Software Open Access

SLiMSuite v1.8.1 (2019-05-27)

Richard J. Edwards

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    <subfield code="a">slimsuite</subfield>
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    <subfield code="a">bioinformatics</subfield>
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    <subfield code="a">motif discovery</subfield>
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    <subfield code="a">sequence analysis</subfield>
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    <subfield code="c">2019-05-27</subfield>
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    <subfield code="u">University of New South Wales</subfield>
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    <subfield code="a">Richard J. Edwards</subfield>
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    <subfield code="a">SLiMSuite v1.8.1 (2019-05-27)</subfield>
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    <subfield code="a">GNU General Public License v3.0 or later</subfield>
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    <subfield code="a">&lt;p&gt;Please see the &lt;a href=""&gt;SLiMSuite GitHub repo&lt;/a&gt; for updates to this code since release.&lt;/p&gt;

&lt;p&gt;This update has fast-forwarded the SLiMSuite release to &lt;code&gt;v1.8.1&lt;/code&gt; to be consistent with the &lt;code&gt;tools/;/code&gt; wrapper script. A top level &lt;code&gt;;/code&gt; file can now be run to access the main tools and functions of the package.&lt;/p&gt;

&lt;p&gt;&lt;a href=""&gt;SLiMSuite REST servers&lt;/a&gt; have been updated to match this release.&lt;/p&gt;

&lt;p&gt;A summary of the changes since the last release is given below.&lt;/p&gt;

&lt;p&gt;SLiMSuite updates&lt;/p&gt;

&lt;p&gt;Updates in Error/:&lt;/p&gt;

&lt;p&gt;&lt;strong&gt;&amp;bull; SLiMSuite:&lt;/strong&gt; &lt;em&gt;Created/Renamed/moved.&lt;/em&gt;&lt;br&gt;
&amp;rarr; Version 1.4.0: SLiMSuite v1.4.0 (2018-07-02) release. Added this top level file to track overall version number.&lt;br&gt;
&amp;rarr; Version 1.4.1: SLiMBench v2.18.3 - Added better handling of motifs without TP occurrences for OccBench. Added minocctp=INT.&lt;/p&gt;

&lt;p&gt;Updates in extras/:&lt;/p&gt;


&lt;p&gt;&lt;strong&gt;&amp;bull; rje_pydocs:&lt;/strong&gt; &lt;em&gt;Updated from Version 2.16.7.&lt;/em&gt;&lt;br&gt;
&amp;rarr; Version 2.16.8: Updated to to parse https.&lt;br&gt;
&amp;rarr; Version 2.16.9: Tweaked docstring parsing.&lt;/p&gt;

&lt;p&gt;Updates in libraries/:&lt;/p&gt;

&lt;p&gt;&lt;strong&gt;&amp;bull; rje:&lt;/strong&gt; &lt;em&gt;Updated from Version 4.19.0.&lt;/em&gt;&lt;br&gt;
&amp;rarr; Version 4.19.1: Added code for catching non-ASCII log filenames.&lt;br&gt;
&amp;rarr; Version 4.20.0: Added quiet mode to log object and output of errors to stderr. Fixed rankList(unique=True)&lt;br&gt;
&amp;rarr; Version 4.21.0: Added hashlib MD% functions.&lt;br&gt;
&amp;rarr; Version 4.21.1: Fixed bug where silent=T wasn&amp;#39;t running silent.&lt;/p&gt;

&lt;p&gt;&lt;strong&gt;&amp;bull; rje_blast_V2:&lt;/strong&gt; &lt;em&gt;Updated from Version 2.22.2.&lt;/em&gt;&lt;br&gt;
&amp;rarr; Version 2.23.3: Fixed LocalIDCut error for GABLAM and QAssemble stat filtering.&lt;/p&gt;

&lt;p&gt;&lt;strong&gt;&amp;bull; rje_db:&lt;/strong&gt; &lt;em&gt;Updated from Version 1.9.0.&lt;/em&gt;&lt;br&gt;
&amp;rarr; Version 1.9.1: Updated logging of adding/removing fields: default is now when debugging only.&lt;/p&gt;

