Closed issues:
- Sorting by reference index seems doesn't work or sorted by DESC order? #1204
- master won't compile #1200
- VCF format tag SB field parse error in loading #1199
- Publish sources JAR with snapshots #1195
- Type SparkFunSuite in package org.bdgenomics.utils.misc is not available #1193
- MDTagging fails on GRCh38 #1192
- Fix stack overflow in IndelRealigner serialization #1190
- Delete
./scripts/commit-pr.sh
#1188 - Hadoop globStatus returns null if no glob matches #1186
- Swapping out IntervalRDD under GenomicRDDs #1184
- How to get "SO coordinate" instead of "SO unsorted"? #1182
- How to read glob of multiple parquet Genotype #1179
- Update command line doc and examples in README.md #1176
- FastqRecordConverter needs cleanup and tests #1172
- TransformFormats write to .gff3 file path incorrectly writes as parquet #1168
- Should be able to merge shards across two different file systems #1165
- RG ID gets written as the index, not the record group name #1162
- Users should be able to save files as
-single
without merging them #1161 - Users should be able to set size of buffer used for merging files #1160
- Bump Hadoop-BAM to 7.7.0 #1158
- adam-shell prints command trace to stdout #1154
- Map IntervalList format column four to feature name or attributes? #1152
- Parquet storage of VariantContext #1151
- vcf2adam unparsable vcf record #1149
- Reorder kryo.register statements in ADAMKryoRegistrator #1146
- Make region joins public again #1143
- Support CRAM input/output #1141
- Transform should run with spark.kryo.requireRegistration=true #1136
- adam-shell not handling bash args correctly #1132
- Remove Gene and related models and parsing code #1129
- Generate Scoverage reports when running CI #1124
- Remove PairingRDD #1122
- SAMRecordConverter.convert takes unused arguments #1113
- Add Pipe API #1112
- Improve coverage in Feature unit tests #1106
- K-mer.scala code #1105
- add -single file output option to ADAM2Vcf #1102
- adam2vcf Fails with Sample not serializable #1100
- ReferenceRegion.apply(AlignmentRecord) should not NPE on unmapped reads #1099
- Add outer region join implementations #1098
- VariantContextConverter never returns DatabaseVariantAnnotation #1097
- loadvcf: conflicting require statement #1094
- ADAM version 0.19.0 will not run on Spark version 2.0.0 #1093
- Be more rigorous with FileSystem.get #1087
- Remove network-connected and default test-related Maven profiles #1073
- Releases should get pushed to Spark Packages #1067
- Invalid POM for cli on 0.19.0 #1066
- scala.MatchError RegExp does not catch colons in value part properly #1061
- Support writing IntervalList header for features #1059
- Add -single support when writing features in native formats #1058
- Remove workaround for gzip/BGZF compressed VCF headers #1057
- Clean up if clauses in Transform #1053
- Adam-0.18.2 can not load Adam-0.14.0 adamSave function data (sam) #1050
- filterByOverlappingRegion Incorrect for Genotypes #1042
- Move Interval trait to utils, added in #75 #1041
- Remove implicit GenomicRDD to RDD conversion #1040
- VCF sample metadata - proposal for a GenotypedSampleMetadata object #1039
- [build system] ADAM test builds pollute /tmp, leaving lots of cruft... #1038
- adamMarkDuplicates function in AlignmentRecordRDDFunctions class can not mark the same read? #1037
- test MarkDuplicatesSuite with two similar read in ref and start position and different avgPhredScore, error! #1035
- Explore protocol buffers vs Avro #1031
- Increase Avro dependency version to 1.8.0 #1029
- ADAM specific logging #1024
- Reenable Travis CI for pull request builds #1023
- Bump Apache Spark version to 1.6.1 in Jenkins #1022
- ADAM compatibility with Spark 2.0 #1021
- ADAM to BAM conversion failing on 1000G file #1013
- Factor out *RDDFunctions classes #1011
- Port single file BAM and header code to VCF #1009
- Roll Jenkins JDK 8 changes into ./scripts/jenkins-test #1008
- Support GFF3 format #1007
- Separate fat jar build from adam-cli to new maven module #1006
- adam-cli POM invalid: maven.build.timestamp #1004
- Sub-partitioning of Parquet file for ADAM #1003
- Flattening the Genotype schema #1002
- install adam 0.19 error! #1001
- How to solve it please? #1000
- Has the project realized alignment reads to reference genome algorithm? #996
- All file-based input methods should support running on directories, compressed files, and wildcards #993
- Contig to ContigName Change not reflected in AlignmentRecordField #991
- Add homebrew guidelines to release checklist or automate PR generation #987
- fix deprecation warnings #985
- rename
fragments
package #984 - Explore if SeqDict data can be factored out more aggressively #983
- Make "Adam" all caps in filename Adam2Fastq.scala #981
- Adam2Fastq should output reverse complement when 0x10 flag is set for read #980
- Allow lowercase letters in jar/version names #974
- Add stringency parameter to flagstat #973
- Arg-array parsing problem in adam-submit #971
- Pass recordGroup parameter to loadPairedFastq #969
- Send a number of partitions to sc.textFile calls #968
- adamGetReferenceString doesn't reduce pairs correctly #967
- Update ADAM formula in homebrew-science to version 0.19.0 #963
- BAM output in ADAM appears to be corrupt #962
- Remove code workarounds necessary for Spark 1.2.1/Hadoop 1.0.x support #959
- Issue with version 18.0.2 #957
- Expose sorting by reference index #952
- .rgdict and .seqdict files are not placed in the adam directory #945
- Why does count_kmers not return k-mers that are split between two records? #930
- Load legacy file formats to Spark SQL Dataframes #912
- Clean up RDD method names #910
- Load/store sequence dictionaries alongside Genotype RDDs #909
- vcf2adam -print_metrics throws IllegalStateException on Spark 1.5.2 or later #902
