctgccccaccggaatacg
+cgtgccttccgggaagatcagcacccaggcgcctttcttcaggcactcgtcgccctgctt
+ggccagttgcttgagggccagcttgggctggctgcggtcgatggcgatgggcttgagcag
+ggccagggcccagccgaagaacggcacgtagagcagctcgcgcttgagtacctggctgag
+tggctcgaagaagccggagaggaagaaggtttcccaggtgctctggtgcttggagaggat
+cacgcagggcttttccgggatgttctccagtccgcgcacctcgtagcggatgccggcgac
+cacgcgggtcagccagatcgcgaagcggcaccagttctgtaccacgaagcggtagcgggc
+gcggaacggcaggatcggcgcgatgaagaagctgagggtgccccagacgaacgcgctggc
+ggacagcagcaggtaaaagaggacggttctgatggcctgcactgtcgacatgtattctga
+ccttactgaagtaatgcgctggcgactgccgccagatcgtcgaatatcagggtgccctct
+ggcaagggcttgcccagcgtacgtacaccttttccggtctttaccaataccggctgacaa
+tcgacggcccgcgccgcctccaggtcaccgatgctgtcgccgacgaaccagatacccgac
+agatcgaccccgtagtgctcgccgatctgccgcagcatacccggcttcggcttgcggcag
+tcgcaaccgtcgtccggtccatgcggacaatagacgatgaggccgacctcgccgccctgc
+tccgcgaccagttcgcgcaagcgcgcatgcatggcctcgagcactgccaggtcgtaatag
+ccacgggcgatgccggactggttggtagccaccgcgacggtccagccggcctggctcagg
+cgggcgatggcctcgatcgagctggggatggggatccactcgtcgagggtcttgatgtaa
+tcgtcggagtcgaggttgatgactccatcgcggtcgagaatcagcagggaacgggacatc
+gatgcgcagttggccatgaacggaaaggatcgattctacctcagccagccggagcatcgc
+ggatggatcgacgagccccctacgctggacaatctgtactagattcaataatggcaatgg
+aatggcaatcccaggccagggagtcatttggcacgcagcagtgggtgtctcggagtacgt
+gcgaaccccttggcgggtggatcaccggagtaacgcagtaagcgcctatcgcatgccagc
+acggccgaccggccgtgtttccaccacaggtggagcgggcgtgacgacggggagttccgg
+ggcgtctgcccgttcccaaggacggtaaccgtgaaacgcctgaaaaagacactgcacctt
+tcaagcttgtccctcgcttccctggctctttcttccgccgccctggcggccgctccggtc
+atgctcgaccagggcaaggaatggaccgaaagccaccgccaggacttctacagccgcgac
+cagggctcgcaggtgatgcccctgccctggctcaaggcgttgcgacagccggatggaacg
+cctttcctcgccgacagcctggcccgctacggctatttgcccaaccccaaggcgcccgcg
+gaaggcctgccggtgggcttcaccgtagccggcacgggcgcccggcagatggtcggcatg
+acctgttcggcctgccatacccggcagatcgaggtgaagggcactgcctatcggatcgac
+ggcggtccggcgatcgtcgacttccaggcattcctcgccgacctcgatcgggccgtggga
+ccgctgaccagcgatgacgccgccttcgacgccttcgccaagccgatcctcggggccaat
+ccgcctcccggtgcgcgcgacgctctgctcgcggcggtgaaggaatggtacgagccctat
+cacacgctgatcgagcgcgcgctgcccaaggacacctggggaccggcgcggctggacgcg
+gtatcgatgatcttcaaccgccttaccgggctggatatcggcaccgcgccgccctacctg
+attcccgacaacatcaaggcggccgatgcgccggtgcgctatccgttcctgtggaacgcg
+gcgcggcagaacaagacccagtggcccggcttcgccgccaacggcaacgacctgctcggc
+ctggcgcgcaatgtcggcgaggtctacggggtgttcgccaccttccacccgcagaagagc
+aagttccacctgctgggcatggactacctgaagatcaactcggccaacttccacgggctg
+ggcaagctggaagacctgatcaagaagatcggcccgccgaagtggccctgggcggtggac
+aagcacctggccaggaaaggcgcgctgatcttcgcccgcaagaccgacgaaggtggctgc
+gtggagtgccacggcatccggatcaaggacctggtgctttgggacactccgctgagggac
+gtcggcagcgacagccgccagcacgccatcctcgatggccaggtgcagaccggcgtgatg
diff --git a/t/data/RunTradis/test.tagged.fastq b/t/data/RunTradis/test.tagged.fastq
new file mode 100644
index 0000000..036f778
--- /dev/null
+++ b/t/data/RunTradis/test.tagged.fastq
@@ -0,0 +1,112 @@
+ at HS21_09876:1:1105:9650:48712#84
+TAAGATTCAGGGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG
++
+CCCFFFFFHHHHCEE8EEFGFFGFIFGGFGEEHFFFGGGFGFGEGEEEFGFGFF
+ at HS21_09876:1:1106:8638:38957#84
+TGAGAGTCAGGGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG
++
+B at CFFFFFHHHHCEF7FHFFFFGFEGEFFEHEGEGFGGGEGFGFGGFEHGFEFD
+ at HS21_09876:1:1105:9650:48712#83
+TAAGAGTCAGGGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG
++
+CCCFFFFFHHHHCEE8EEFGFFGFIFGGFGEEHFFFGGGFGFGEGEEEFGFGFF
+ at HS21_09876:1:1106:8638:38957#83
+TAAGAGTCAGGGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG
++
