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JAL-2909 fix up tests and ensure we don’t test bam as a writable format

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JAL-3821 data file for failing test

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    ./J03321_rna.embl.txt
JAL-3821 less ambiguous base class name for EMBL and GenBank flat file parsers

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JAL-3821 failing test

JAL-3691 automatic insertion of Locale.ROOT to toUpperCase() and toLowerCase() and added import java.util.Locale appropriately

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JAL-3853 - tweak test again - since failed a few commits after f6cb90d43782ca99cf2b1cbee2dc76bca3d1d466

JAL-3853 patch sequence annotation report code and tweak the test. When merging from 2.11.2 develop there will be conflicts that need merging re HTMLXML tags

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WIP
WIP
JAL-3808 example exonerate cdna2genome and coding2genome test data and test

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Merge branch 'Jalview-JS/develop' into merge_js_develop also patched new code from JAL-3690 refactorings

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JAL-3628 Test for doubly saved single backup file scheme

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    ./testProps_singlefilebackup.jvprops
JAL-3779 apply properties to all groups with given name, not just first

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JAL-3779 apply properties to all groups with given name, not just first

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Merge branch 'feature/JAL-3469clinvarVCF' into spike/clinvar

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JAL-3725 fix tests for EMBLFlatFile parser when mapping doesn’t include stop codon

JAL-3576 IntervalStore updated to v1.2

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JAL-3675 2.11.1.1 java 8 compatible patch for JAL-3615 from feature/JAL-3615gzipXfam

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JAL-3615 code tidy, improve unit test

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JAL-2656 Java 8 compatible test for gzipped, refactored for unit test

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JAL-3692 parse multiline CDS location correctly

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JAL-1260 unit test for FileFormats updated for GenBank/ENA

JAL-1260 unit test for FileFormats updated for GenBank/ENA

JAL-1260 file formats and IdentifyFile updates for GenBank and ENA

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JAL-1260 file formats and IdentifyFile updates for GenBank and ENA

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JAL-1260 refactored GenBank (and EMBL) flat file parser

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    ./GenBankFileTest.java
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JAL-1260 refactored GenBank (and EMBL) flat file parser

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    ./GenBankFileTest.java
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JAL-3490 merged with 2.11.2 develop

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