Biostar170742.java:29: package com.github.lindenb.jvarkit.util.picard does not exist
import com.github.lindenb.jvarkit.util.picard.GenomicSequence;
^
Biostar170742.java:30: package com.github.lindenb.jvarkit.util.picard does not exist
import com.github.lindenb.jvarkit.util.picard.SAMSequenceDictionaryProgress;
^
Biostar170742.java:32: package htsjdk.samtools does not exist
import htsjdk.samtools.Cigar;
^
Biostar170742.java:33: package htsjdk.samtools does not exist
import htsjdk.samtools.CigarElement;
^
Biostar170742.java:34: package htsjdk.samtools does not exist
import htsjdk.samtools.CigarOperator;
^
Biostar170742.java:35: package htsjdk.samtools does not exist
import htsjdk.samtools.SAMRecord;
^
Biostar170742.java:36: package htsjdk.samtools does not exist
import htsjdk.samtools.SAMRecordIterator;
^
Biostar170742.java:37: package htsjdk.samtools does not exist
import htsjdk.samtools.SamReader;
^
Biostar170742.java:38: package htsjdk.samtools.reference does not exist
import htsjdk.samtools.reference.IndexedFastaSequenceFile;
^
Biostar170742.java:39: package htsjdk.samtools.util does not exist
import htsjdk.samtools.util.CloserUtil;
^
Biostar170742.java:42: cannot find symbol
symbol: class AbstractBiostar170742
public class Biostar170742 extends AbstractBiostar170742
^
Biostar170742.java:44: package org.slf4j does not exist
private static final org.slf4j.Logger LOG = com.github.lindenb.jvarkit.util.log.Logging.getLog(Biostar170742.class);
^
Biostar170742.java:44: package com.github.lindenb.jvarkit.util.log does not exist
private static final org.slf4j.Logger LOG = com.github.lindenb.jvarkit.util.log.Logging.getLog(Biostar170742.class);
^
Biostar170742.java:51: cannot find symbol
symbol : variable super
location: class com.github.lindenb.jvarkit.tools.biostar.Biostar170742
if(super.faidx==null)
^
Biostar170742.java:53: cannot find symbol
symbol : method wrapException(java.lang.String)
location: class com.github.lindenb.jvarkit.tools.biostar.Biostar170742
return wrapException("Reference sequence was not defined");
^
Biostar170742.java:56: cannot find symbol
symbol : class SamReader
location: class com.github.lindenb.jvarkit.tools.biostar.Biostar170742
SamReader sfr=null;
^
Biostar170742.java:57: cannot find symbol
symbol : class SAMRecordIterator
location: class com.github.lindenb.jvarkit.tools.biostar.Biostar170742
SAMRecordIterator iter=null;
^
Biostar170742.java:58: cannot find symbol
symbol : class GenomicSequence
location: class com.github.lindenb.jvarkit.tools.biostar.Biostar170742
GenomicSequence genomicSequence = null;
^
Biostar170742.java:59: cannot find symbol
symbol : class IndexedFastaSequenceFile
location: class com.github.lindenb.jvarkit.tools.biostar.Biostar170742
IndexedFastaSequenceFile indexedFastaSequenceFile= null;
^
Biostar170742.java:62: cannot find symbol
symbol : class IndexedFastaSequenceFile
location: class com.github.lindenb.jvarkit.tools.biostar.Biostar170742
indexedFastaSequenceFile = new IndexedFastaSequenceFile(super.faidx);
^
Biostar170742.java:62: cannot find symbol
symbol : variable super
location: class com.github.lindenb.jvarkit.tools.biostar.Biostar170742
indexedFastaSequenceFile = new IndexedFastaSequenceFile(super.faidx);
^
Biostar170742.java:64: cannot find symbol
symbol : method openSamReader(java.lang.String)
location: class com.github.lindenb.jvarkit.tools.biostar.Biostar170742
sfr = openSamReader(inputName);
^
Biostar170742.java:65: cannot find symbol
symbol : variable super
location: class com.github.lindenb.jvarkit.tools.biostar.Biostar170742