+B at CFFFFFHHHHCEF7FHFFFFGFEGEFFEHEGEGFGGGEGFGFGGFEHGFEFD
+ at HS21_09876:1:1204:19746:42237#83
+TAAGAGTCAGGGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG
++
+CCCFFFFFHHHHCBF2GGFFEFGEEFFFEEHEEHFFFFGFGFFFGGGGHGFEFF
+ at HS21_09876:1:2210:2408:11148#83
+TAAGAGTCAGGGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG
++
+BBCFFFFFHHHHCBF,GGFF<FEHFFEGFGFEEEGFGGGFGFFFGGGFHGFEFF
+ at HS21_09876:1:2210:16541:84795#83
+TAAGAGTCAGGGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG
++
+BCCFFFFFHHFDB at F%GEFDCFGHE<FD>GEEEGFFGGFFGFFBG8FGFGFEEE
+ at HS21_09876:1:1201:6607:66324#83
+TAAGAGTCAGCCCACCGACGGCTCCGGATGGCTGACCCGCTGCTGGATGGGGCT
++
+BCCDFBDEHHHHCDF8EHFEGFAGIFEDEGFEFFGFEGFEGFGFGEGGHGFEFD
+ at HS21_09876:1:2102:12312:75235#83
+TAAGAGTCAGCCCACCGACGGCTCCGGATGGCTGACCCGCTGCTGGATGGGGCT
++
+BCCDFFFFHHHHCDH8EHFFGFAGDFIEEEGEFFGFFGFFGFFEGEFFFGFEFE
+ at HS21_09876:1:1106:16061:54950#83
+TAAGAGTCAGGGGATGGGGCTGATCTCGGCCATGGTCTCGCTGACCCAGGCTTC
++
+BBBDFFFFHHFHCBD4GHFFGFEEC<FCGEFEGHGFFEGFGFFFGDFGDGFDFF
+ at HS21_09876:1:2101:14032:85058#83
+TAAGAGTCAGGAATCGAGCGCGCGCTGCCCAAGGACACCTGGGGACCGGCGCGG
++
+BCCDFFFFHHHHCEH5GHFFFFGEDC;GHFFEHGGFFGFEGFFJGDGFHGFGFF
+ at HS21_09876:1:2111:11125:6617#83
+TAAGAGTCAGGAATCGAGCGCGCGCTGCCCAAGGACACCCGGGGACCGGCGCGG
++
+BCCDDDDDFHHG2BH8HEFGFFGH;EFGHFGEGGGFEGGFGFFGGDGEHGFEFF
+ at HS21_09876:1:2202:3163:76297#83
+TAAGAGTCAGGAATCGAGCGCGCGCTGCCCAAGGACACCTGGGGACCGGCGCGG
++
+BCCDFDDDHHHHCEH8EGFEGFGEIFDGHFGEHECFFGGFGFFDGEGGHGFEFF
+ at HS21_09876:1:2205:20175:3703#83
+TAAGAGTCAGGAATCGAGCGCGCGCTGCCCAAGGACACCTGGGGACCGGCGCGG
++
+BCCDFFFEHHH>8BI2A<FEFFGCE<EDFDDEHH?F=GFFGF3FGEGGHGDDFE
+ at HS21_09876:1:2205:6527:34286#83
+TAAGAGTCAGGAATCGAGCGCGCGCTGCCCAAGGACACCTGGGGACCGGCGCGG
++
+BCCDFFFFHHHGBDH4HHFGFFGFDFDGHEGEHGGFEGFJGFGGGEGFHGFFFF
+ at HS21_09876:1:1201:10071:48582#83
+TAAGAGTCAGGCCCCAAGGACACCTGGGGACCGGCGCGGCTGGACGCGGTATCG
++
+CCCDFFFFHHHHCDI8EHFGFFGEFFFGGFGEFGGFFGGFGFG8G8ECFGFFAE
+ at HS21_09876:1:2107:20205:78513#83
+TAAGAGTCAGGCCCCGAGGACACCTGGGGACCGGCGCGGCTGGACGCGGTATCG
++
+BCCFFFFFHHHHCEI%EGFFEFEGIFGDGFE>GDGFFGFEBFGDGEGEH;EFDD
+ at HS21_09876:1:2207:12005:97464#83
+TAAGAGTCAGGCCCCAAGGACACCTGGGGACCGGCGCGGCTGGACGCGGTATCG
++
+BCCDFFFFHHHGBBH0EG?<FFEHCBGEE>DEDF?FFGFE1FE89EEGD;;@?D
+ at HS21_09876:1:1208:12319:4648#83
+TAAGAGTCAGCAACCTGGGGACCGGCGCGGCTGGACGCGGTATCGATGATCTTC
++
+B=BDFFFDH>AA>EF8EIFFGFGEC<F;FEEEG3?FFG/E=F?DG89C=GAD?E
+ at HS21_09876:1:2209:14024:59451#83
+TAAGAGTCAGCCCGGTGCGCTACCCGTTCCTGTGGAACGCGGCGCGGCAGAACA
++
+BCCDFFFFHHFHCBF.E<FEFFGHHGE;H>GEFHFFFGFFGFFFGEFGFGFGFF
+ at HS21_09876:2:1211:5990:82312#83
+TAAGAGTCAGTTTTCGGTCACCGCGGTGCGCAACCTGCACCCGGTGACCCTCTC
++
+BCCFFFFFHHHGFEH0FFDDDGCF7GFD1GCFGFGGFGFFGHEFF?FFFEEDEE
+ at HS21_09876:2:2103:19946:55809#83
+TAAGAGTCAGGGGTCATAACGCCGCGGAGATTCTCTCGCGCGGTCAGCAGAAGC
++
+BBCFDEFFHHHHEAE'EFFEGGGFHEFAHGFHG at GEFHFEGFGFFF<FGEEDCE
+ at HS21_09876:2:1104:10740:37072#83
+TAAGAGTCAGCCCACCGACGGCTCCGGATGGCTGACCCGCTGCTGGATGGGGCT
++
+BBBDDFFFHHHHFAE,FIGDEG;FHFFHH>FAGGFFF;><GHA9<F<FGE=F at C
+ at HS21_09876:2:2201:4547:41892#83
+TAAGAGTCAGCCCACCGACGGCTCCGGATGGCTGACCCGCTGCTGGATGGGGCT
++
+BCCDFFFFHHGGEEE7EFGEDGEDHGGAHFGHGFDGFCFEGFAFFFDFBEEEDE
+ at HS21_09876:2:2213:12056:100809#83
+TAAGAGTCAGGGGATGGGGCTGATCTCGGCCATGGTCTCGCTGACCCAGGCTTC
++
+BBCDDDDDHDBFEE?,B>DFG=EDF:GHHEG6GGDGFFFFGGF6FFEFGC1BFF
+ at HS21_09876:1:1115:10349:43433#83
+TTTTCGACAACCTTTTGCCTGCCGGAGAAACACGCAGTTGCTACCNNACNCTNN
++
+8,(,*A<A2;DGE4B>HGFEDDCFG8CE=FF8BB7ED?FEEE522!!<2!:0!!