- error: no reads in first split: bad BAM file or tiny split size? #896
- FastaConverter.FastaDescriptionLine not kryo-registered #893
- Work With ADAM fasta2adam in a distributed mode #881
- vcf2adam -> Exception in thread "main" java.lang.NoSuchMethodError: scala.Predef$.$conforms()Lscala/Predef$$less$colon$less; #871
- Code coverage profile is broken #849
- Building Adam on OS X 10.10.5 with Java 1.8 #835
- Normalize AlignmentRecord.recordGroup* fields onto a separate record type #828
- Gracefully handle missing Spark- and Hadoop-versions in jenkins-test; document how to set them. #827
- Use Adam File with Hive #820
- How do we handle reads that don't have original quality scores when converting to FASTQ with original qualities? #818
- SAMFileHeader "sort order" attribute being un-set during file-save job #800
- Use same sort order as Samtools #796
- RNAME and RNEXT fields jumbled on transform BAM->ADAM->BAM #795
- Support loading multiple indexed read files #787
- Duplicate OUTPUT command line argument metaVar in adam2fastq #776
- Allow Variant to ReferenceRegion conversion #768
- Spark Errors References Deprecated SPARK_CLASSPATH #767
- Spark Errors References Deprecated SPARK_CLASSPATH #766
- adam2vcf fails with -coalesce #735
- Writing to a BAM file with adamSAMSave consistently fails #721
- BQSR on C835.HCC1143_BL.4 uses excessive amount of driver memory #714
- Support writing RDD[Feature] to various file formats #710
- adamParquetSave has a menacing false error message about *.adam extension #681
- BAMHeader not set when running on a cluster #676
- spark 1.3.1 upgarde to hortonworks HDP 2.2.4.2-2? #675
Symbol
case class is nucleotide-centric #672- xAssembler cannot be build using mvn #658
- adam-submit VerifyError #642
- vcf2adam : Unsupported type ENUM #638
- Update CDH documentation #615
- Remove and generalize plugin code #602
- Fix record oriented shuffle #599
- Migrate preprocessing stages out of ADAM #598
- Publish/socialize a roadmap #591
- Eliminate format detection and extension checks for loading data #587
- Improve error message when we can't find a ReferenceRegion for a contig #582
- Do reference partitioners restrict a partition to contain keys from a single contig? #573
- Connection refused errors when transforming BAM file with BQSR #516
- ReferenceRegion shouldn't extend Ordered #511
- Documentation for common usecases #491
- Improve handling of "*" sequences during BQSR #484
- Original qualities are parsed out, but left in attribute fields #483
- Need a FileLocator that mirrors the use of Path in HDFS #477
- FileLocator should support finding "child" locators. #476
- Add S3 based Parquet directory loader #463
- Should FASTQ output use reads' "original qualities"? #436
- VcfStringUtils unused? #428
- We should be able to filter genotypes that overlap a region #422
- Create a simplified vocabulary for naming projections. #419
- Update documentation #406
- Bake off different region join implementations #395
- Handle no-ops more intelligently when creating MD tags #392
- Remove all the commands in the "CONVERSION OPERATIONS"
CommandGroup
#373 - Fail to Write RDD into HDFS with Parquet Format #344
- Refactor ReferencePositionWithOrientation #317
- Add docs about SPARK_LOCAL_IP #305
- PartitionAndJoin should throw an exception if it sees an unmapped read #297
- Add insert size calculation #296
- Newbie questions - learning resources? Reading a range of records from Adam? #281
- Add variant effect ontology #261
- Don't flatten optional SAM tags into a string #240
- Characterize impact of partition size on pileup creation #163
- Need to support BCF output format #153
- Allow list of commands to be injected into adam-cli AdamMain #132
- Parse out common annotations stored in VCF format #118
- Update normalization code to enable normalization of sequences with more than two indels #64
- Add clipping heuristic to indel realigner #63
- BQSR should support recalibration across multiple ADAM files #58
Merged and closed pull requests:
- fix SB tag parsing #1209 (fnothaft)
- Fastq record converter #1208 (fnothaft)
- Doc suggested partitionSize in ShuffleRegionJoin #1207 (jpdna)
- Test demonstrating region join failure #1206 (jpdna)
- fix SB tag parsing #1203 (jpdna)
- fix build #1201 (ryan-williams)
- [ADAM-1192] Correctly handle other whitespace in FASTA description. #1198 (fnothaft)
- [ADAM-1190] Manually (un)pack IndelRealignmentTarget set. #1191 (fnothaft)
- [ADAM-1188] Delete scripts/commit-pr.sh #1189 (fnothaft)
- [ADAM-1186] Mask null from fs.globStatus. #1187 (fnothaft)
- Fastq record converter #1185 (zyxue)
- [ADAM-1182] isSorted=true should write SO:coordinate in SAM/BAM/CRAM header. #1183 (fnothaft)
- Add scoverage aggregator and fail on low coverage. #1181 (fnothaft)
- [ADAM-1179] Improve error message when globbing a parquet file fails. #1180 (fnothaft)
- [ADAM-1176] Update command line doc and examples in README.md #1177 (heuermh)
- Refactor CLIs for merging sharded files #1167 (fnothaft)
- Update Hadoop-BAM to version 7.7.0 #1166 (heuermh)
- [ADAM-1162] Write record group string name. #1163 (fnothaft)
- Map IntervalList format column four to feature name #1159 (heuermh)
- Make AlignmentRecordConverter public so that it can be used from other projects #1157 (tomwhite)
- added predicate option to loadCoverage #1156 (akmorrow13)
- [ADAM-1154] Change set -x to set -e in ./bin/adam-shell. #1155 (fnothaft)
- Remove Gene and related models and parsing code #1153 (heuermh)
- Reorder kryo.register statements in ADAMKryoRegistrator #1148 (heuermh)
- Updated GenomicPartitioners to accept additional key. #1147 (akmorrow13)
- [ADAM-1141] Add support for saving/loading AlignmentRecords to/from CRAM. #1145 (fnothaft)
- misc pom/test/resource improvements #1142 (ryan-williams)