&lt;p&gt;&lt;strong&gt;&amp;bull; rje_disorder:&lt;/strong&gt; &lt;em&gt;Updated from Version 1.2.0.&lt;/em&gt;&lt;br&gt;
&amp;rarr; Version 1.3.0: Switched default behaviour to be md5acc=T.&lt;br&gt;
&amp;rarr; Version 1.4.0: Fixed up disorder=parse and disorder=foldindex.&lt;br&gt;
&amp;rarr; Version 1.5.0: Added iupred2 and anchor2 parsing from URL using accnum. Made default disorder=iushort2.&lt;/p&gt;

&lt;p&gt;&lt;strong&gt;&amp;bull; rje_genbank:&lt;/strong&gt; &lt;em&gt;Updated from Version 1.5.3.&lt;/em&gt;&lt;br&gt;
&amp;rarr; Version 1.5.4: Added recognition of *.gbff for genbank files.&lt;/p&gt;

&lt;p&gt;&lt;strong&gt;&amp;bull; rje_obj:&lt;/strong&gt; &lt;em&gt;Updated from Version 2.2.2.&lt;/em&gt;&lt;br&gt;
&amp;rarr; Version 2.3.0: Added quiet mode to object and stderr output.&lt;br&gt;
&amp;rarr; Version 2.4.0: Added vLog() and bugLog() methods.&lt;br&gt;
&amp;rarr; Version 2.4.1: Fixed bug where silent=T wasn&amp;#39;t running silent.&lt;/p&gt;

&lt;p&gt;&lt;strong&gt;&amp;bull; rje_paf:&lt;/strong&gt; &lt;em&gt;Created/Renamed/moved.&lt;/em&gt;&lt;br&gt;
&amp;rarr; Version 0.0.0: Initial Compilation.&lt;br&gt;
&amp;rarr; Version 0.1.0: Initial working version. Compatible with GABLAM v2.30.0 and Snapper v1.7.0.&lt;br&gt;
&amp;rarr; Version 0.2.0: Added endextend=X : Extend minimap2 hits to end of sequence if with X bp [10]&lt;br&gt;
&amp;rarr; Version 0.3.0: Added mapsplice mode for dealing with transcript mapping.&lt;br&gt;
&amp;rarr; Version 0.3.1: Correct PAF splicing bug.&lt;br&gt;
&amp;rarr; Version 0.4.0: Added TmpDir and forking for GABLAM conversion.&lt;br&gt;
&amp;rarr; Version 0.5.0: Added uniquehit=T/F : Option to use *.hitunique.tdt table of unique coverage for GABLAM coverage stats [False]&lt;/p&gt;

&lt;p&gt;&lt;strong&gt;&amp;bull; rje_ppi:&lt;/strong&gt; &lt;em&gt;Updated from Version 2.8.1.&lt;/em&gt;&lt;br&gt;
&amp;rarr; Version 2.9.0: Added ppiout=FILE : Save pairwise PPI file following processing (if rest=None) [None]&lt;/p&gt;

&lt;p&gt;&lt;strong&gt;&amp;bull; rje_qsub:&lt;/strong&gt; &lt;em&gt;Updated from Version 1.9.2.&lt;/em&gt;&lt;br&gt;
&amp;rarr; Version 1.9.3: Updates the order of the qsub -S /bin/bash flag.&lt;/p&gt;

&lt;p&gt;&lt;strong&gt;&amp;bull; rje_rmd:&lt;/strong&gt; &lt;em&gt;Created/Renamed/moved.&lt;/em&gt;&lt;br&gt;
&amp;rarr; Version 0.0.0: Initial Compilation.&lt;/p&gt;

&lt;p&gt;&lt;strong&gt;&amp;bull; rje_samtools:&lt;/strong&gt; &lt;em&gt;Updated from Version 1.20.0.&lt;/em&gt;&lt;br&gt;
&amp;rarr; Version 1.20.1: Fixed mlen bug. Added catching of unmapped reads in SAM file. Fixed RLen bug. Changed softclip defaults.&lt;br&gt;
&amp;rarr; Version 1.20.2: Fixed readlen coverage bug and acut bug.&lt;/p&gt;