+ at HS21_09876:1:1211:4356:84410#83
+TTCTCGACAACCTTTTGCCTGCCGGAGAAACACGCAGTTGCTACCTGACTCTTA
++
+>E52EHFGFFGGFFFGHGHEEEGFGEGFGFGFGCGGFGFGFDHHHHFFFFFCCC
+ at HS21_09876:1:1101:19209:27276#83
+CGCACAGCCGTGTGGAAAAAACCGCTGTGGATAACCATCTCGGCCTGACTCTTA
++
+CEF4GHFDFFEEIFECHFGEFFGFEFGFGFFFGDHGHGFEFFHHHHFFFFFCCC
diff --git a/t/data/RunTradis/test.tagged.fastq.gz b/t/data/RunTradis/test.tagged.fastq.gz
new file mode 100644
index 0000000..d4b5f3f
Binary files /dev/null and b/t/data/RunTradis/test.tagged.fastq.gz differ
diff --git a/t/data/RunTradis/test2.tagged.fastq b/t/data/RunTradis/test2.tagged.fastq
new file mode 100644
index 0000000..598b411
--- /dev/null
+++ b/t/data/RunTradis/test2.tagged.fastq
@@ -0,0 +1,452 @@
+ at HS21_09876:1:1207:4978:63940#75
+TAAGAGTCAGGGGATAGAAACGGTTAATGCTCTTGGGACGGCGCTTTTCTGTGC
++
+CCCFFFFFHHGHC7E4EEFGFFGGFFFCEG at EHGFFEGFEGFFEGEHFFGFGFE
+ at HS21_09876:1:1203:13201:16985#75
+TAAGAGTCAGCGGGTTAATGCTCTTGGGACGGCGCTTTTCTGTGCATAACTCGA
++
+BCCFFFFFGHHHCED9GEFDEFGFIFEGCEFEHGGFGGFFGFFGGEFGHGEGFF
+ at HS21_09876:1:1105:14817:70208#75
+TAAGAGTCAGGCCTCTTGGGACGGCGCTTTTCTGTGCATAACTCGACGAAGCCC
++
+CCCFFFFFHHHHCEF8HHFGCFGGEFEFEGGEFFGFFGFFGFGFGEGGHGFEFE
+ at HS21_09876:1:1101:1155:30938#75
+TAAGAGTCAGGTTGCATAACTCGACGAAGCCCAGCAACTGCGTGTTTCTCCGGC
++
+B=?DDDEFHCFHBDD,AEFEGDGGCFFGE>DEAHEFFFCFGFFFDEGEFGFFFE
+ at HS21_09876:1:2204:6930:62477#75
+TAAGAGTCAGGGGCAAAAGGTTGTCGAGAACCGGTGTCGAGGCTGTTTCCTTCC
++
+BBCFFFFFHHHHCEF5GHFFCFDGEFBCHFFEFFGFFGFFGFFDGEEGFGFGFE
+ at HS21_09876:1:2211:14592:36752#75
+TAAGAGTCAGGGGTCACCGCGGTGCGCAACCTGCACCCGGTGACCCTCTCCCCC
++
+CCCFFFFFHFHH9BF%GGFFEFDGFFF;EFFEHGGFEGFFGFFEGDEFHGFGFE
+ at HS21_09876:1:1101:1117:56616#75
+TAAGAGTCAGGGGCCTGCACCGTATTCGGCCAGGTGATGTTGGCCAACGGCATC
++
+=:=DADDDFFHHCDF8EEFGGFGEEFDGHEEEGGCFFFFFGFGFGCGGFGE at ED
+ at HS21_09876:1:1106:9993:12675#75
+TAAGAGTCAGGGGCCTGCACCGTATTCGGCCAGGTGATGTTGGCCAACGGCATC
++
+BBBFFFFFHHFHCBI2DEFGGFGEFFFGHGIEHHGFFGFFGFFJGEHFFGFDFE
+ at HS21_09876:1:2205:12308:83747#75
+TAAGAGTCAGGGGCCTGCACCGTATTCGGCCAGGTGATGTTGGCCAACGGCATC
++
+BCCFFFFFHHHHC at F7EEFGFFGFEFGGGFHEGEFFFGFFGFFECDEGHGFFFF
+ at HS21_09876:1:2211:5325:48675#75
+TAAGAGTCAGGGGCCTGCACCGTATTCGGCCAGGTGATGTTGGCCAACGGCATC
++
+1:B4A2AD2ACF57<'GE4EEFG9 at FDDGGIEE?F:=8FEGFGDGACGFGEDA:
+ at HS21_09876:1:1202:13852:46659#75
+TAAGAGTCAGGGGCCAACGGCATCGCCAGCAACCTGGGGATTTCCCGTGAGCGC
++
+CCCFFFFFHHHHCEH8EEFGFFDG7FG;EFFEAHEFGGFFBFGEGEGGFGEGFF
+ at HS21_09876:1:1110:4160:49896#75
+TAAGAGTCAGAAACTCTCCCACTGCAACTGATCAACCCGGACAGCTTTCGGTTG
++
+BCBFFFFDHHHHCDF8AEFGCFGHDFGCHGDEFFGFFGGFGFGFG8GGHGFFFE
+ at HS21_09876:1:2205:9754:20814#75
+TAAGAGTCAGAAACTCTCCCACTGCAACTGATCAACCCGGACAGCTTTCGGTTG
++
+BBCFDEFEHHHHCEE4EIFGGFAFEFGGHFFEGEFFGGFEGFFFGEFEHGFEFF
+ at HS21_09876:1:1104:13063:60859#75
+TAAGAGTCAGGGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG
++
+CCCFFFFFHHH>0 at F,GEFE3CHEEFDC2FEEAG?FCEFED=F8CEEEH;;EDE
+ at HS21_09876:1:1107:8692:25384#75
+TAAGAGTCAGGGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG
++
+@@CFFFFFHHHHA at E7EIFEEFGE-<FF>F at EHDCFF8G>GFFBGCCCHGF:AD
+ at HS21_09876:1:1109:11137:7630#75
+TAAGAGTCAGGGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG
++
+BCCFFFFFHHGHCBF8EEFDEFGEEFGG>GFEGGCFFGGFGFFEGGFFHGFEFF
+ at HS21_09876:1:1110:7663:40978#75
+TAAGAGTCAGGGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG
++
+BB@=DADDHDFH?7D9EGFFEFGFEFF;>FDED?FFEGGEGFGFACFFFGFFFE
+ at HS21_09876:1:1201:5332:2719#75
+TAAGAGTCAGGGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG
