# Cannoli Changelog #


### Version 0.1.0 ###

**Closed issues:**

 - Default Docker images to those on BioContainers registry [\#92](https://github.com/bigdatagenomics/cannoli/issues/92)
 - Bump to ADAM 0.23.0 [\#89](https://github.com/bigdatagenomics/cannoli/issues/89)
 - Jenkins compile error due to upstream 0.23.0-SNAPSHOT changes [\#87](https://github.com/bigdatagenomics/cannoli/issues/87)
 - Error with snpEff [\#86](https://github.com/bigdatagenomics/cannoli/issues/86)
 - Add wrapper for RealTimeGenomics/rtg-tools vcfeval [\#84](https://github.com/bigdatagenomics/cannoli/issues/84)
 - Incorrect case for snpEff when using docker [\#83](https://github.com/bigdatagenomics/cannoli/issues/83)
 - Cannoli-BWA Command Failure // Re Open [\#78](https://github.com/bigdatagenomics/cannoli/issues/78)
 - Cannoli-BWA Command Failure [\#77](https://github.com/bigdatagenomics/cannoli/issues/77)
 - All commands invoked via docker should use --rm=true [\#76](https://github.com/bigdatagenomics/cannoli/issues/76)
 - FreeBayes Issue [\#75](https://github.com/bigdatagenomics/cannoli/issues/75)
 - Read in Fragment not found [\#74](https://github.com/bigdatagenomics/cannoli/issues/74)
 - Cannoli Command [\#73](https://github.com/bigdatagenomics/cannoli/issues/73)
 - FileNotFoundException while loading file from HDFS [\#66](https://github.com/bigdatagenomics/cannoli/issues/66)
 - Create script for releasing to Sonatype OSS repository [\#63](https://github.com/bigdatagenomics/cannoli/issues/63)
 - Compile errors with latest ADAM 0.23.0-SNAPSHOT version [\#55](https://github.com/bigdatagenomics/cannoli/issues/55)
 - Rename FastqInterleaver --> InterleaveFastq [\#51](https://github.com/bigdatagenomics/cannoli/issues/51)
 - Remove SequenceDictionaryReader per ADAMContext.loadSequenceDictionary [\#48](https://github.com/bigdatagenomics/cannoli/issues/48)
 - Move adam-cli to provided scope [\#46](https://github.com/bigdatagenomics/cannoli/issues/46)
 - NoSuchMethodError when running cannoli locally [\#45](https://github.com/bigdatagenomics/cannoli/issues/45)
 -  BCF not yet supported  [\#44](https://github.com/bigdatagenomics/cannoli/issues/44)
 - Interleaver should support uBAM [\#39](https://github.com/bigdatagenomics/cannoli/issues/39)
 - Use --interleaved for bowtie2 [\#36](https://github.com/bigdatagenomics/cannoli/issues/36)
 - Use ADAM tab5 formatter for bowtie [\#33](https://github.com/bigdatagenomics/cannoli/issues/33)
 - Add ability to specify docker command [\#28](https://github.com/bigdatagenomics/cannoli/issues/28)
 - Bump BWA docker version argument [\#27](https://github.com/bigdatagenomics/cannoli/issues/27)
 - BWA-Mount index files into docker container [\#25](https://github.com/bigdatagenomics/cannoli/issues/25)
 - Disable incremental mode in the Scala build [\#23](https://github.com/bigdatagenomics/cannoli/issues/23)
 - Update plugin dependency versions to match bigdatagenomics/adam [\#20](https://github.com/bigdatagenomics/cannoli/issues/20)
 - Bowtie error: reads file does not look like a FASTQ file [\#18](https://github.com/bigdatagenomics/cannoli/issues/18)
 - Update ADAM dependency version to 0.22.0 [\#16](https://github.com/bigdatagenomics/cannoli/issues/16)
 - Add ability to force load format for BWA [\#14](https://github.com/bigdatagenomics/cannoli/issues/14)
 - Add a FASTQ interleaver [\#12](https://github.com/bigdatagenomics/cannoli/issues/12)
 - Properly handle sequence and read group metadata from BWA [\#10](https://github.com/bigdatagenomics/cannoli/issues/10)
 - Set up CI [\#9](https://github.com/bigdatagenomics/cannoli/issues/9)
 - Need to double escape tabs in BWA native [\#7](https://github.com/bigdatagenomics/cannoli/issues/7)
 - Migrate repository to bigdatagenomics organization [\#6](https://github.com/bigdatagenomics/cannoli/issues/6)
 - Allow BWA to save Fragments instead of AlignmentRecords [\#4](https://github.com/bigdatagenomics/cannoli/issues/4)

