<commit_before>## 0.7.9 (in progress)

- Redo Illumina sequencer integration to be up to date with current
  code base. Uses external bcl2fastq demultiplexing and new bcbio integrated
  analysis server. Provide documentation on setting up automated infrastructure.
- Perform de-duplication of BAM files as part of streaming alignment process
  using samblaster or biobambam's bammarkduplicates. Removes need for secondary
  split of files and BAM preparation unless recalibration and realignment
  needed. Enables pre-processing of input files for structural variant detection.
- Rework batched regional analysis in variant calling to remove custom cases and
  simplify structure. Filtering now happens explicitly on the combined batch
  file. This is functionally equivalent to previous filters but now the workflow
  is clearer. Avoids special cases for tumor/normal inputs.
- Perform regional splitting of samples grouped by batch instead of globally,
  enabling multiple organisms and experiments within a single input sample YAML.
- Add temporary directory usage to enable use of local high speed scratch disk
  on setups with large enough global temporary storage.
- Update FreeBayes to latest version and provide improved filtering for high
  depth artifacts.
- Update VQSR support for GATK to be up to date with latest best
  practices. Re-organize GATK and filtering to be more modular to help with
  transition to GATK 3.x gVCF approaches.
- Provide configuration option, `remove_lcr`, to filter out variants in low
  complexity regions.
- Improve Galaxy upload for LIMS supports: enable upload of FastQC as PDF
  reports with wkhtmltopdf installed. Provide tabular summaries of mapped reads.
- Improve checks for pre-aligned BAMs: ensure correct sample names and
  provide more context on errors around mismatching reference genomes.
- GATK HaplotypeCaller: ensure genotype depth annotation with DepthPerSampleHC
  annotation. Enable GATK 3.1 hardware specific optimizations.
- Use bgzipped VCFs for dbSNP, Cosmic and other resources to save disk
  space. Upgrade to Cosmic v68.
- Avoid VCF concatenation errors when first input file is empty. Thanks to
  <NAME>.

## 0.7.8 (March 21, 2014)

- Add a check for mis-specified FASTQ format in the sample YAML file. Thanks
  to <NAME>.
- Updated RNA-seq integration tests to have more specific tags (singleend, Tophat,
  STAR, explant).
- Fix contig ordering after Tophat alignment which was preventing GATK-based
  tools from running.
- Allow calculation of RPKM on more deeply sampled genes by setting
  `--max-bundle-frags` to 2,000,000. Thanks to <NAME>.
- Provide cleaner installation process for non-distributable tools like
  GATK. The `--tooplus` argument now handles jars from the GATK site or Appistry
  and correctly updates manifest version information.
- Use bgzipped/tabix indexed variant files throughout pipeline instead of raw
  uncompressed VCFs. Reduces space requirements and enables parallelization on
  non-shared filesystems or temporary space by avoiding transferring
  uncompressed outputs.
- Reduce memory usage during post-alignment BAM preparation steps (PrintReads
  downsampling, deduplication and realignment prep) to avoid reaching memory cap
  on limited systems like SLURM. Do not include for IndelRealigner which needs
  memory in high depth regions.
- Provide explicit targets for coverage depth (`coverage_depth_max` and
  `coverage_depth_min`) instead of `coverage_depth` enumeration. Provide
  downsampling of reads to max depth during post-alignment preparation to avoid
  repetitive centromere regions with high depth.
- Ensure read group information correctly supplied with bwa aln. Thanks to Miika
  Ahdesmaki.
- Fix bug in retrieval of snpEff databases on install. Thanks to <NAME>.
- Fix bug in normal BAM preparation for tumor/normal variant calling. Thanks to
  <NAME>.<commit_msg>Added oncofuse update to changelog.<commit_after>## 0.7.9 (in progress)

- Redo Illumina sequencer integration to be up to date with current
  code base. Uses external bcl2fastq demultiplexing and new bcbio integrated
  analysis server. Provide documentation on setting up automated infrastructure.
- Perform de-duplication of BAM files as part of streaming alignment process
  using samblaster or biobambam's bammarkduplicates. Removes need for secondary
  split of files and BAM preparation unless recalibration and realignment
  needed. Enables pre-processing of input files for structural variant detection.
- Rework batched regional analysis in variant calling to remove custom cases and
  simplify structure. Filtering now happens explicitly on the combined batch
  file. This is functionally equivalent to previous filters but now the workflow
  is clearer. Avoids special cases for tumor/normal inputs.
- Perform regional splitting of samples grouped by batch instead of globally,
  enabling multiple organisms and experiments within a single input sample YAML.
- Add temporary directory usage to enable use of local high speed scratch disk
  on setups with large enough global temporary storage.
- Update FreeBayes to latest version and provide improved filtering for high
  depth artifacts.
- Update VQSR support for GATK to be up to date with latest best
  practices. Re-organize GATK and filtering to be more modular to help with
  transition to GATK 3.x gVCF approaches.
- Provide configuration option, `remove_lcr`, to filter out variants in low
  complexity regions.
- Improve Galaxy upload for LIMS supports: enable upload of FastQC as PDF
  reports with wkhtmltopdf installed. Provide tabular summaries of mapped reads.
- Improve checks for pre-aligned BAMs: ensure correct sample names and
  provide more context on errors around mismatching reference genomes.
- GATK HaplotypeCaller: ensure genotype depth annotation with DepthPerSampleHC
  annotation. Enable GATK 3.1 hardware specific optimizations.
- Use bgzipped VCFs for dbSNP, Cosmic and other resources to save disk
  space. Upgrade to Cosmic v68.
- Avoid VCF concatenation errors when first input file is empty. Thanks to
  <NAME>.
- Added preliminary support for oncofuse for calling gene fusion events. Thanks
  to @tanglingfung.

## 0.7.8 (March 21, 2014)

- Add a check for mis-specified FASTQ format in the sample YAML file. Thanks
  to <NAME>.
- Updated RNA-seq integration tests to have more specific tags (singleend, Tophat,
  STAR, explant).
- Fix contig ordering after Tophat alignment which was preventing GATK-based
  tools from running.
- Allow calculation of RPKM on more deeply sampled genes by setting
  `--max-bundle-frags` to 2,000,000. Thanks to <NAME>.
- Provide cleaner installation process for non-distributable tools like
  GATK. The `--tooplus` argument now handles jars from the GATK site or Appistry
  and correctly updates manifest version information.
- Use bgzipped/tabix indexed variant files throughout pipeline instead of raw
  uncompressed VCFs. Reduces space requirements and enables parallelization on
  non-shared filesystems or temporary space by avoiding transferring
  uncompressed outputs.
- Reduce memory usage during post-alignment BAM preparation steps (PrintReads
  downsampling, deduplication and realignment prep) to avoid reaching memory cap
  on limited systems like SLURM. Do not include for IndelRealigner which needs
  memory in high depth regions.
- Provide explicit targets for coverage depth (`coverage_depth_max` and
  `coverage_depth_min`) instead of `coverage_depth` enumeration. Provide
  downsampling of reads to max depth during post-alignment preparation to avoid
  repetitive centromere regions with high depth.
- Ensure read group information correctly supplied with bwa aln. Thanks to Miika
  Ahdesmaki.
- Fix bug in retrieval of snpEff databases on install. Thanks to <NAME>.
- Fix bug in normal BAM preparation for tumor/normal variant calling. Thanks to
  <NAME>.
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