++
+BCCFFFFFHHHHADF4EHFEEFGFEFEGCG at EEFCFFGFFGFGFGEEGHGFFFD
+ at HS21_09876:1:1204:12364:36595#75
+TAAGAGTCAGGGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG
++
+CCCFFFFFHHHHCBD2EGFF<FGEIFFD>FFEDFEFFGFFGFGEGEGEHGFGFF
+ at HS21_09876:1:2102:4320:20528#75
+TAAGAGTCAGGGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG
++
+BBBFFFDDFFHHCEF2EEFGCFGEEGED>G at EEGEFGGGEGFGEBCEGHGFEED
+ at HS21_09876:1:2102:17907:93005#75
+TAAGAGTCAGGGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG
++
+CCCFFFFFHHHHCEE5EEFFEFGEEFEGFEEEDFCFGGFFGFFGGGFGHGFEFF
+ at HS21_09876:1:2104:19430:56353#75
+TAAGAGTCAGGGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG
++
+BBCDFFFEHHHHCBH5FGFEEFGEDEFG>EHEEEEFFGGEGFFEGDGGFGFGFE
+ at HS21_09876:1:2106:8768:77924#75
+TAAGAGTCAGGGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG
++
+BBCFFFFFHHHHCBE7EGFFEFG87CEDFEFEFHCFFGFFGFFEGEGEHGFEDF
+ at HS21_09876:1:2109:3560:75405#75
+TAAGAGTCAGGGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG
++
+B@@DFDDFHHHHCBD,FGFE<FGEIEEG>FIEGGFFGGGFGFFEGEFGFGFEFD
+ at HS21_09876:1:2201:7109:15683#75
+TAAGAGTCAGGGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG
++
+BBCFFFFFHHHHCBF5GHFECFGEFFEGEGEEEFFFEGFFGFFGGGEFHGFEFF
+ at HS21_09876:1:2204:5779:59154#75
+TAAGAGTCAGGGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG
++
+CCCFFFFEHHHHCEF7EEFF<DGHIEFD>E at EHGFFFGGEGFFDCEEGHGEFFE
+ at HS21_09876:1:2210:14908:13619#75
+TAAGAGTCAGGGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG
++
+BBCFFFFFHFHHC7H,EEFG<FGC7CDD>DEEAFGF=GA>GFG8GCGGHGFDFD
+ at HS21_09876:1:2210:1263:58662#75
+TAAGAGTCAGGGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG
++
+BBBFFFFFHHHGBBH4HE?FE at GC7GFDFEDEAHCFFG;>GFGFG8EEHGF at DD
+ at HS21_09876:1:2211:14421:77160#75
+TAAGAGTCAGGGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG
++
+CCCFFFFFHFFF;EE-HEFFCFGCDFGDFFHEDFFFGGFEGFGEGEGGHGFGEF
+ at HS21_09876:1:1107:18833:61679#75
+TAAGAGTCAGGGGGCTGATCTCGGCCATGGTCTCGCTGACCCAGGCTTCGGCGC
++
+CCCFFFFFHHHH87E,G24E<9<F@<F;2>IE-FGFFG/1GFFFGEGE=;FGFC
+ at HS21_09876:1:1201:13166:59616#75
+TAAGAGTCAGGGGGCTGATCTCGGCCATGGTCTCGCTGACCCAGGCTTCGGCGC
++
+BCCFFFFFHHHHCDF5GEFFEFEFEFFDEGGEHGEFEEFFGFGFGDEGHGFGFD
+ at HS21_09876:1:1205:1312:68078#75
+TAAGAGTCAGGGGGCTGATCTCGGCCATGGTCTCGCTGACCCAGGCTTCGGCGC
++
+B@@FFFFFHHHHCDE,GEFCEFEFEFDGCGFEGGGFFEFEGFFEGECEHGFFFE
+ at HS21_09876:1:2101:9743:73722#75
+TAAGAGTCAGGGGGCTGATCTCGGCCATGGTCTCGCTGACCCAGGCTTCGGCGC
++
+BCCFFFFFHHHHCDF7EEFFEFGFEFBDFEHEEFGFFFFFGFGFGEEEFGFEFE
+ at HS21_09876:1:2112:4406:21609#75
+TAAGAGTCAGGGGGCTGATCTCGGCCATGGTCTCGCTGACCCAGGCTTCGGCGC
++
+BBCDFFFFHHHD-<<+8=F<EADG7FFBEGFEEFG9F4FEGF?FGGEEHGFEEE
+ at HS21_09876:1:2207:15792:48961#75
+TAAGAGTCAGGGGGCTGATCTCGGCCATGGTCTCGCTGACCCAGGCTTCGGCGC
++
+BCCFFFFFHHHGCEF,AGFCCFDEEFD;CGIEAECFF8GFGFF8GEGGFGFEFE
+ at HS21_09876:1:1102:3356:32350#75
+TAAGAGTCAGGGGACATCGATGCGCAGTTGGCCATGAACGGAAAGGATCGATTC
++
+CCCFFFFFHHHHC at F8EHFEEFGEIFDDEGGEGGFFFGFFGFFEGEFGHGFEFE
+ at HS21_09876:1:1108:19283:13217#75
+TAAGAGTCAGGGGACATCGATGCGCAGTTGGCCATGAACGGAAAGGATCGATTC
++
+B at CBDDBDHHHH8BF2EHFF<FGHFFDCGFFEGEGFEGFFGFFDGDGFHGFDFD
+ at HS21_09876:1:1201:19929:5101#75
+TAAGAGTCAGCCCCCTACGCTGGACAATCTGTACTAGATTCAATAATGGCAATG
++
+BCCDFFFFHHHHCEH7GHFFFFGGEFGFFFFEDHGFGGFEGFFGGEGFHGFDFF
+ at HS21_09876:1:2105:4638:75190#75
+TAAGAGTCAGCCCCCTACGCTGGACAATCTGTACTAGATTCAATAATGGCAATG
++
+BBCDFFFFHCFHCEH7GEFGFFGEEFDEFFFEGHGFGGFFGFGDGEGFHGFEFE