&lt;p&gt;&lt;strong&gt;&amp;bull; rje_seq:&lt;/strong&gt; &lt;em&gt;Updated from Version 3.25.0.&lt;/em&gt;&lt;br&gt;
&amp;rarr; Version 3.25.1: Fixed -long_seqids retrieval bug.&lt;br&gt;
&amp;rarr; Version 3.25.2: Fixed 9spec filtering bug.&lt;/p&gt;

&lt;p&gt;&lt;strong&gt;&amp;bull; rje_seqlist:&lt;/strong&gt; &lt;em&gt;Updated from Version 1.29.0.&lt;/em&gt;&lt;br&gt;
&amp;rarr; Version 1.30.0: Updated and improved DNA2Protein.&lt;br&gt;
&amp;rarr; Version 1.31.0: Added genecounter to rename option for use with other programs, e.g. PAGSAT.&lt;br&gt;
&amp;rarr; Version 1.31.1: Fixed edit bug when not in DNA mode.&lt;br&gt;
&amp;rarr; Version 1.32.0: Added genomesize and NG50/LG50 to DNA summarise.&lt;br&gt;
&amp;rarr; Version 1.32.1: Fixed LG50/L50 bug.&lt;/p&gt;

&lt;p&gt;&lt;strong&gt;&amp;bull; rje_sequence:&lt;/strong&gt; &lt;em&gt;Updated from Version 2.6.0.&lt;/em&gt;&lt;br&gt;
&amp;rarr; Version 2.7.0: Added shift=X to maskRegion() for 1-L input. Fixed cterminal maskRegion.&lt;/p&gt;

&lt;p&gt;&lt;strong&gt;&amp;bull; rje_slimcore:&lt;/strong&gt; &lt;em&gt;Updated from Version 2.9.0.&lt;/em&gt;&lt;br&gt;
&amp;rarr; Version 2.10.0: Added seqfilter=T/F : Whether to apply sequence filtering options (goodX, badX etc.) to input [False]&lt;br&gt;
&amp;rarr; Version 2.10.1: Fixed default results file bug.&lt;br&gt;
&amp;rarr; Version 2.10.2: Improved handling and REST output of disorder scores.&lt;br&gt;
&amp;rarr; Version 2.11.0: Modified qregion=X,Y to be 1-L numbering.&lt;/p&gt;

&lt;p&gt;&lt;strong&gt;&amp;bull; rje_slimlist:&lt;/strong&gt; &lt;em&gt;Updated from Version 1.7.3.&lt;/em&gt;&lt;br&gt;
&amp;rarr; Version 1.7.4: Modified concetanation of SLiMSuite results to use &amp;quot;|&amp;quot; in place of &amp;quot;#&amp;quot; for better compatibility.&lt;/p&gt;

&lt;p&gt;&lt;strong&gt;&amp;bull; rje_uniprot:&lt;/strong&gt; &lt;em&gt;Updated from Version 3.25.0.&lt;/em&gt;&lt;br&gt;
&amp;rarr; Version 3.25.1: Fixed proteome download bug following Uniprot changes.&lt;br&gt;
&amp;rarr; Version 3.25.2: Fixed Uniprot protein extraction issues by using curl. (May not be a robust fix!)&lt;/p&gt;

&lt;p&gt;Updates in tools/:&lt;/p&gt;