- [ADAM-1136] Transform runs successfully with kryo registration required #1138 (fnothaft)
- [ADAM-1132] Fix improper quoting of bash args in adam-shell. #1133 (fnothaft)
- Remove StructuralVariant and StructuralVariantType, add names field to Variant #1131 (heuermh)
- Remove StructuralVariant and StructuralVariantType, add names field to Variant #1130 (heuermh)
- PR #1108 with issue #1122 #1128 (fnothaft)
- [ADAM-1038] Eliminate writing to /tmp during CI builds. #1127 (fnothaft)
- Update for bdg-formats code style changes #1126 (heuermh)
- [ADAM-1124] Add Scoverage and generate coverage reports in Jenkins. #1125 (fnothaft)
- [ADAM-1093] Move to support Spark 2.0.0. #1123 (fnothaft)
- remove duplicated dependency #1119 (ryan-williams)
- Clean up ADAMContext #1118 (fnothaft)
- [ADAM-993] Support loading files using globs and from directory paths. #1117 (fnothaft)
- [ADAM-1087] Migrate away from FileSystem.get #1116 (fnothaft)
- [ADAM-1099] Make reference region not throw NPE. #1115 (fnothaft)
- Add pipes API #1114 (fnothaft)
- [ADAM-1105] Use assembly jar in adam-shell. #1111 (fnothaft)
- Add outer joins #1109 (fnothaft)
- Modified CalculateDepth to calcuate coverage from alignment files #1108 (akmorrow13)
- Resolves various single file save/header issues #1104 (fnothaft)
- [ADAM-1100] Resolve Sample Not Serializable exception #1101 (fnothaft)
- added loadIndexedVcf and loadIndexedBam for multiple ReferenceRegions #1096 (akmorrow13)
- Added support for Indexed VCF files #1095 (akmorrow13)
- [ADAM-582] Eliminate .get on option in FragmentCoverter. #1091 (fnothaft)
- [ADAM-776] Rename duplicate OUTPUT metaVar in ADAM2Fastq. #1090 (fnothaft)
- refactored ReferenceFile to require SequenceDictionary #1086 (akmorrow13)
- [ADAM-1073] Remove network-connected and default test-related Maven profiles #1082 (heuermh)
- [ADAM-1053] Clean up Transform #1081 (fnothaft)
- [ADAM-1061] Clean up attributes regex and denormalized fields #1080 (fnothaft)
- Extended TwoBitFile and NucleotideContigFragmentRDDFunctions to behave more similar #1079 (akmorrow13)
- Refactor variant and genotype annotations #1078 (heuermh)
- [ADAM-1039] Add basic support for Sample record. #1077 (fnothaft)
- Remove code workarounds necessary for Spark 1.2.1/Hadoop 1.0.x support #1076 (heuermh)
- [ADAM-194] Use separate filtersFailed and filtersPassed arrays for variant quality filters #1075 (heuermh)
- Whitespace code style fixes #1074 (heuermh)
- [ADAM-1006] Split überjar out to adam-assembly submodule. #1072 (fnothaft)
- Remove code coverage profile #1071 (heuermh)
- [ADAM-768] ReferenceRegion from variant/genotypes #1070 (fnothaft)
- [ADAM-1044] Support VCF annotation ANN field #1069 (heuermh)
- [ADAM-1067] Add release documentation and scripting for Spark Packages. #1068 (fnothaft)
- [ADAM-602] Remove plugin code. #1065 (fnothaft)
- Refactoring
org.bdgenomics.adam.io
package. #1064 (fnothaft) - Cleanup in org.bdgenomics.adam.converters package. #1062 (fnothaft)
- [ADAM-1057] Remove workaround for gzip/BGZF compressed VCF headers #1057 (heuermh)
- Cleanup on
org.bdgenomics.adam.algorithms.smithwaterman
package. #1056 (fnothaft) - Documentation cleanup and minor refactor on the consensus package. #1055 (fnothaft)
- Add KEYS with public code signing keys #1054 (heuermh)
- Adding GA4GH 0.5.1 converter for reads. #1052 (fnothaft)
- [ADAM-1011] Refactor to add GenomicRDDs for all Avro types #1051 (fnothaft)
- removed interval trait and redirected to interval in utils-intervalrdd #1046 (akmorrow13)
- [ADAM-952] Expose sorting by reference index. #1045 (fnothaft)
- overlap query reflects new formats #1043 (erictu)
- Changed loadIndexedBam to use hadoop-bam InputFormat #1036 (fnothaft)
- Increase Avro dependency version to 1.8.0 #1034 (heuermh)
- Improved README fix using feedback from other approach review. #1034 (InvisibleTech)
- Error in the README.md for kmer.scala example, need to get rdd first. #1032 (InvisibleTech)
- Add fragmentEndPosition to NucleotideContigFragment #1030 (heuermh)
- Logging to be done by ADAM utils code rather than Spark #1028 (jpdna)
- add maxScore #1027 (xubo245)
- [ADAM-1008] Modify jenkins-test script to support Java 8 build. #1026 (fnothaft)
- whitespace change, do not merge #1025 (shaneknapp)
- require kryo registration in tests #1020 (ryan-williams)
- print full stack traces on test failures #1019 (ryan-williams)
- bump commons-io version #1017 (ryan-williams)
- exclude javadoc jar in adam-shell #1016 (ryan-williams)
- [ADAM-909] Refactoring variation RDDs. #1015 (fnothaft)
- Modified CalculateDepth to get coverage on whole alignment adam files #1010 (akmorrow13)
- [ADAM-1004] Remove recursive maven.build.timestamp declaration #1005 (heuermh)
- Maint 2.11 0.19.0 #999 (tushu1232)
- [ADAM-710] Add saveAs methods for feature formats GTF, BED, IntervalList, and NarrowPeak #998 (heuermh)
- Moving Adam2Fastq to ADAM2Fastq #995 (heuermh)
- Update release doc for CHANGES.md and homebrew #994 (heuermh)
- Update to AlignmentRecordField and its usages as contig changed to co… #992 (jpdna)
- [ADAM-974] Short term fix for multiple ADAM cli assembly jars check #990 (heuermh)
- Update hadoop-bam dependency version to 7.5.0 #989 (heuermh)
- Replaced Contig with ContigName in AlignmentRecord and related changes #988 (jpdna)
- fix some deprecation/style things and rename a pkg #986 (ryan-williams)
- Fix Adam2fastq in case of read with both reverse and unmapped flags #982 (jpdna)
- [ADAM-510] Refactoring RDD function names #979 (heuermh)
- Use .adam/_{seq,rg}dict.avro paths for Avro-formatted dictionaries #978 (heuermh)
- Remove unused file VcfHeaderUtils.scala #977 (heuermh)
- add validation stringency to bam parsing, flagstat #976 (ryan-williams)
- more permissible jar regex in adam-submit #975 (ryan-williams)