+ at HS21_09876:1:2207:17913:29384#75
+TAAGAGTCAGCCCCCTACGCTGGACAATCTGTACTAGATTCAATAATGGCAATG
++
+BCCDFFFFHHHHCDH9EHFGGFGHDFGDHGEEHGGFGGGFGFFEGEGFHGDEFF
+ at HS21_09876:1:2112:7251:38022#75
+TAAGAGTCAGTTTCCCAAGGACGGTAACCGTGAAACGCCTGAAAAAGACACTGC
++
+BBCFFFFDFFHF-7())EF=F8GE+EE2FF5+EEF7=/AF=F/FGDCE=G;@AD
+ at HS21_09876:1:1104:16812:95781#75
+TAAGAGTCAGGGGGCAAGGAATGGACCGAAAGCCACCGCCAGGACTTCTACAGC
++
+BCBFFFFFHHHHCDH%GEFGGCGEEFFGHGGEDFGFFGFFGFGFGCFGFGFGFD
+ at HS21_09876:1:2107:10172:88839#75
+TAAGAGTCAGGGGCAAGGAATGGACCGAAAGCCACCGCCAGGACTTCTACAGCC
++
+CCCFFFFFHHHHCBE-GIFEE at GECFFDHEIEFHGFFGGFAFGEGDFFHGFDFF
+ at HS21_09876:1:2101:13178:6874#75
+TAAGAGTCAGGGGTGATGCCCCTGCCCTGGCTCAAGGCGTTGCGACAGCCGGAT
++
+BCCDFFFFHA?FC7<7E2FDFF<EDFFEEEF>HEGFGGFEGFE?GDGG=GDFBE
+ at HS21_09876:1:2207:5093:25809#75
+TAAGAGTCAGCCCCCTGCCCTGGCTCAAGGCGTTGCGACAGCCGGATGGAACGC
++
+BBCDDEFDHHFFCBF,FEFECFGFFFF;HGGEFFEFEGFFGFGDGEGGHGFFBE
+ at HS21_09876:1:1105:3593:46102#75
+TAAGAGTCAGGGGCTCAAGGCGTTGCGACAGCCGGATGGAACGCCTTTCCTCGC
++
+CCCFFFFFHHHHCDE4EGFGECGFEFFEGFEEGFEFEGGEGFFJGFFGHGFGFF
+ at HS21_09876:1:1214:11162:39342#75
+TAAGAGTCAGGGGCTCAAGGCGTTGCGACAGCCGGATGGAACGCCTTTCCTCGC
++
+BCCDDFFFHHHHCB<&3GFEFFGGEFFDFGDEHGECGGGFGFFFGEEGFDFEFD
+ at HS21_09876:1:2103:18144:97839#75
+TAAGAGTCAGGGGCTCAAGGCGTTGCGACAGCCGGATGGAACGCCTTTCCTCGC
++
+CCCFFFFFHHGFCEE'EIFFGFDFDFECGGHEFGGFFCGFGFGDGEGEHGFEFD
+ at HS21_09876:1:1109:10864:56828#75
+TAAGAGTCAGCCCGCTGACCAGCGATGACGCCGCCTTCGACGCCTTCGCCAAGC
++
+BCCDFFFFHHHFABE2EHFGCFEEE<FCHGFEHEGFEGFE=FGFGEECHGFFFE
+ at HS21_09876:1:2102:16237:67170#75
+TAAGAGTCAGGGGACAAGCACCTGGCCAGGAAAGGCGCGCTGATCTTCGCCCGC
++
+B at CFFFFFHHHHCBF8GEFEGFGECFFEFEIEFEGFGGGFGFFGGEGEHGFGFD
+ at HS21_09876:1:1107:14911:52768#75
+TAAGAGTCAGGGGGACACTCCGCTGAGGGACGTCGGCAGCGACAGCCGCCAGCA
++
+CCCFFFFFHHA?8B<48<?<E9EEI<B;>DFEAF?FEGAD==GE98EG=G@@ED
+ at HS21_09876:1:2108:6881:4925#75
+TAAGAGTCAGGGGGACACTCCGCTGAGGGACGTCGGCAGCGACAGCCGCCAGCA
++
+CCCFFFEEHHHHCEE0EEFGFFGGEFDGHEFEEFGFGFGFGFGDGDEEHGDEFE
+ at HS21_09876:1:1111:18499:9859#75
+TAAGAGTCAGCCCGCTGAGGGACGTCGGCAGCGACAGCCGCCAGCACGCCATCC
++
+BBCFFFFFHHHHCEF0GEFDEFEFIFFGGGFEHDGFFGGFGFFEGEGFHGFGFF
+ at HS21_09876:1:1210:19511:97335#75
+TAAGAGTCAGCCCGCTGAGGGACGTCGGCAGCGACAGCCGCCAGCACGCCATCC
++
+CCCFFFFDHFFHCDH7HGFGGFGEIFFGHGHEFFGFFGFEGFFGGGGEHGFEFD
+ at HS21_09876:1:1103:13218:78186#75
+TAAGAGTCAGCCCGTAGCGGTGGCCGGTTCGATCCTGCAGCACTTCGTGCCGAT
++
+CCCFFFFFHHHHCDF7EEFDC9GEFFECEEFEHGGFGGFFGFFFGGFGFGFFFC
+ at HS21_09876:1:2107:11891:7630#75
+TAAGAGTCAGCCCGTAGCGGTGGCCGGTTCGATCCTGCAGCACTTCGTGCCGAT
++
+ at CCFFDDDHFFHCED0GIFDEFGEEFFDEFIEEFEFFEFEGFFBGEFGFGFEFD
+ at HS21_09876:1:2201:9833:67072#75
+TAAGAGTCAGCCCGTAGCGGTGGCCGGTTCGATCCTGCAGCACTTCGTGCCGAT
++
+CCCFFFFFHHHHCEE5GHFDEFGHDFEDFEGEEHGFGGFFGFGFGDGGFGFEFC
+ at HS21_09876:2:2101:20921:89053#75
+TAAGAGTCAGGGGATAGAAACGGTTAATGCTCTTGGGACGGCGCTTTTCTGTGC
++
+CCCFFFFFHHHHD9E0FEFEGGGFHFFHHGGFGCFGFHFFGGGFFFFFGFEEEF
+ at HS21_09876:2:2205:9713:92092#75
+TAAGAGTCAGGGGATAGAAACGGTTAATGCTCTTGGGACGGCGCTTTTCTGTGC
++
+CCCFFFFFHHHGED<6?EFEDG;:EEC;=GEAG at GFF;FGGCA9F>DFDFCE at E
+ at HS21_09876:2:2208:11577:65116#75
+TAAGAGTCAGGGGATAGAAACGGTTAATGCTCTTGGGACGGCGCTTTTCTGTGC
++
+BBCFFDFFDFFA at AE3F3@D:GGFD:FHD>=FGFGD<A>1GDAGF?<FG?EBFC
+ at HS21_09876:2:2210:17556:49545#75
+TAAGAGTCAGGGGATAGAAACGGTTAATGCTCTTGGGACGGCGCTTTTCTGTGC
++
+B at BFFFFFHHHHF9E1FDGEE=GDDEFAH>FEGGDEFGFFGDG9FF<FEFH:FB
+ at HS21_09876:2:1203:11706:53883#75
+TAAGAGTCAGGGGCAAAAGGTTGTCGAGAACCGGTGTCGAGGCTGTTTCCTTCC