&lt;p&gt;&lt;strong&gt;&amp;bull; buscomp:&lt;/strong&gt; &lt;em&gt;Created/Renamed/moved.&lt;/em&gt;&lt;br&gt;
&amp;rarr; Version 0.0.0: Initial Compilation.&lt;br&gt;
&amp;rarr; Version 0.1.0: Basic working version.&lt;br&gt;
&amp;rarr; Version 0.2.0: Functional version with basic RMarkdown HTML output.&lt;br&gt;
&amp;rarr; Version 0.3.0: Added ratefas=FILELIST: Additional fasta files of assemblies to rate with BUSCOMPSeq (No BUSCO run) [].&lt;br&gt;
&amp;rarr; Version 0.4.0: Implemented forking and tidied up output a little.&lt;br&gt;
&amp;rarr; Version 0.5.0: Updated genome stats and RMarkdown HTML output. Reorganised assembly loading and proeccessing. Added menus.&lt;br&gt;
&amp;rarr; Version 0.5.1: Reorganised code for clearer flow and documentation. Unique and missing BUSCO output added.&lt;br&gt;
&amp;rarr; Version 0.5.2: Dropped paircomp method and added Rmarkdown control methods. Updated Rmarkdown descriptions. Updated log output.&lt;br&gt;
&amp;rarr; Version 0.5.3: Tweaked log output and fixed a few minor bugs.&lt;br&gt;
&amp;rarr; Version 0.5.4: Deleted some excess code and tweaked BUSCO percentage plot outputs.&lt;br&gt;
&amp;rarr; Version 0.5.5: Fixed minlocid bug and cleared up minimap temp directories. Added LnnIDxx to BUSCOMP outputs.&lt;br&gt;
&amp;rarr; Version 0.5.6: Added uniquehit=T/F : Option to use *.hitunique.tdt table of unique coverage for GABLAM coverage stats [False]&lt;br&gt;
&amp;rarr; Version 0.6.0: Added more minimap options, changed defaults and dev generation of a table changes in ratings from BUSCO to BUSCOMP.&lt;br&gt;
&amp;rarr; Version 0.6.1: Fixed bug that was including Duplicated sequences in the buscomp.fasta file. Added option to exclude from BUSCOMPSeq compilation.&lt;br&gt;
&amp;rarr; Version 0.6.2: Fixed bug introduced that had broken manual group review/editing.&lt;br&gt;
&amp;rarr; Version 0.7.0: Updated the defaults in the light of test analyses. Tweaked Rmd report.&lt;br&gt;
&amp;rarr; Version 0.7.1: Fixed unique group count bug when some genomes are not in a group. Fixed running with non-standard options.&lt;br&gt;
&amp;rarr; Version 0.7.2: Added loadsummary=T/F option to regenerate summaries and fixed bugs running without BUSCO results.&lt;/p&gt;

&lt;p&gt;&lt;strong&gt;&amp;bull; comparimotif_V3:&lt;/strong&gt; &lt;em&gt;Updated from Version 3.13.0.&lt;/em&gt;&lt;br&gt;
&amp;rarr; Version 3.14.0: Modified memsaver mode to take different input formats.&lt;/p&gt;

&lt;p&gt;&lt;strong&gt;&amp;bull; gablam:&lt;/strong&gt; &lt;em&gt;Updated from Version 2.29.0.&lt;/em&gt;&lt;br&gt;
&amp;rarr; Version 2.30.0: Added mapper=X : Program to use for mapping files against each other (blast/minimap) [blast]&lt;br&gt;
&amp;rarr; Version 2.30.1: Fixed BLAST LocalIDCut error for GABLAM and QAssemble stat filtering.&lt;/p&gt;

&lt;p&gt;&lt;strong&gt;&amp;bull; gopher:&lt;/strong&gt; &lt;em&gt;Updated from Version 3.4.3.&lt;/em&gt;&lt;br&gt;
&amp;rarr; Version 3.5.0: Added separate outputs for trees with different alignment programs.&lt;br&gt;
&amp;rarr; Version 3.5.1: Added capacity to run DNA GOPHER with tblastx. (Not tested!)&lt;br&gt;
&amp;rarr; Version 3.5.2: Added acc=LIST as alias for uniprotid=LIST and updated docstring for REST to make it clear that rest=X needed.&lt;/p&gt;

&lt;p&gt;&lt;strong&gt;&amp;bull; haqesac:&lt;/strong&gt; &lt;em&gt;Updated from Version 1.12.0.&lt;/em&gt;&lt;br&gt;
&amp;rarr; Version 1.13.0: Modified qregion=X,Y to be 1-L numbering.&lt;/p&gt;