**Merged and closed pull requests:**

 - [CANNOLI-92] Use BioContainers Docker images with version tags by default. [\#96](https://github.com/bigdatagenomics/cannoli/pull/96) ([heuermh](https://github.com/heuermh))
 - Add hadoopConfiguration to VCFOutFormatter ctr. [\#93](https://github.com/bigdatagenomics/cannoli/pull/93) ([heuermh](https://github.com/heuermh))
 - [CANNOLI-89] Bump ADAM dependency version to 0.23.0. [\#90](https://github.com/bigdatagenomics/cannoli/pull/90) ([heuermh](https://github.com/heuermh))
 - Fix compile error due to upstream 0.23.0-SNAPSHOT changes. [\#88](https://github.com/bigdatagenomics/cannoli/pull/88) ([heuermh](https://github.com/heuermh))
 - [CANNOLI-83] Fix case for snpEff when using docker. [\#85](https://github.com/bigdatagenomics/cannoli/pull/85) ([heuermh](https://github.com/heuermh))
 - Replace cannoli ascii logo. [\#82](https://github.com/bigdatagenomics/cannoli/pull/82) ([heuermh](https://github.com/heuermh))
 - Add docker support to bowtie and bowtie2. [\#81](https://github.com/bigdatagenomics/cannoli/pull/81) ([heuermh](https://github.com/heuermh))
 - [CANNOLI-76] Add --rm flag to docker run. [\#80](https://github.com/bigdatagenomics/cannoli/pull/80) ([heuermh](https://github.com/heuermh))
 - Adding code of contact adapted from the Contributor Convenant, version 1.4. [\#79](https://github.com/bigdatagenomics/cannoli/pull/79) ([heuermh](https://github.com/heuermh))
 - Adding wrapper for BCFtools norm. [\#71](https://github.com/bigdatagenomics/cannoli/pull/71) ([heuermh](https://github.com/heuermh))
 - Adding wrapper for samtools mpileup. [\#70](https://github.com/bigdatagenomics/cannoli/pull/70) ([heuermh](https://github.com/heuermh))
 - Adding wrapper for vt normalize. [\#68](https://github.com/bigdatagenomics/cannoli/pull/68) ([heuermh](https://github.com/heuermh))
 - [CANNOLI-45] Move to multimodule Maven build, add cannoli-submit script [\#62](https://github.com/bigdatagenomics/cannoli/pull/62) ([heuermh](https://github.com/heuermh))
 - Update move_to scripts for Spark version 2.1.0. [\#61](https://github.com/bigdatagenomics/cannoli/pull/61) ([heuermh](https://github.com/heuermh))
 - Fix compile error in FragmentRDD.apply [\#60](https://github.com/bigdatagenomics/cannoli/pull/60) ([heuermh](https://github.com/heuermh))
 - [CANNOLI-33] Use ADAM tab5 formatter for bowtie. [\#59](https://github.com/bigdatagenomics/cannoli/pull/59) ([heuermh](https://github.com/heuermh))
 - [CANNOLI-48] Remove SequenceDictionaryReader. [\#58](https://github.com/bigdatagenomics/cannoli/pull/58) ([heuermh](https://github.com/heuermh))
 - [CANNOLI-55] Fix compile errors due to upstream commit 0afbda96. [\#57](https://github.com/bigdatagenomics/cannoli/pull/57) ([heuermh](https://github.com/heuermh))
 - Fix compile issues with most recent ADAM version 0.23.0-SNAPSHOT. [\#56](https://github.com/bigdatagenomics/cannoli/pull/56) ([heuermh](https://github.com/heuermh))
 - [CANNOLI-51] Rename FastqInterleaver --> InterleaveFastq [\#53](https://github.com/bigdatagenomics/cannoli/pull/53) ([heuermh](https://github.com/heuermh))
 - Code style fixes. [\#52](https://github.com/bigdatagenomics/cannoli/pull/52) ([heuermh](https://github.com/heuermh))