++
+B at CFFFFFHHHHEDE,FFFEGG;:HEFDHGG6GC=>FFFCG;AFFFFFGFEF9E
+ at HS21_09876:2:2103:7357:48165#75
+TAAGAGTCAGCCCATCCACCTGCTGGGCCTGGCGCGTTCATTCCGCAGTGCGCG
++
+CCCFFFFFHHHHDEE3GEDFGGGFEGGFHGFFGGGEFHFFGGGFFFFFDFHFEF
+ at HS21_09876:2:1102:4592:99056#75
+TAAGAGTCAGGGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG
++
+BBCFFFFFHHHHDDE,FFGFFGGF-GIFCFGFGHDDFGFFGGEFFFFFEFFFED
+ at HS21_09876:2:1105:18701:63246#75
+TAAGAGTCAGGGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG
++
+BBCFFFFFHHHHFDE3FFFEFGGDDFFFDEHEGHGFFFFF>GFFFFFFGFEFED
+ at HS21_09876:2:1107:9181:47786#75
+TAAGAGTCAGGGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG
++
+CCCFFFFFHFHHEDE1FFF4GGGEEFGFFGFHGHGFFHFFGEGFFFEFEFEFCE
+ at HS21_09876:2:2101:7072:68459#75
+TAAGAGTCAGGGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG
++
+CCCFFFFFHHHHDEE3FFFFDGGF7EFHAFFGGFGEFHFFGGGFFFFFGFHFFD
+ at HS21_09876:2:2104:11024:92879#75
+TAAGAGTCAGGGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG
++
+CCCFFFFFHHHHDDE7FFDG:GGDEEFF=GGFAHFFFFFGGEEFFFFFGFEFEF
+ at HS21_09876:2:2106:9334:51625#75
+TAAGAGTCAGGGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG
++
+BB at FBDADFHHFEA<1FFG::=GFH0=;1>=FA at D>FAF<>;A9FFFFG?=B9E
+ at HS21_09876:2:2107:14640:85151#75
+TAAGAGTCAGGGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG
++
+BB at BDDFFHHFHFEE,FIDFDGGDFFGF=GHGGHFFFHFHGEGFFF at FGEEEDD
+ at HS21_09876:2:2201:18727:56295#75
+TAAGAGTCAGGGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG
++
+B=BDFFFFHHD>EAE3GDFCD=GEEDGH1>C6GGD>FG3FGHEFFF0F7EEDDC
+ at HS21_09876:2:2203:20492:60041#75
+TAAGAGTCAGGGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG
++
+CCCFFFFEHFFFCEE'FFFFDGGEEGGFAFFFGHGDFHFFGHGFFFFFGEEEEF
+ at HS21_09876:2:1102:1602:23426#75
+TAAGAGTCAGGGGATGGGGCTGATCTCGGCCATGGTCTCGCTGACCCAGGCTTC
++
+BBCFFFFFHHFHDAE6FFDEGGGDC:FDHEGHA at GGFGFFGEGFFFFFGEFBFE
+ at HS21_09876:2:1104:6936:48990#75
+TAAGAGTCAGGGGATGGGGCTGATCTCGGCCATGGTCTCGCTGACCCAGGCTTC
++
+CCCFFFFFHHHHDEE,FFFEGGGDF:F;HFGFGFGEFGFFGGEGFFFFGFFFEF
+ at HS21_09876:2:2101:9813:71457#75
+TAAGAGTCAGGGGATGGGGCTGATCTCGGCCATGGTCTCGCTGACCCAGGCTTC
++
+BCCDFFFFHHHHEEE3FIDEGGGDEDFAHGGGGGGGFFFFGHEFFFFFEFHDEF
+ at HS21_09876:2:2201:13960:2115#75
+TAAGAGTCAGGGGATGGGGCTGATCTCGGCCATGGTCTCGCTGACCCAGGCTTC
++
+BCCFFFFFHHHHFEE4FFGEGGGDFAGDHGHGGGGFFGFFGEDFFFFFDFHDED
+ at HS21_09876:2:2202:14819:44089#75
+TAAGAGTCAGGGGATGGGGCTGATCTCGGCCATGGTCTCGCTGACCCAGGCTTC
++
+CCCFFFFFHHHHD9E4GFFFIGGDF:GDHGGGGHGFFFFFGEEGFFFFEFEEEG
+ at HS21_09876:2:2203:10287:44498#75
+TAAGAGTCAGGGGATGGGGCTGATCTCGGCCATGGTCTCGCTGACCCAGGCTTC
++
+BCCFFFFFHHHHDEE6GIFEGGGDDDGHHGGFGFGFFFFEGFFGFFFFGFEEEF
+ at HS21_09876:2:2206:9622:55348#75
+TAAGAGTCAGGGGATGGGGCTGATCTCGGCCATGGTCTCGCTGACCCAGGCTTC
++
+BBCFFFFFHHHHDDE,FFFEGGGDFAGHHGGFGHFDFFFFGGDFFFFFDEHEEE
+ at HS21_09876:2:1101:1182:4708#75
+TAAGAGTCAGGGGGCTGATCTCGGCCATGGTCTCGCTGACCCAGGCTTCGGCGC
++
+BBBFFFFFHHGHF=E6EFFEEGGGFDGGEGFAGFGFFCFFGHEFFFEFFGFEED
+ at HS21_09876:2:2207:16105:64688#75
+TAAGAGTCAGGGGGCTGATCTCGGCCATGGTCTCGCTGACCCAGGCTTCGGCGC
++
+BCCFFFFFHHHHFEE1FFDDDGBFEGCFAFFEGHDEFCFEGDF9F;<FDFHF at F
+ at HS21_09876:2:2208:6290:56164#75
+TAAGAGTCAGGGGGCTGATCTCGGCCATGGTCTCGCTGACCCAGGCTTCGGCGC
++
+BCCFFFFFHHHHFEE7FEFDEGCFFGFHHEFHGFGGFAFFGGGGFF at FGEEFCG
+ at HS21_09876:2:1103:10943:7841#75
+TAAGAGTCAGGGGACATCGATGCGCAGTTGGCCATGAACGGAAAGGATCGATTC
++
+BCBFFFFFHHHHFDE8FFFFDGGFEECFHGHFGFFDFFFFGGFFFFFFGFEDEF
+ at HS21_09876:2:2105:16580:94645#75
