jalview

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JAL-2909 separate reverse and forward strand reads. fix subtle bug in handling inserts. gross hack & WIP to try to get reference sequences added to alignment (doesn’t work - see FIXME)

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    /src/jalview/datamodel/CigarParser.java
JAL-2909 recognise .bam extension in URL and allow location spec as suffix - e.g. file:///…mybam.bam#2:121212-150000

JAL-2909 soft clip and handclap features (should use SO terms for ‘Clipped’)

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    /src/jalview/datamodel/CigarParser.java
JAL-2909 add sequence feature for quality

JAL-2909 add sequence feature for insertions

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    /src/jalview/datamodel/CigarParser.java
JAL-2909 Updated tests

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    /src/jalview/datamodel/CigarParser.java
JAL-2909 fixed another insertions bug

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    /src/jalview/datamodel/CigarParser.java
JAL-2909 Fixed a bug in the insertions code

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    /src/jalview/datamodel/CigarParser.java
JAL-2909 Gaps at start of reads only from start of alignment window

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    /src/jalview/datamodel/CigarParser.java
JAL-2909 Wire up coordinates dialog with bam file reader

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    /src/jalview/gui/BamFileOptionsChooser.java
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    /src/jalview/io/AlignmentFileReaderI.java
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    /src/jalview/io/AppletFormatAdapter.java
JAL-2909 Tidy up bam file cigar code

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    /src/jalview/datamodel/CigarParser.java
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    /src/jalview/gui/BamFileOptionsChooser.java
JAL-2909 Bam file parsing with insertions, first pass

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    /src/jalview/datamodel/CigarParser.java
JAL-2909 Changes to htsjdk import control

JAL-2909 Cigar parsing tests

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    /test/jalview/datamodel/CigarParserTest.java
JAL-2909 Partial insertions

JAL-2909 Modified classpath

JAL-2909 Insertions almost

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    /lib/htsjdk-2.12.0.jar
JAL-2909 Read in a bam file - but strand/location unaware

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    /src/jalview/io/BamFile.java
JAL-2909 Removed buggy CIGAR parsing code which was not used

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    /src/jalview/datamodel/CigarBase.java
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    /src/jalview/datamodel/SeqCigar.java
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    /test/jalview/datamodel/SeqCigarTest.java
JAL-2858 update release date and rejig what's new message

JAL-2858 fix what's new

JAL-2858 update latest release notes link in TOC

JAL-2859 release notes

JAL-2858 update release notes

JAL-2858 release notes for 2.10.3b1 (including revision to EnsemblGenomes client as per JAL-2679)

JAL-2858 bump version number for 2.10.3b1

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    /resources/lang/Messages.properties
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    /resources/lang/Messages_es.properties
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    /src/jalview/gui/StructureChooser.java
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    /src/jalview/jbgui/GStructureChooser.java
JAL-2679 update query id to actual case of retrieved gene

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    /src/jalview/ext/ensembl/EnsemblGene.java
JAL-2679 case-insensitive comparison of query and retrieved accession

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    /src/jalview/ext/ensembl/EnsemblFeatures.java
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    /src/jalview/ext/ensembl/EnsemblGene.java
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    /src/jalview/ext/ensembl/EnsemblSeqProxy.java
JAL-2679 use object_type=Transcript for lookup of Parent for Protein

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    /src/jalview/ext/ensembl/EnsemblCdna.java
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    /src/jalview/ext/ensembl/EnsemblGene.java
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    /src/jalview/ext/ensembl/EnsemblGenome.java
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    /src/jalview/ext/ensembl/EnsemblLookup.java
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    /src/jalview/ext/ensembl/EnsemblSeqProxy.java
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    /src/jalview/ext/ensembl/EnsemblSymbol.java