<commit_before>## 1.1.9 (in progress)
- Fix for get VEP cache.
- Support Picard's new syntax for ReorderSam (REFERENCE -> SEQUENCE_DICTIONARY).
- Adds filtering of nucleosome free (NF) regions for ATAC-seq.
- Add peak calling on NF regions.
- Add uploading of full and NF BAM for ATAC-seq.
- Add documentation describing ATAC-seq outputs.
- Remove mitochondrial reads from ChIP/ATAC-seq calling.
- Add ENCODE library complexity metrics for ATAC/ChIP-seq to MultiQC report 
  (see https://www.encodeproject.org/data-standards/terms/#library for a description of the metrics)
- Add STAR sample-specific 2-pass. This helps assign a moderate number of reads per genes. Thanks
  to @naumenko-sa for the intial implementation and push to get this going.

## 1.1.8 (28 October 2019)
- Add `antibody` configuration option. Setting a specific antibody for ChIP-seq will use appropriate
  settings for that antibody. See the documentation for supported antibodies.
- Add `use_lowfreq_filter` for forcing vardict to report variants with low allelic frequency,
 useful for calling somatic variants in panels with high coverage.
- Fix for checking for pre-existing inputs with python3.
- Add `keep_duplicates` option for ChIP/ATAC-seq which does not remove duplicates before peak calling.
  Defaults to False.
- Add `keep_multimappers` for ChIP/ATAC-seq which does not remove multimappers before peak calling.
  Defaults to False.
- Remove ethnicity as a required column in PED files.

## 1.1.7 (10 October 2019)
=======
- hot fix for dataclasses not being supported in 3.6. Use namedtuple instead.

## 1.1.6 (10 October 2019)

- GATK ApplyBQSRSpark: avoid StreamClosed issue with GATK 4.1+
- RNA-seq: fixes for cufflinks preparation due to python3 transition.
- RNA-seq: output count tables from tximport for genes and transcripts. These
  are in `bcbioRNASeq/results/date/genes/counts` and `bcbioRNASeq/results/data/transcripts/counts`.
- qualimap (RNA-seq): disable stranded mode for qualimap, as it gives incorrect
  results with the hisat2 aligner and for RNA-seq just setting it to unstranded
- Add `quantify_genome_alignments` option to use genome alignments to quantify
  with Salmon.
- Add `--validateMappings` flag to Salmon read quantification mode.
- VEP cache is not installing anymore from bcbio run<commit_msg>Add note about transcriptome indexing fix.<commit_after>## 1.1.9 (in progress)
- Fix for get VEP cache.
- Support Picard's new syntax for ReorderSam (REFERENCE -> SEQUENCE_DICTIONARY).
- Adds filtering of nucleosome free (NF) regions for ATAC-seq.
- Add peak calling on NF regions.
- Add uploading of full and NF BAM for ATAC-seq.
- Add documentation describing ATAC-seq outputs.
- Remove mitochondrial reads from ChIP/ATAC-seq calling.
- Add ENCODE library complexity metrics for ATAC/ChIP-seq to MultiQC report 
  (see https://www.encodeproject.org/data-standards/terms/#library for a description of the metrics)
- Add STAR sample-specific 2-pass. This helps assign a moderate number of reads per genes. Thanks
  to @naumenko-sa for the intial implementation and push to get this going.
- Index transcriptomes only once for pseudo/quasi aligner tools. This fixes race conditions that
  can happen.

## 1.1.8 (28 October 2019)
- Add `antibody` configuration option. Setting a specific antibody for ChIP-seq will use appropriate
  settings for that antibody. See the documentation for supported antibodies.
- Add `use_lowfreq_filter` for forcing vardict to report variants with low allelic frequency,
 useful for calling somatic variants in panels with high coverage.
- Fix for checking for pre-existing inputs with python3.
- Add `keep_duplicates` option for ChIP/ATAC-seq which does not remove duplicates before peak calling.
  Defaults to False.
- Add `keep_multimappers` for ChIP/ATAC-seq which does not remove multimappers before peak calling.
  Defaults to False.
- Remove ethnicity as a required column in PED files.

## 1.1.7 (10 October 2019)
=======
- hot fix for dataclasses not being supported in 3.6. Use namedtuple instead.

## 1.1.6 (10 October 2019)

- GATK ApplyBQSRSpark: avoid StreamClosed issue with GATK 4.1+
- RNA-seq: fixes for cufflinks preparation due to python3 transition.
- RNA-seq: output count tables from tximport for genes and transcripts. These
  are in `bcbioRNASeq/results/date/genes/counts` and `bcbioRNASeq/results/data/transcripts/counts`.
- qualimap (RNA-seq): disable stranded mode for qualimap, as it gives incorrect
  results with the hisat2 aligner and for RNA-seq just setting it to unstranded
- Add `quantify_genome_alignments` option to use genome alignments to quantify
  with Salmon.
- Add `--validateMappings` flag to Salmon read quantification mode.
- VEP cache is not installing anymore from bcbio run
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