+TAAGAGTCAGGGGACATCGATGCGCAGTTGGCCATGAACGGAAAGGATCGATTC
++
+CCCDFFFFHHHGEDE3GEFGGGG6FGGHHFHFGFGFFGFEGFEFFFFFGFEFCG
+ at HS21_09876:2:2201:10169:48549#75
+TAAGAGTCAGGGGACATCGATGCGCAGTTGGCCATGAACGGAAAGGATCGATTC
++
+CCCFFFFFHHHHFEE6GFFDEGGFHEFFHFHFGGGDFFFFGFGFFFFFGFEECC
+ at HS21_09876:2:1206:3642:93629#75
+TAAGAGTCAGCCCCCTACGCTGGACAATCTGTACTAGATTCAATAATGGCAATG
++
+BCCDFFFFHHFBEA<'F>@EFGG:EEFH=FCEG3FF<;FFGHFFFFDFGECEDF
+ at HS21_09876:2:1212:2848:49763#75
+TAAGAGTCAGCCCCCTACGCTGGACAATCTGTACTAGATTCAATAATGGCAATG
++
+BCCDDEFFHGGHFDE,DDEDHG;E;FG;HFGEGFGDFF3FGEGFFFFF7FFF9D
+ at HS21_09876:2:2101:18079:59533#75
+TAAGAGTCAGCCCGTGAAACGCCTGAAAAAGACACTGCACCTTTCAAGCTTGTC
++
+@@@DDDDDHHA+9AB1F>G01AG:CD1H=>CEA3F3FA><G;GF</CFBEC/B8
+ at HS21_09876:2:2203:9677:46062#75
+TAAGAGTCAGGAAAAAAGACACTGCACCTTTCAAGCTTGTCCCTCGTTTCCCTG
++
+BCCFFFFFHHHHFDE1FEDEGGCGHGFHHGGFGHGFFHFFGEGFFFFFGFEEED
+ at HS21_09876:2:1205:13947:81320#75
+TAAGAGTCAGGGGGCAAGGAATGGACCGAAAGCCACCGCCAGGACTTCTACAGC
++
+CCCFFFFFHHHHDEE6FFGEGGGFHGGFHGGGGGGFFFFFGFGFFFFFEFEDEG
+ at HS21_09876:2:1208:6932:10738#75
+TAAGAGTCAGGGGGCAAGGAATGGACCGAAAGCCACCGCCAGGACTTCTACAGC
++
+B at CDDEFFHDHHCEE7FFGEGGGEDEGFHFHEGFGGFHFFGFGEFFFFGEEFDE
+ at HS21_09876:2:2106:12096:83091#75
+TAAGAGTCAGGGGGCAAGGAATGGACCGAAAGCCACCGCCAGGACTTCTACAGC
++
+BCCFFFFFHHHHDEE0GFDEIGGGEGGGHGGFGHGFFFFFGFGFFFFFDEEECE
+ at HS21_09876:2:2106:9969:96661#75
+TAAGAGTCAGGGGGCAAGGAATGGACCGAAAGCCACCGCCAGGACTTCTACAGC
++
+BBBFFADDAF?D1AE6FFFGEGGEDGCDHGGAG at D>FAFEGEGFFFEFGFEEEE
+ at HS21_09876:2:1111:18613:97316#75
+TAAGAGTCAGCCCCCTGCCCTGGCTCAAGGCGTTGCGACAGCCGGATGGAACGC
++
+BBCBDFFFHHHHDAE,EFFFGGGEEEGADEHFGCGDFGFFGGGFFFFFDGEFCE
+ at HS21_09876:2:2112:7311:2729#75
+TAAGAGTCAGCCCCCTGCCCTGGCTCAAGGCGTTGCGACAGCCGGATGGAACGC
++
+BCCDFEFEHFFH7EE)GEGFFGGGCEI;HGGFGFGFFHFEGEG6FFDFECC76D
+ at HS21_09876:2:2209:5184:70364#75
+TAAGAGTCAGCCCCCTGCCCTGGCTCAAGGCGTTGCGACAGCCGGATGGAACGC
++
+CCCFFFFFHFFHDEE7FFFGFGGGDGGHHGGFGFGDFCFFGEEGFFFFEFFFEF
+ at HS21_09876:2:2206:10363:37150#75
+TAAGAGTCAGGGGGCTTCACCGTAGCCGGCACGGGCGCCCGGCAGATGGTCGGC
++
+BBBFFFFFHHHHDDE1FF at HIGGE?GGFHFEFGHGEFFFFGFGFFFFFGEEFBE
+ at HS21_09876:2:1211:8018:71514#75
+TAAGAGTCAGCCCGCTGACCAGCGATGACGCCGCCTTCGACGCCTTCGCCAAGC
++
+BBCDDEDFHHGHDAE,FEDE:2;ECF=H=>GF5 at G>FGFH3CGFFF at FDEEF9E
+ at HS21_09876:2:2207:12305:87719#75
+TAAGAGTCAGCCCGCTGACCAGCGATGACGCCGCCTTCGACGCCTTCGCCAAGC
++
+@@CADAADFFFFFEE6FEGFGGGFEFFHHGGFGHGFFHFEGHEFFFEFGFEDEB
+ at HS21_09876:2:1109:4620:60950#75
+TAAGAGTCAGAAAGCAGATCCTCGGGGCCAATCCGCCTCCCGGTGCGCGCGACG
++
+CCCFFFFFHHHHDEE4FFFEGGGHFGGFHFCFGFGEFHFFGGEGFFFFDFEFCE
+ at HS21_09876:2:1108:17674:57476#75
+TAAGAGTCAGCCCTTCCACCCGCAGAAGAGCAAGTTCCACCTGCTGGGCATGGA
++
+CCCFFFFFHHHHFEE4FFDGIGGGFGGFHGGFGGGFFFFFGFFFFFFFDFHFEC
+ at HS21_09876:2:1208:4027:38154#75
+TAAGAGTCAGCCCTTCCACCCGCAGAAGAGCAAGTTCCACCTGCTGGGCATGGA
++
+BCCFFFFFHHHHFEE6GFFEIGGGCGFFHGGFGGGEFGFFGFGFFFFFDFHFFE
+ at HS21_09876:2:2104:21108:77778#75
+TAAGAGTCAGCCCTTCCACCCGCAGAAGAGCAAGTTCCACCTGCTGGGCATGGA
++
+CCCFFFFFHHHHDEE,EFFGFGGDEEGHHGGFGCGFFCFFGFEFFFDFGCHFE8
+ at HS21_09876:2:1105:10717:93499#75
+TAAGAGTCAGGGGGACACTCCGCTGAGGGACGTCGGCAGCGACAGCCGCCAGCA
++
+CCCFFFFFHHHHDEB6DFFFDG;EEFFFAGHFGFGFFAFFGEGFFFFFGCH:9F
+ at HS21_09876:2:2107:17307:90872#75
+TAAGAGTCAGCCCGCTGAGGGACGTCGGCAGCGACAGCCGCCAGCACGCCATCC
++
+BCCDFEFDHHFHDAE7FFFFFGGFHGGHHGFFGGGEFFFFGGEFFFFFDFHEEG
+ at HS21_09876:2:2108:10562:66996#75
+TAAGAGTCAGCCCGCTGAGGGACGTCGGCAGCGACAGCCGCCAGCACGCCATCC
++
+CCCFFFFEHHFFDEE6FFDIGGGF>GFHHGFFGFGFFFFFGEGFFFFFDFFFCD
