--rsrs option crashes #49
Description
I would like to use HaploGrep to classify a FASTA sample with respect to the RSRS, but the option does not seem to work. I get the error:
`[classify, --in, simulations/Q1.fa, --out, here, --format, fasta, --rsrs]
phylotree17_FU1_rsrs.xml
Parameters:
Input format: fasta
Phylotree version: 17_FU1
Reference: RSRS
Extended report: false
Skip alignment rules: false
Used metric: kulczynski
Chip array data: false
Lineage: 0
Start Classification...
[M::bwa_idx_load_from_disk] read 0 ALT contigs
java.io.FileNotFoundException: phylotree17_FU1_rsrs.xml (No such file or directory)
at java.base/java.io.FileInputStream.open0(Native Method)
at java.base/java.io.FileInputStream.open(FileInputStream.java:213)
at java.base/java.io.FileInputStream.(FileInputStream.java:155)
at phylotree.PhylotreeManager.getPhylotree(PhylotreeManager.java:53)
at genepi.haplogrep.util.HgClassifier.run(HgClassifier.java:25)
at genepi.commands.HaplogrepCommand.call(HaplogrepCommand.java:178)
at genepi.commands.HaplogrepCommand.call(HaplogrepCommand.java:20)
at picocli.CommandLine.executeUserObject(CommandLine.java:1953)
at picocli.CommandLine.access$1300(CommandLine.java:145)
at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2352)
at picocli.CommandLine$RunLast.handle(CommandLine.java:2346)
at picocli.CommandLine$RunLast.handle(CommandLine.java:2311)
at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179)
at picocli.CommandLine.execute(CommandLine.java:2078)
at genepi.App.main(App.java:59)
java.net.MalformedURLException
at java.base/java.net.URL.(URL.java:702)
at java.base/java.net.URL.(URL.java:564)
at java.base/java.net.URL.(URL.java:511)
at java.xml/com.sun.org.apache.xerces.internal.impl.XMLEntityManager.setupCurrentEntity(XMLEntityManager.java:649)
at java.xml/com.sun.org.apache.xerces.internal.impl.XMLVersionDetector.determineDocVersion(XMLVersionDetector.java:150)
at java.xml/com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(XML11Configuration.java:860)
at java.xml/com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(XML11Configuration.java:824)
at java.xml/com.sun.org.apache.xerces.internal.parsers.XMLParser.parse(XMLParser.java:141)
at java.xml/com.sun.org.apache.xerces.internal.parsers.AbstractSAXParser.parse(AbstractSAXParser.java:1216)
at java.xml/com.sun.org.apache.xerces.internal.jaxp.SAXParserImpl$JAXPSAXParser.parse(SAXParserImpl.java:635)
at org.jdom.input.SAXBuilder.build(SAXBuilder.java:489)
at org.jdom.input.SAXBuilder.build(SAXBuilder.java:807)
at phylotree.Phylotree.(Phylotree.java:60)
at phylotree.PhylotreeManager.getPhylotree(PhylotreeManager.java:60)
at genepi.haplogrep.util.HgClassifier.run(HgClassifier.java:25)
at genepi.commands.HaplogrepCommand.call(HaplogrepCommand.java:178)
at genepi.commands.HaplogrepCommand.call(HaplogrepCommand.java:20)
at picocli.CommandLine.executeUserObject(CommandLine.java:1953)
at picocli.CommandLine.access$1300(CommandLine.java:145)
at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2352)
at picocli.CommandLine$RunLast.handle(CommandLine.java:2346)
at picocli.CommandLine$RunLast.handle(CommandLine.java:2311)
at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179)
at picocli.CommandLine.execute(CommandLine.java:2078)
at genepi.App.main(App.java:59)
Caused by: java.lang.NullPointerException
at java.base/java.net.URL.(URL.java:608)
... 24 more
`
However the program works without the --rsrs flag.