 - Update adam dependency version to 0.23.0-SNAPSHOT. [\#49](https://github.com/bigdatagenomics/cannoli/pull/49) ([heuermh](https://github.com/heuermh))
 - [CANNOLI-46] Move adam-cli to provided scope. [\#47](https://github.com/bigdatagenomics/cannoli/pull/47) ([heuermh](https://github.com/heuermh))
 - [CANNOLI-33] Use ADAM tab5 formatter for bowtie [\#42](https://github.com/bigdatagenomics/cannoli/pull/42) ([heuermh](https://github.com/heuermh))
 - Adding sample reads tool. [\#41](https://github.com/bigdatagenomics/cannoli/pull/41) ([heuermh](https://github.com/heuermh))
 - [CANNOLI-39] Add support for exporting interleaved FASTQ as unaligned BAM. [\#40](https://github.com/bigdatagenomics/cannoli/pull/40) ([fnothaft](https://github.com/fnothaft))
 - Use --interleaved for bowtie2 [\#37](https://github.com/bigdatagenomics/cannoli/pull/37) ([heuermh](https://github.com/heuermh))
 - Add placeholder publish_scaladoc.sh script [\#31](https://github.com/bigdatagenomics/cannoli/pull/31) ([heuermh](https://github.com/heuermh))
 - [CANNOLI-28] Allow docker command to be specified. [\#30](https://github.com/bigdatagenomics/cannoli/pull/30) ([fnothaft](https://github.com/fnothaft))
 - [CANNOLI-25] Properly support loading BWA indices via SparkFiles API. [\#26](https://github.com/bigdatagenomics/cannoli/pull/26) ([fnothaft](https://github.com/fnothaft))
 - Disable incremental mode in the Scala build. [\#24](https://github.com/bigdatagenomics/cannoli/pull/24) ([heuermh](https://github.com/heuermh))
 - Update examples in readme [\#22](https://github.com/bigdatagenomics/cannoli/pull/22) ([heuermh](https://github.com/heuermh))
 - Prep for move to bigdatagenomics org [\#19](https://github.com/bigdatagenomics/cannoli/pull/19) ([fnothaft](https://github.com/fnothaft))
 - [CANNOLI-16] Update ADAM dependency version to 0.22.0 [\#17](https://github.com/bigdatagenomics/cannoli/pull/17) ([heuermh](https://github.com/heuermh))
 - [CANNOLI-14] Add switches to force loading from Interleaved FASTQ/Parquet. [\#15](https://github.com/bigdatagenomics/cannoli/pull/15) ([fnothaft](https://github.com/fnothaft))
 - [CANNOLI-12] Add a FASTQ interleaver. [\#13](https://github.com/bigdatagenomics/cannoli/pull/13) ([fnothaft](https://github.com/fnothaft))
 - [CANNOLI-10] Attach record groups and sequence dictionary to BWA output. [\#11](https://github.com/bigdatagenomics/cannoli/pull/11) ([fnothaft](https://github.com/fnothaft))
 - [CANNOLI-7] Escape tabs in @RG line when running BWA without docker. [\#8](https://github.com/bigdatagenomics/cannoli/pull/8) ([fnothaft](https://github.com/fnothaft))
 - [CANNOLI-4] Add ability to save Fragments from BWA. [\#5](https://github.com/bigdatagenomics/cannoli/pull/5) ([fnothaft](https://github.com/fnothaft))
 - Add Docker arguments to Freebayes and SnpEff. [\#3](https://github.com/bigdatagenomics/cannoli/pull/3) ([heuermh](https://github.com/heuermh))
 - Add BWA runner. [\#2](https://github.com/bigdatagenomics/cannoli/pull/2) ([fnothaft](https://github.com/fnothaft))
 - SupportedHeaderLines renamed to DefaultHeaderLines [\#1](https://github.com/bigdatagenomics/cannoli/pull/1) ([waltermblair](https://github.com/waltermblair))