+ at HS21_09876:2:1204:3124:19338#75
+TAAGAGTCAGGGGTGCAGACCGGCGTGATGGAGGGCGCGCGGATGCCGTTCGGC
++
+CCCFFFFFHHHHDAE6FFGEIGGEHDGHHGGFGFDEFFFEGEEFFFFFDEEFFF
+ at HS21_09876:2:1104:8314:51088#75
+TAAGAGTCAGCCCGTAGCGGTGGCCGGTTCGATCCTGCAGCACTTCGTGCCGAT
++
+CCCFFFFFHGDFFEE1GFGEFGGEDDGDH>GAGFGFFHFFGGECFFFFGFHBDC
+ at HS21_09876:2:1205:9430:9196#75
+TAAGAGTCAGCCCGTAGCGGTGGCCGGTTCGATCCTGCAGCACTTCGTGCCGAT
++
+BBCDFFFFHHHHDEE7FFFGDGGEHEFHHFHFGFGDFFFFGGGFFFFFDFEFCC
+ at HS21_09876:2:1211:6841:16284#75
+TAAGAGTCAGCCCGTAGCGGTGGCCGGTTCGATCCTGCAGCACTTCGTGCCGAT
++
+BCCFFFFFHHHHDDE1FEDEE=GEFGFHHGGEGFG>FFFCGCG at FF@FDGF at DE
+ at HS21_09876:2:2101:5488:100342#75
+TAAGAGTCAGCCCGTAGCGGTGGCCGGTTCGATCCTGCAGCACTTCGTGCCGAT
++
+CCCFFFDDHHHHDEE3FFGCD=GFEGFHHEGEGFFDFGFEGDEFFFFFGFEFB8
+ at HS21_09876:2:2109:9412:27195#75
+TAAGAGTCAGCCCGTAGCGGTGGCCGGTTCGATCCTGCAGCACTTCGTGCCGAT
++
+BCCFFFFEHGBCC@<,D>GF:CGFDGGD=GG6ACDDF at FFGDECFFFF7EEDE.
+ at HS21_09876:2:2208:5757:63730#75
+TAAGAGTCAGCCCGTAGCGGTGGCCGGTTCGATCCTGCAGCACTTCGTGCCGAT
++
+BCCDDEFFHFHHFEE6FIFEEGGFEFIF=GHGGHGFFH>FGEG9FFEFDFHFEB
diff --git a/t/data/RunTradis/test2.tagged.fastq.gz b/t/data/RunTradis/test2.tagged.fastq.gz
new file mode 100644
index 0000000..0e187f2
Binary files /dev/null and b/t/data/RunTradis/test2.tagged.fastq.gz differ
diff --git a/t/data/TradisPlot/expected.plot.gz b/t/data/TradisPlot/expected.plot.gz
new file mode 100644
index 0000000..34168ba
Binary files /dev/null and b/t/data/TradisPlot/expected.plot.gz differ
diff --git a/t/data/TradisPlot/sample.fastq b/t/data/TradisPlot/sample.fastq
new file mode 100644
index 0000000..c10bf1f
--- /dev/null
+++ b/t/data/TradisPlot/sample.fastq
@@ -0,0 +1,52 @@
+ at IL2_4334:7:5:6843:6843
+CAACGTTTTCTGCGTGTTGCCGATATTCTGGAAAGCA
++
+=8>;A<@>=B;FF8>CCF:=CC-7(C>/22C:4;<=;
+ at IL2_4334:7:5:18259:13400
+CAACGTTTTCTGCGTGTTGCCGATATTCTGGAAAGCA
++
+<8:=B>=B(B88A?C@@A;;B at +21AA/38><8=C;>
+ at IL2_4334:7:15:5608:3756
+CAACGTTTTCTGCGTGTTGCCGATATTTTGGAAAGCA
++
+9AA9:17<988@=@AB6=:?;:-08C=&,6C@:8A4=
+ at IL2_4334:7:18:16351:15714
+CAACGTTTTCTGCGTGTTGCCGATATTCTGGAAAGCA
++
+<===?;=@<<>FCBFF=:B7?A+4/A>(22@?64?5@
+ at IL2_4334:7:39:12877:7020
+CAACGTTTTCTGCGTGTTGCCGATATTCTGGAAAGCA
++
+=B?=<>ACB=@;FFF=FFA<AC071??/84C=;3?75
+ at IL2_4334:7:42:14437:19550
+CAACGTTTTCTGCGTGTTGCCGATATTCTGGAAAGCA
++
+<7=B8 at B=;8;DF;CF;F;8A?2<6;:18;81;<;8C
+ at IL2_4334:7:53:4426:3757
+CAACGTTTTCTGCGTGTTGCCGATATTCTGGAAAGCA
++
+=B<7<:9B@:@AF at A>?F@<F=47. at A,11D<45D9<
+ at IL2_4334:7:79:9021:16833
+CAACGTTTTCTGCGTGTTGCCGATATTCTGGAAAGCA
++
+;A:7A;CBFBFA?ABCC>86 at B:C?A>6=:6<CB:>C
+ at IL2_4334:6:120:19845:10197
+TNAGAGACAGGTATTACTCTGCATCANTNAANNGAGA
++
+:)::9:9;BA;1CB7F:BCC==7 at 5A)=%76%%0B67
+ at IL2_4334:7:82:17494:18362
+CAACGTTTTCTGCGTGTTGCCGATATTCTGGAAAGCA
++
+<79:<9;7<>8=CB@:C:AB=7410=C-46;,75>>F
+ at IL2_4334:7:84:7230:17356
+CAACGTTTTCTGCGTGTTGCCGATATTCTGGAAAGCA
++
+DADFDFFDDD>8:=>=?@48 at 87A4@F6>??BF??B@
+ at IL2_4334:6:120:19846:21043
+TNAGAGACAGTGTCTAGGGCATCACTNANGGNNGAGG
++
+<)72:19:?>:A>C?@@??CC@?:6;)5%>9%%;;;<
+ at IL2_4334:6:120:19846:19594
+TNAGAGACAGATCCTATGGGGCTGAANTNTNNNGTGA
++
+:)7:782?=AC<;@=5444@:B;>?*%)%4%%%?161
\ No newline at end of file
diff --git a/t/data/TradisPlot/test.mapped.bam b/t/data/TradisPlot/test.mapped.bam
new file mode 100644
index 0000000..57a47a6
Binary files /dev/null and b/t/data/TradisPlot/test.mapped.bam differ
--
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