- fix bash arg array processing in adam-submit #972 (ryan-williams)
- adamGetReferenceString reduces pairs correctly, fixes #967 #970 (erictu)
- A few improvements #966 (ryan-williams)
- improve SW performance by replacing functional reductions with imperative ones #965 (noamBarkai)
- [ADAM-962] Fix corrupt single-file BAM output. #964 (fnothaft)
- [ADAM-960] Updating bdg-utils dependency version to 0.2.4 #961 (heuermh)
- [ADAM-946] Fixes to FlagStat for Samtools concordance issue #954 (jpdna)
- Use hadoop-bam BAMInputFormat to do loadIndexedBam #953 (andrewmchen)
- Add -print_metrics option to Jenkins build #947 (heuermh)
- adam2vcf doesn't have info fields #939 (andrewmchen)
- [ADAM-893] Register missing serializers. #933 (fnothaft)
Closed issues:
- Update bdg-utils dependency version to 0.2.4 #960
- Drop support for Spark version 1.2.1, Hadoop version 1.0.x #958
- Exception occurs when running tests on master #956
- Flagstat results still don't match samtools flagstat #946
- readInFragment value is not properly read from parquet file into RDD[AlignmentRecord] #942
- adam2vcf -sort_on_save flag broken #940
- Transform -limit_projection requires .sam.seqdict file #937
- MarkDuplicates fails if library name is not set #934
- fastqtobam or sam #928
- Vcf2Adam uses SB field instead of FS field for fisher exact test for strand bias #923
- Add back limit_projection on Transform #920
- BAM header is not getting set on partition 0 with headerless BAM output format #916
- Add numParts apply method to GenomicRegionPartitioner #914
- Add Spark version 1.6.x to Jenkins build matrix #913
- Target Spark 1.5.2 as default Spark version #911
- Move to bdg-formats 0.7.0 #905
- secondOfPair and firstOfPair flag is missing in the newest 0.18 adam transformed results from BAM #903
- Future pull request #900
- error in vcf2adam #899
- Importing directory of VCFs seems to fail #898
- How to filter genotypeRDD on sample names? org.apache.spark.SparkException: Task not serializable? #891
- Add Spark version 1.5.x to Jenkins build matrix #889
- Transform DAG causes stages to recompute #883
- adam-submit buildinfo is confused #880
- move_to_scala_2.11 and maven-javadoc-plugin #863
- NativeCodeLoader: Unable to load native-hadoop library for your platform... using builtin-java classes where applicable #837
- Fix record oriented shuffle #599
- Avro.GenericData error with ADAM 0.12.0 on reading from ADAM file #290
Merged and closed pull requests:
- [ADAM-960] Updating bdg-utils dependency version to 0.2.4 #961 (heuermh)
- [ADAM-946] Fixes to FlagStat for Samtools concordance issue #954 (jpdna)
- Fix for travis build, replace reads2ref with reads2fragments #950 (heuermh)
- [ADAM-940] Fix adam2vcf -sort_on_save flag #949 (massie)
- Remove BuildInformation and extraneous git-commit-id-plugin configuration #948 (heuermh)
- Update readme for spark 1.5.2 and hadoop 2.6.0 #944 (heuermh)
- [ADAM-942] Replace first/secondInRead with readInFragment #943 (heuermh)
- [ADAM-937] Adding check for aligned read predicate or limit projection flags and non-parquet input path #938 (heuermh)
- [ADAM-934] Properly handle unset library name during duplicate marking #935 (fnothaft)
- [ADAM-911] Move to Spark 1.5.2 and Hadoop 2.6.0 as default versions. #932 (fnothaft)
- added start and end values to Interval Trait. Used for IntervalRDD #931 (akmorrow13)
- Removing buildinfo command #929 (heuermh)
- Removing symbolic test resource links, read from test classpath instead #927 (heuermh)
- Changed fisher strand bias field for VCF2Adam from SB to FS #924 (andrewmchen)
- [ADAM-920] Limit tag/orig qual flags in Transform. #921 (fnothaft)
- Change the README to use adam-shell -i instead of pasting #919 (andrewmchen)
- [ADAM-916] New strategy for writing header. #917 (fnothaft)
- [ADAM-914] Create a GenomicRegionPartitioner given a partition count. #915 (fnothaft)
- Squashed #907 and ran format-sources #908 (fnothaft)
- Various small fixes #907 (huitseeker)
- ADAM-599, 905: Move to bdg-formats:0.7.0 and migrate metadata #906 (fnothaft)
- Rewrote the getType method to handle all ploidy levels #904 (NeillGibson)
- Single file save from #733, rebased #901 (fnothaft)
- Added is* genotype methods from HTS-JDK Genotype to RichGenotype #895 (NeillGibson)
- [ADAM-891] Mark SparkContext as @transient. #894 (fnothaft)
- Update README URLs based on HTTP redirects #892 (ReadmeCritic)
- adding --version command line option #888 (heuermh)
- Add exception in move_to_scala_2.11.sh for maven-javadoc-plugin #887 (heuermh)
- Fix tightlist bug in Pandoc #885 (massie)
- [ADAM-883] Add caching to Transform pipeline. #884 (fnothaft)
- ISSUE 877: Minor fix to commit script to support https.
- ISSUE 876: Separate command line argument words by underscores
- ISSUE 875: P Operator parsing for MDTag
- ISSUE 873: [ADAM-872] Modify regex to capture release and SNAPSHOT jars but not javadoc or sources jars
- ISSUE 866: [ADAM-864] Don't force shuffle if reducing partition count.
- ISSUE 856: export valid fastq
- ISSUE 847: Updating build dependency versions to latest minor versions
- ISSUE 870: [ADAM-867] add pull requests missing from 0.18.0 release to CHANGES.md
- ISSUE 869: [ADAM-868] make release branch and tag names consistent
- ISSUE 862: [ADAM-861] use -d to check for repo assembly dir
- ISSUE 860: New release and pr-commit scripts
- ISSUE 859: [ADAM-857] Corrected handling of env vars in bin scripts
- ISSUE 854: [ADAM-853] allow main class in adam-submit to be specified
- ISSUE 852: [ADAM-851] Slienced Parquet logging.
- ISSUE 850: [ADAM-848] TwoBitFile now support nBlocks and maskBlocks
- ISSUE 846: Updating maven build plugin dependency versions
- ISSUE 845: [ADAM-780] Make DecadentRead package private.
- ISSUE 844: [ADAM-843] Aggressively project out metadata fields.