&lt;p&gt;&lt;strong&gt;&amp;bull; pagsat:&lt;/strong&gt; &lt;em&gt;Updated from Version 2.4.0.&lt;/em&gt;&lt;br&gt;
&amp;rarr; Version 2.5.0: Reduced the executed code when mapfas=T assessment=F. (Recommended first run.) Added renaming.&lt;br&gt;
&amp;rarr; Version 2.5.1: Added recognition of *.gbff for genbank files.&lt;br&gt;
&amp;rarr; Version 2.6.0: Added mapper=X : Program to use for mapping files against each other (blast/minimap) [blast]&lt;br&gt;
&amp;rarr; Version 2.6.1: Switch failure to find key report files to a long warning, not program exit.&lt;br&gt;
&amp;rarr; Version 2.6.2: Fixed bugs with mapper=minimap mode and started adding more internal documentation.&lt;br&gt;
&amp;rarr; Version 2.6.3: Fixed default behaviour to run report=T mode.&lt;br&gt;
&amp;rarr; Version 2.6.4: Fixed summary table merge bug.&lt;br&gt;
&amp;rarr; Version 2.6.5: Fixed compile path bug.&lt;br&gt;
&amp;rarr; Version 2.6.6: Fixed BLAST LocalIDCut error for GABLAM and QAssemble stat filtering.&lt;br&gt;
&amp;rarr; Version 2.6.7: Generalised compile path bug fix.&lt;br&gt;
&amp;rarr; Version 2.6.8: Added ChromXcov fields to PAGSAT Compare.&lt;/p&gt;

&lt;p&gt;&lt;strong&gt;&amp;bull; pingu_V4:&lt;/strong&gt; &lt;em&gt;Updated from Version 4.9.0.&lt;/em&gt;&lt;br&gt;
&amp;rarr; Version 4.9.1: Fixed Pairwise parsing and filtering for more flexibility of input. Fixed fasid=X bug and ppiseqfile names.&lt;br&gt;
&amp;rarr; Version 4.10.0: Added hubfield and spokefield options for parsing hublist.&lt;/p&gt;

&lt;p&gt;&lt;strong&gt;&amp;bull; qslimfinder:&lt;/strong&gt; &lt;em&gt;Updated from Version 2.2.0.&lt;/em&gt;&lt;br&gt;
&amp;rarr; Version 2.3.0: Modified qregion=X,Y to be 1-L numbering.&lt;/p&gt;

&lt;p&gt;&lt;strong&gt;&amp;bull; samphaser:&lt;/strong&gt; &lt;em&gt;Created/Renamed/moved.&lt;/em&gt;&lt;br&gt;
&amp;rarr; Version 0.0.0: Initial Compilation.&lt;br&gt;
&amp;rarr; Version 0.1.0: Updated SAMPhaser to be more memory efficient.&lt;br&gt;
&amp;rarr; Version 0.2.0: Added reading of sequence and generation of SNP-altered haplotype blocks.&lt;br&gt;
&amp;rarr; Version 0.2.1: Fixed bug in which zero-phasing sequences were being excluded from blocks output.&lt;br&gt;
&amp;rarr; Version 0.3.0: Made a new unzip process.&lt;br&gt;
&amp;rarr; Version 0.4.0: Added RGraphics for unzip.&lt;br&gt;
&amp;rarr; Version 0.4.1: Fixed MeanX bug in devUnzip.&lt;br&gt;
&amp;rarr; Version 0.4.2: Made phaseindels=F by default: mononucleotide indel errors will probably add phasing noise. Fixed basefile R bug.&lt;br&gt;
&amp;rarr; Version 0.4.3: Fixed bug introduced by adding depthplot code. Fixed phaseindels bug. (Wasn&amp;#39;t working!)&lt;br&gt;
&amp;rarr; Version 0.4.4: Modified mincut=X to adjust for samtools V1.12.0.&lt;br&gt;
&amp;rarr; Version 0.4.5: Updated for modified RJE_SAMTools output.&lt;br&gt;
&amp;rarr; Version 0.4.6: splitzero=X : Whether to split haplotigs at zero-coverage regions of X+ bp (-1 = no split) [100]&lt;br&gt;
&amp;rarr; Version 0.5.0: snptable=T/F : Output filtered alleles to SNP Table [False]&lt;br&gt;
&amp;rarr; Version 0.6.0: Converted haplotig naming to be consistent for PAGSAT generation. Updated for rje_samtools v1.21.1.&lt;br&gt;
&amp;rarr; Version 0.7.0: Added skiploci=LIST and phaseloci=LIST : Optional list of loci to skip phasing []&lt;br&gt;
&amp;rarr; Version 0.8.0: poordepth=T/F : Whether to include reads with poor track probability in haplotig depth plots (random track) [False]&lt;/p&gt;