out = super.openFileOrStdoutAsPrintStream();
^
Biostar170742.java:69: cannot find symbol
symbol : class SAMSequenceDictionaryProgress
location: class com.github.lindenb.jvarkit.tools.biostar.Biostar170742
final SAMSequenceDictionaryProgress progress = new SAMSequenceDictionaryProgress(sfr.getFileHeader());
^
Biostar170742.java:69: cannot find symbol
symbol : class SAMSequenceDictionaryProgress
location: class com.github.lindenb.jvarkit.tools.biostar.Biostar170742
final SAMSequenceDictionaryProgress progress = new SAMSequenceDictionaryProgress(sfr.getFileHeader());
^
Biostar170742.java:73: cannot find symbol
symbol : class SAMRecord
location: class com.github.lindenb.jvarkit.tools.biostar.Biostar170742
final SAMRecord rec= progress.watch(iter.next());
^
Biostar170742.java:75: cannot find symbol
symbol : class Cigar
location: class com.github.lindenb.jvarkit.tools.biostar.Biostar170742
final Cigar cigar = rec.getCigar();
^
Biostar170742.java:82: cannot find symbol
symbol : class GenomicSequence
location: class com.github.lindenb.jvarkit.tools.biostar.Biostar170742
genomicSequence = new GenomicSequence(indexedFastaSequenceFile, rec.getReferenceName());
^
Biostar170742.java:89: cannot find symbol
symbol : class CigarElement
location: class com.github.lindenb.jvarkit.tools.biostar.Biostar170742
for(final CigarElement ce: cigar.getCigarElements())
^
Biostar170742.java:91: cannot find symbol
symbol : class CigarOperator
location: class com.github.lindenb.jvarkit.tools.biostar.Biostar170742
final CigarOperator op = ce.getOperator();
^
Biostar170742.java:92: cannot find symbol
symbol : variable CigarOperator
location: class com.github.lindenb.jvarkit.tools.biostar.Biostar170742
if(op.equals(CigarOperator.S))
^
Biostar170742.java:94: operator + cannot be applied to int,CigarElement.getLength
readpos+=ce.getLength();
^
Biostar170742.java:94: inconvertible types
found : <nulltype>
required: int
readpos+=ce.getLength();
^
Biostar170742.java:97: cannot find symbol
symbol : variable CigarOperator
location: class com.github.lindenb.jvarkit.tools.biostar.Biostar170742
if(op.equals(CigarOperator.H))
^
Biostar170742.java:163: cannot find symbol
symbol : variable RETURN_OK
location: class com.github.lindenb.jvarkit.tools.biostar.Biostar170742
return RETURN_OK;
^
Biostar170742.java:167: cannot find symbol
symbol : method wrapException(java.lang.Exception)
location: class com.github.lindenb.jvarkit.tools.biostar.Biostar170742
return wrapException(err);
^
Biostar170742.java:171: cannot find symbol
symbol : variable CloserUtil
location: class com.github.lindenb.jvarkit.tools.biostar.Biostar170742
CloserUtil.close(out);
^
Biostar170742.java:172: cannot find symbol
symbol : variable CloserUtil
location: class com.github.lindenb.jvarkit.tools.biostar.Biostar170742
CloserUtil.close(iter);
^
Biostar170742.java:173: cannot find symbol
symbol : variable CloserUtil
location: class com.github.lindenb.jvarkit.tools.biostar.Biostar170742
CloserUtil.close(sfr);
^
Biostar170742.java:174: cannot find symbol
symbol : variable CloserUtil
location: class com.github.lindenb.jvarkit.tools.biostar.Biostar170742
CloserUtil.close(indexedFastaSequenceFile);
^
Biostar170742.java:49: method does not override or implement a method from a supertype
@Override
^
Biostar170742.java:180: cannot find symbol
symbol : method instanceMain(java.lang.String[])
location: class com.github.lindenb.jvarkit.tools.biostar.Biostar170742
new Biostar170742().instanceMain(args);
^
42 errors