- ISSUE 840: fix flagstat output file encoding
- ISSUE 839: let flagstat write to file
- ISSUE 831: Support loading paired fastqs
- ISSUE 830: better validation when saving paired fastqs
- ISSUE 829: fix
Long != null
warnings - ISSUE 819: Implement custom ReferenceRegion hashcode
- ISSUE 816: [ADAM-793] adding command to convert ADAM nucleotide contig fragments to FASTA files
- ISSUE 815: Upgrade to bdg-formats:0.6.0, add Fragment datatype converters
- ISSUE 814: [ADAM-812] fix for javadoc errors on JDK8
- ISSUE 813: [ADAM-808] build an assembly cli jar with maven shade plugin
- ISSUE 810: [ADAM-807] workaround for git-commit-id/git-commit-id-maven-plugin#61
- ISSUE 809: [ADAM-785] Add support for all numeric array (TYPE=B) tags
- ISSUE 806: [ADAM-755] updating utils dependency version to 0.2.3
- ISSUE 805: Better transform error when file doesn't exist
- ISSUE 803: fix unmapped-read sorting
- ISSUE 802: stop writing contig names as md5 sums
- ISSUE 798: fix SAM-attr conversion bug; int[]'s not byte[]'s
- ISSUE 790: optionally add MDTags to reads with
transform
- ISSUE 782: Fix SAM Attribute parser for numeric array tags
- ISSUE 773: [ADAM-772] fix some bash var quoting
- ISSUE 765: [ADAM-752] Build for many combos of Spark/Hadoop versions.
- ISSUE 764: More involved README restructuring
- ISSUE 762: [ADAM-132] allowing list of commands to be injected into adam-cli ADAMMain
- ISSUE 784: [ADAM-783] Write @SQ header lines in sorted order.
- ISSUE 792: [ADAM-791] Add repartition parameter to Fasta2ADAM.
- ISSUE 781: [ADAM-777] Add validation stringency flag for BQSR.
- ISSUE 757: We should print a warning message if the user has ADAM_OPTS set.
- ISSUE 770: [ADAM-769] Fix serialization issue in known indel consensus model.
- ISSUE 763: Clean up README links, other nits
- ISSUE 749: Remove adam-cli jar from classpath during adam-submit
- ISSUE 754: Bump ADAM to Spark 1.4
- ISSUE 753: Bump Spark to 1.4
- ISSUE 748: Fix for mdtag issues with insertions
- ISSUE 746: Upgrade to Parquet 1.8.1.
- ISSUE 744: [ADAM-743] exclude conflicting jackson dependencies
- ISSUE 737: Reverse complement negative strand reads in fastq output
- ISSUE 731: Fixed bug preventing use of TLEN attribute
- ISSUE 730: [ADAM-729] Stuff TLEN into attributes.
- ISSUE 728: [ADAM-709] Remove FeatureHierarchy and FeatureHierarchySuite
- ISSUE 719: [ADAM-718] Use filesystem path to get underlying file system.
- ISSUE 712: unify header-setting between BAM/SAM and VCF
- ISSUE 696: include SequenceRecords from second-in-pair reads
- ISSUE 698: class-ify ShuffleRegionJoin, force setting seqdict
- ISSUE 706: restore clause guarding pruneCache check
- ISSUE 705: GeneFeatureRDDFunctions → FeatureRDDFunctions
- ISSUE 691: fix BAM/SAM header setting when writing on cluster
- ISSUE 688: make adamLoad public
- ISSUE 694: Fix parent reference in distribution module
- ISSUE 684: a few region-join nits
- ISSUE 682: [ADAM-681] Remove menacing error message about reqd .adam extension
- ISSUE 680: [ADAM-674] Delete Bam2ADAM.
- ISSUE 678: upgrade to bdg utils 0.2.1
- ISSUE 668: [ADAM-597] Move correction out of ADAM and into a downstream project.
- ISSUE 671: Bug fix in ReferenceUtils.unionReferenceSet
- ISSUE 667: [ADAM-666] Clean up key not found error in partitioner code.
- ISSUE 656: Update Vcf2ADAM.scala
- ISSUE 652: added filterByOverlappingRegion in GeneFeatureRDDFunctions
- ISSUE 650: [ADAM-649] Support transform of all BAM/SAM files in a directory.
- ISSUE 647: [ADAM-646] Special case reads with '*' quality during BQSR.
- ISSUE 645: [ADAM-634] Create a local ParquetLister for testing purposes.
- ISSUE 633: [Adam] Tests for SAMRecordConverter.scala
- ISSUE 641: [ADAM-640] Fix incorrect exclusion for org.seqdoop.htsjdk.
- ISSUE 632: [ADAM-631] Allow VCF conversion to sort on output after coalescing.
- ISSUE 628: [ADAM-627] Makes ReferenceFile trait extend Serializable.
- ISSUE 637: check for mac brew alternate spark install structure
- ISSUE 624: Conceptual fix for duplicate marking and sorting stragglers
- ISSUE 629: [ADAM-604] Remove normalization code.
- ISSUE 630: Add flatten command.
- ISSUE 619: [ADAM-540] Move to new HTSJDK release; should support Java 8.
- ISSUE 626: [ADAM-625] Enable globbing for BAM.
- ISSUE 621: Removes the predicates package.
- ISSUE 620: [ADAM-600] Adding RegionJoin trait.
- ISSUE 616: [ADAM-565] Upgrade to Parquet filter2 API.
- ISSUE 613: [ADAM-612] Point to proper k-mer counters.
- ISSUE 588: [ADAM-587] Clean up loading checks.
- ISSUE 592: [ADAM-513] Remove ReferenceMappable trait.
- ISSUE 606: [ADAM-605] Remove visualization code.
- ISSUE 596: [ADAM-595] Delete the 'comparisons' code.
- ISSUE 590: [ADAM-589] Removed pileup code.
- ISSUE 586: [ADAM-452] Fixes SM attribute on ADAM to BAM conversion.
- ISSUE 584: [ADAM-583] Add k-mer counting functionality for nucleotide contig fragments
- ISSUE 570: A few small conversion fixes
- ISSUE 579: [ADAM-578] Update end of read when trimming.
- ISSUE 564: [ADAM-563] Add warning message when saving Parquet files with incorrect extension
- ISSUE 576: Changed hashCode implementations to improve performance of BQSR
- ISSUE 569: Typo in the narrowPeak parser
- ISSUE 568: Moved the Timers object from bdg-utils back to ADAM
- ISSUE 478: Move non-genomics code
- ISSUE 550: [ADAM-549] Added documentation for testing and CI for ADAM.
- ISSUE 555: Makes maybeLoadVCF private.