&lt;p&gt;&lt;strong&gt;&amp;bull; seqmapper:&lt;/strong&gt; &lt;em&gt;Updated from Version 2.2.0.&lt;/em&gt;&lt;br&gt;
&amp;rarr; Version 2.3.0: Added GABLAM-free method.&lt;/p&gt;

&lt;p&gt;&lt;strong&gt;&amp;bull; seqsuite:&lt;/strong&gt; &lt;em&gt;Updated from Version 1.19.1.&lt;/em&gt;&lt;br&gt;
&amp;rarr; Version 1.20.0: Added rje_paf.PAF.&lt;br&gt;
&amp;rarr; Version 1.21.0: Added NG50 and LG50 to batch summarise.&lt;br&gt;
&amp;rarr; Version 1.22.0: Added BUSCOMP to programs.&lt;br&gt;
&amp;rarr; Version 1.23.0: Added rje_ppi.PPI to programs.&lt;/p&gt;

&lt;p&gt;&lt;strong&gt;&amp;bull; slimbench:&lt;/strong&gt; &lt;em&gt;Updated from Version 2.18.2.&lt;/em&gt;&lt;br&gt;
&amp;rarr; Version 2.18.3: Added better handling of motifs without TP occurrences for OccBench. Added minocctp=INT.&lt;br&gt;
&amp;rarr; Version 2.18.4: Fixed ELMBench rating bug.&lt;br&gt;
&amp;rarr; Version 2.18.5: Fixed Balanced=F bug.&lt;br&gt;
&amp;rarr; Version 2.19.0: Implemented dataset=LIST: List of headers to split dataset into. If blank, will use datatype defaults. []&lt;/p&gt;

&lt;p&gt;&lt;strong&gt;&amp;bull; slimfarmer:&lt;/strong&gt; &lt;em&gt;Updated from Version 1.9.0.&lt;/em&gt;&lt;br&gt;
&amp;rarr; Version 1.10.0: Added appending contents of jobini file to slimsuite=F farm commands.&lt;/p&gt;

&lt;p&gt;&lt;strong&gt;&amp;bull; slimfinder:&lt;/strong&gt; &lt;em&gt;Updated from Version 5.3.4.&lt;/em&gt;&lt;br&gt;
&amp;rarr; Version 5.3.5: Fixed slimcheck and advanced stats models bug.&lt;br&gt;
&amp;rarr; Version 5.4.0: Modified qregion=X,Y to be 1-L numbering.&lt;/p&gt;

&lt;p&gt;&lt;strong&gt;&amp;bull; slimparser:&lt;/strong&gt; &lt;em&gt;Updated from Version 0.5.0.&lt;/em&gt;&lt;br&gt;
&amp;rarr; Version 0.5.1: Minor docs and bug fixes.&lt;br&gt;
&amp;rarr; Version 0.6.0: Improved functionality as replacement pureapi with rest=jobid and rest=check functions.&lt;/p&gt;

&lt;p&gt;&lt;strong&gt;&amp;bull; slimsuite:&lt;/strong&gt; &lt;em&gt;Updated from Version 1.7.1.&lt;/em&gt;&lt;br&gt;
&amp;rarr; Version 1.8.0: Added BUSCOMP and basic test function.&lt;br&gt;
&amp;rarr; Version 1.8.1: Updated documentation and added IUPred2. General tidy up and new example data for protocols paper.&lt;/p&gt;

&lt;p&gt;&lt;strong&gt;&amp;bull; smrtscape:&lt;/strong&gt; &lt;em&gt;Updated from Version 2.2.2.&lt;/em&gt;&lt;br&gt;
&amp;rarr; Version 2.2.3: Fixed bug where SMRT subreads are not returned by seqlist in correct order. Fixed RQ=0 bug.&lt;/p&gt;

&lt;p&gt;&lt;strong&gt;&amp;bull; snapper:&lt;/strong&gt; &lt;em&gt;Updated from Version 1.6.1.&lt;/em&gt;&lt;br&gt;
&amp;rarr; Version 1.7.0: Added mapper=minimap setting, compatible with GABLAM v2.30.0 and rje_paf v0.1.0.&lt;/p&gt;

&lt;p&gt;&amp;copy; RJ Edwards 2019. Last modified 27 May 2019.&lt;/p&gt;

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