- ISSUE 558: Makes Features2ADAMSuite use SparkFunSuite
- ISSUE 557: Randomize ports and turn off Spark UI to reduce bind exceptions in tests
- ISSUE 552: Create test suite for FlagStat
- ISSUE 554: privatize ADAMContext.maybeLoad{Bam,Fastq}
- ISSUE 551: [ADAM-386] Multiline FASTQ input
- ISSUE 542: Variants Visualization
- ISSUE 545: [ADAM-543][ADAM-544] Fix issues with ADAM scripts and classpath
- ISSUE 535: [ADAM-441] put a check in for Nothing. Throws an IAE if no return type is provided
- ISSUE 546: [ADAM-532] Fix wigFix intermittent test failure
- ISSUE 534: [ADAM-528][ADAM-533] Adds new RegionJoin impl that is shuffle-based
- ISSUE 531: [ADAM-529] Attaching scaladoc to released distribution.
- ISSUE 413: [ADAM-409][ADAM-520] Added local wigfix2bed tool
- ISSUE 527: [ADAM-526]
VcfAnnotation2ADAM
only counts once - ISSUE 523: don't open non-.adam-extension files as ADAM files
- ISSUE 521: quieting wget output
- ISSUE 482: [ADAM-462] Coverage region calculation
- ISSUE 515: [ADAM-510] fix for bash syntax error; add ADDL_JARS check to adam-submit
- ISSUE 509: Add a 'distribution' module to create assemblies
- ISSUE 508: Upgrade from Parquet 1.4.3 to 1.6.0rc4
- ISSUE 498: [ADAM-496] Changes VCF to flat ADAM command name and usage
- ISSUE 500: [ADAM-495] Require SPARK_HOME for adam-submit
- ISSUE 501: [ADAM-499] Add -onlyvariants option to vcf2adam
- ISSUE 507: [ADAM-505] Removed
adam-local
from docs - ISSUE 504: [ADAM-502] Add missing Long implicit to ColumnReaderInput
- ISSUE 503: [ADAM-473] Make RecordCondition and FieldCondition public
- ISSUE 494: Fix foreach block for vcf ingest
- ISSUE 492: Documentation cleanup and style improvements
- ISSUE 481: [ADAM-480] Switch assembly to single goal.
- ISSUE 487: [ADAM-486] Add port option to viz command.
- ISSUE 469: [ADAM-461] Fix ReferenceRegion and ReferencePosition impl
- ISSUE 440: [ADAM-439] Fix ADAM to account for BDG-FORMATS-35: Avro uses Strings
- ISSUE 470: added ReferenceMapping for Genotype, filterByOverlappingRegion for GenotypeRDDFunctions
- ISSUE 468: refactor RDD loading; explicitly load alignments
- ISSUE 474: Consolidate documentation into a single location in source.
- ISSUE 471: Fixed typo on MAVEN_OPTS quotation mark
- ISSUE 467: [ADAM-436] Optionally output original qualities to fastq
- ISSUE 451: add
adam view
command, analogous tosamtools view
- ISSUE 466: working examples on .sam included in repo
- ISSUE 458: Remove unused val from Reads2Ref
- ISSUE 438: Add ability to save paired-FASTQ files
- ISSUE 457: A few random Predicate-related cleanups
- ISSUE 459: a few tweaks to scripts/jenkins-test
- ISSUE 460: Project only the sequence when kmer/qmer counting
- ISSUE 450: Refactor some file writing and reading logic
- ISSUE 455: [ADAM-454] Add serializers for Avro objects which don't have serializers
- ISSUE 447: Update the contribution guidelines
- ISSUE 453: Better null handling for isSameContig utility
- ISSUE 417: Stores original position and original cigar during realignment.
- ISSUE 449: read “OQ” attr from structured SAMRecord field
- ISSUE 446: Revert "[ADAM-237] Migrate to Chill serialization libraries."
- ISSUE 437: random nits
- ISSUE 434: Few transform tweaks
- ISSUE 435: [ADAM-403] Remove seqDict from RegionJoin
- ISSUE 431: A few tweaks, typo corrections, and random cleanups
- ISSUE 430: [ADAM-429] adam-submit now handles args correctly.
- ISSUE 427: Fixes for indel realigner issues
- ISSUE 418: [ADAM-416] Removing 'ADAM' prefix
- ISSUE 404: [ADAM-327] Adding gene, transcript, and exon models.
- ISSUE 414: Fix error in
adam-local
alias - ISSUE 415: Update README.md to reflect Spark 1.1
- ISSUE 412: [ADAM-411] Updated usage aliases in README. Fixes #411.
- ISSUE 408: [ADAM-405] Add FASTQ output.
- ISSUE 385: [ADAM-384] Adds import from FASTQ.
- ISSUE 400: [ADAM-399] Fix link to schemas.
- ISSUE 396: [ADAM-388] Sets Kryo serialization with --conf args
- ISSUE 394: [ADAM-393] Adds knobs to SparkContext creation in SparkFunSuite
- ISSUE 391: [ADAM-237] Migrate to Chill serialization libraries.
- ISSUE 380: Rewrite of MarkDuplicates which seems to improve performance
- ISSUE 387: fix some deprecation warnings
- ISSUE 376: [ADAM-375] Upgrade to Hadoop-BAM 7.0.0.
- ISSUE 378: [ADAM-360] Upgrade to Spark 1.1.0.
- ISSUE 379: Fix the position of the jar path in the submit.
- ISSUE 383: Make Mdtags handle '=' and 'X' cigar operators
- ISSUE 369: [ADAM-369] Improve debug output for indel realigner
- ISSUE 377: [ADAM-377] Update to Jenkins scripts and README.
- ISSUE 374: [ADAM-372][ADAM-371][ADAM-365] Refactoring CLI to simplify and integrate with Spark model better
- ISSUE 370: [ADAM-367] Updated alias in README.md
- ISSUE 368: erasure, nonexhaustive-match, deprecation warnings
- ISSUE 354: [ADAM-353] Fixing issue with SAM/BAM/VCF header attachment when running distributed
- ISSUE 357: [ADAM-357] Added Java Plugin hook for ADAM.
- ISSUE 352: Fix failing MD tag
- ISSUE 363: Adding maven assembly plugin configuration to create tarballs
- ISSUE 364: [ADAM-364] Fixing remaining cs.berkeley.edu URLs.
- ISSUE 362: Remove mention of uberjar from README
- ISSUE 343: Allow retrying on failure for HTTPRangedByteAccess
- ISSUE 349: Fix for a NullPointerException when hostname is null in Task Metrics
- ISSUE 347: Bug fix for genome browser
- ISSUE 346: Genome visualization
- ISSUE 342: [ADAM-309] Update to bdg-formats 0.2.0
- ISSUE 333: [ADAM-332] Upgrades ADAM to Spark 1.0.1.
- ISSUE 341: [ADAM-340] Adding the TrackedLayout trait and implementation.
- ISSUE 337: [ADAM-335] Updated README.md to reflect migration to appassembler.
- ISSUE 311: Adding several simple normalizations.
- ISSUE 330: Make mismatch and deletes positions accessible
- ISSUE 334: Moving code coverage into a profile
- ISSUE 329: Add count of mismatches to mdtag
- ISSUE 328: [ADAM-326] Adding a 5-second retry on the HttpRangedByteAccess test.
- ISSUE 325: Adding documentation for commit/issue nomenclature and rebasing
- ISSUE 308: Fixing the 'index 0' bug in features2adam
- ISSUE 306: Adding code for lifting over between sequences and the reference genome.
- ISSUE 320: Remove extraneous implicit methods in ReferenceMappingContext
- ISSUE 314: Updates to indel realigner to improve performance and accuracy.
- ISSUE 319: Adding scripts for publishing scaladoc.
- ISSUE 315: Added table of (wall-clock) stage durations when print_metrics is used
- ISSUE 312: Fixing sources jar
- ISSUE 313: Making the CredentialsProperties file optional
- ISSUE 267: Parquet and indexed Parquet RDD implementations, and indices.
- ISSUE 301: Add Beacon's AlleleCount
- ISSUE 293: Add aggregation and display of metrics obtained from Spark
- ISSUE 295: Fix broken link to ADAM specification for storing reads.
- ISSUE 292: Cleaning up scaladoc generation warnings.
- ISSUE 289: Modifying interleaved fastq format to be hadoop version independent.
- ISSUE 288: Add ADAMFeature to Kryo registrator
- ISSUE 286: Removing some debug printout that was left in.
- ISSUE 287: Cleaning hadoop dependencies
- ISSUE 285: Refactoring read groups to increase the amount of data stored.
- ISSUE 284: Cleaning up build warnings.
- ISSUE 280: Move to bdg-formats
- ISSUE 283: Fix reference name comment
- ISSUE 282: Minor cleanup on interleaved FASTQ input format.
- ISSUE 277: Implemented HTTPRangedByteAccess.
- ISSUE 274: Added clarifying note to
ADAMVariantContext
- ISSUE 279: Simplify format-source
- ISSUE 278: Use maven license plugin to ensure source has correct license
- ISSUE 268: Adding fixed depth prefix trie implementation
- ISSUE 273: Fixes issue in reference models where strings are not sanitized on collection from avro.
- ISSUE 272: Created command categories
- ISSUE 269: Adding k-mer and q-mer counting.
- ISSUE 271: Consolidate Parquet logging configuration
- ISSUE 264: Parquet-related Utility Classes
- ISSUE 259: ADAMFlatGenotype is a smaller, flat version of a genotype schema
- ISSUE 266: Removed extra command 'BuildInformation'
- ISSUE 263: Added AdamContext.referenceLengthFromCigar
- ISSUE 260: Modifying conversion code to resolve #112.
- ISSUE 258: Adding an 'args' parameter to the plugin framework.
- ISSUE 262: Adding reference assembly name to ADAMContig.
- ISSUE 256: Upgrading to Spark 1.0
- ISSUE 257: Adds toString method for sequence dictionary.
- ISSUE 255: Add equals, canEqual, and hashCode methods to MdTag class
- ISSUE 254: Cleanup import statements
- ISSUE 250: Adding ADAM to SAM conversion.
- ISSUE 248: Adding utilities for read trimming.
- ISSUE 252: Added a note about rebasing-off-master to CONTRIBUTING.md
- ISSUE 249: Cosmetic changes to FastaConverter and FastaConverterSuite.
- ISSUE 251: CHANGES.md is updated at release instead of per pull request
- ISSUE 247: For #244, Fragments were incorrect order and incomplete
- ISSUE 246: Making sample ID field in genotype nullable.
- ISSUE 245: Adding ADAMContig back to ADAMVariant.
- ISSUE 243: Rebase PR#238 onto master
- ISSUE 242: Upgrade to Parquet 1.4.3
- ISSUE 241: Fixes to FASTA code to properly handle indices.
- ISSUE 239: Make ADAMVCFOutputFormat public
- ISSUE 233: Build up reference information during cigar processing
- ISSUE 234: Predicate to filter conversion
- ISSUE 235: Remove unused contiglength field
- ISSUE 232: Add
-pretty
and-o
to theprint
command - ISSUE 230: Remove duplicate mdtag field
- ISSUE 231: Helper scripts to run an ADAM Console.
- ISSUE 226: Fix ReferenceRegion from ADAMRecord
- ISSUE 225: Change Some to Option to check for unmapped reads
- ISSUE 223: Use SparkConf object to configure SparkContext
- ISSUE 217: Stop using reference IDs and use reference names instead
- ISSUE 220: Update SAM to ADAM conversion
- ISSUE 213: BQSR updates
- ISSUE 214: Upgrade to Spark 0.9.1
- ISSUE 211: FastaConverter Refactor
- ISSUE 212: Cleanup build warnings
- ISSUE 210: Remove Scalariform from process-sources phase
- ISSUE 209: Fix Scalariform issues and Maven warnings
- ISSUE 207: Change from deprecated manifest erasure to runtimeClass
- ISSUE 206: Add Scalariform settings to pom
- ISSUE 204: Update Avro code gen to not mark fields as deprecated.
- ISSUE 203: Move package from edu.berkeley.cs.amplab to org.bdgenomics
- ISSUE 199: Updating pileup conversion code to convert sequences that use the X and = (EQ) CIGAR operators
- ISSUE 191: Add repartition parameter
- ISSUE 183: Fixing Job.getInstance call that breaks hadoop 1 compatibility.
- ISSUE 192: Add docs and scripts for creating a release
- ISSUE 193: Issue #137, clarify role of CHANGES.{md,txt}
- ISSUE 187: Add summarize_genotypes command
- ISSUE 178: Upgraded to Hadoop-BAM 0.6.2/Picard 1.107.
- ISSUE 173: Parse annotations out of vcf files
- ISSUE 162: Refactored SequenceDictionary
- ISSUE 180: BQSR using vcf loader
- ISSUE 179: Update maven-surefire-plugin dependency version to 2.17, also create an ...
- ISSUE 175: VariantContext converter refactor
- ISSUE 169: Cleaning up mpileup command
- ISSUE 170: Adding variant field enumerations
- ISSUE 166: Pair-wise genotype concordance of genotype RDDs, with CLI tool
- ISSUE 171: Add back in allele dosage for genotypes.
- ISSUE 167: Fix for Hadoop 1.0.x support
- ISSUE 165: call PluginExecutor in apply method, fixes issue 164
- ISSUE 160: Refactoring FASTA work to break contig sizes.
- ISSUE 78: Upgrade to Spark 0.9 and Scala 2.10
- ISSUE 138: Display Git commit info on command line
- ISSUE 161: Added switches to spark context creation code
- ISSUE 117: Add a "range join" method.
- ISSUE 151: Vcf work concordance and genotype
- ISSUE 150: Remaining variant changes for adam2vcf, unit tests, and CLI modifications
- ISSUE 147: Resurrect VCF conversion code
- ISSUE 148: Moving createSparkContext into core
- ISSUE 142: Enforce Maven and Java versions
- ISSUE 144: Merge of last few days of work on master into this branch
- ISSUE 124: Vcf work rdd master merge
- ISSUE 143: Changing package declaration to match test file location and removing un...
- ISSUE 140: Update README.md
- ISSUE 139: Update README.md
- ISSUE 129: Modified pileup transforms to improve performance + to add options
- ISSUE 116: add fastq interleaver script
- ISSUE 125: Add design doc to CONTRIBUTING document
- ISSUE 114: Changes to RDD utility files for new variant schema
- ISSUE 122: Add IRC Channel to readme
- ISSUE 100: CLI component changes for new variant schema
- ISSUE 108: Adding new PluginExecutor command
- ISSUE 98: Vcf work remove old variant
- ISSUE 104: Added the port erasure to SparkFunSuite's cleanup.
- ISSUE 107: Cleaning up change documentation.
- ISSUE 99: Encoding tag types in the ADAMRecord attributes, adding the 'tags' command
- ISSUE 105: Add initial documentation on contributing
- ISSUE 97: New schema, variant context converter changes, and removal of old genoty...
- ISSUE 79: Adding ability to convert reference FASTA files for nucleotide sequences
- ISSUE 91: Minor change, increase adam-cli usage width to 150 characters
- ISSUE 86: Fixes to pileup code
- ISSUE 88: Added function for building variant context from genotypes.
- ISSUE 81: Update README and cleanup top-level cli help text
- ISSUE 76: Changing hadoop fs call to be compatible with Hadoop 1.
- ISSUE 74: Updated CHANGES.txt to include note about the recursive-load branch.
- ISSUE 73: Support for loading/combining multiple ADAM files into a single RDD.
- ISSUE 72: Added ability to create regions from reads, and to merge adjacent regions
- ISSUE 71: Change RecalTable to use optimized phred calculations
- ISSUE 68: sonatype-nexus-snapshots repository is already in parent oss-parent-7 pom
- ISSUE 67: fix for wildcard exclusion maven warnings
- ISSUE 65: Create a cache for phred -> double values instead of recalculating
- ISSUE 60: Bugfix for BQSR: Offset into qualityScore list was wrong
- ISSUE 66: add pluginDependency section and remove versions in plugin sections
- ISSUE 61: Filter utility for inverse of Projection
- ISSUE 48: Fix read groups mapping and add Y as base type
- ISSUE 36: Adding reads to rods transformation.
- ISSUE 56: Adding Yy as base in MdTag
- ISSUE 53: Fix Hadoop 2.2.0 support, upgrade to Spark 0.8.1
- ISSUE 52: Attributes: Use 't' instead of ',', as , is a valid character
- ISSUE 47: Adding containsRefName to SequenceDictionary
- ISSUE 46: Reduce logging for the actual adamSave job
- ISSUE 45: Make MdTag immutable
- ISSUE 38: Small bugfixes and cleanups to BQSR
- ISSUE 40: Fixing reference position from offset implementation
- ISSUE 31: Fixing a few issues in the ADAM2VCF2ADAM pipeline.
- ISSUE 30: Suppress parquet logging in FieldEnumerationSuite
- ISSUE 28: Fix build warnings
- ISSUE 24: Add unit tests for marking duplicates
- ISSUE 26: Fix unmapped reads in sequence dictionary
- ISSUE 23: Generalizing the Projection class
- ISSUE 25: Adding support for before, after clauses to SparkFunSuite.
- ISSUE 22: Add a unit test for sorting reads
- ISSUE 21: Adding rod functionality: a specialized grouping of pileup data.
- ISSUE 13: Cleaning up VCF<->ADAM pipeline
- ISSUE 20: Added Apache License 2.0 boilerplate to tops of all the GB-(c) files
- ISSUE 19: Allow the Hadoop version to be specified
- ISSUE 17: Fix transform -sort_reads partitioning. Add -coalesce option to transform.
- ISSUE 16: Fixing an issue in pileup generation and in the MdTag util.
- ISSUE 15: Tweaks 1
- ISSUE 12: Subclass testing bug in AdamContext.adamLoad
- ISSUE 11: Missing brackets in VcfConverter.getType
- ISSUE 10: Moved record field name enum over to the projections package.
- ISSUE 8: Fixes to sorting in ReferencePosition
- ISSUE 4: New SparkFunSuite test support class, logging util and new BQSR test.
- ISSUE 1: Fix scalatest configuration and fix unit tests
- ISSUE 14: Converting some of the Option() calls to Some()
- ISSUE 13: Cleaning up VCF<->ADAM pipeline
- ISSUE 9: Adding support for a Sequence Dictionary from BAM files
- ISSUE 8: Fixes to sorting in ReferencePosition
- ISSUE 7: ADAM variant and genotype formats; and a VCF->ADAM converter
- ISSUE 4: New SparkFunSuite test support class, logging util and new BQSR test.
- ISSUE 3: Adding in implicit conversion functions for going between Java and Scala...
- ISSUE 2: Update from Spark 0.7.3 to 0.8.0-incubating
- ISSUE 1: Fix scalatest configuration and fix unit tests