v0.29.6
- MANTA-287 add the unit test of consistency of supporting reads
- MANTA-287 fix a bug in the small assembler by checking consistency when adding a new supporting read of contig
v0.29.5
- [#32] Preserve file path softlinks so that sidecar index files can be found
- Fix field name in denovo variant search script
v0.29.4
- Add a python script to identify de novo calls
- MANTA-285 add option to keep all temp files to support workflow debug
- MANTA-276 mv configure to top-level, mv guides to docs dir, add methods docs
- MANTA-284 improve windows shell support by shortening very long cmdlines
v0.29.3
- MANTA-280 filter supplementary reads without SA tags and read pairs with unmatched mate information
- STARKA-306 fix rare chunk size boundary defect in RangeMap
v0.29.2
- MANTA-277 fix invalid genome region requested during insert size estimation
- Update to pyflow 1.1.12 to improve SGE filesystem delay handling
and fix issue between SGE and recent bash shellshock fix
v0.29.1
- [#22] Add new manta developer guide to source docs
- [#21] improve fragment size estimation for very short fragments
- RNA: Improve fusion detection sensitivity
- MANTA-261 Transfer stable components from Manta windows port
- MANTA-273 fix support for "csi"-style BAM indices
- MANTA-273/[#14] allow bam index filenames in single-extension (Picard) style
v0.29.0
- MANTA-267/[#12] Support contig names with colons (for HLA contigs in 1kg hg38)
- MANTA-252 Complete support for CRAM input
- MANTA-264 Remove samtools from manta dependencies
- MANTA-252 Change default chrom depth to median estimate from alignments
- MANTA-263 Improve performance/stability for references with
large numbers of small contigs
- MANTA-261 Transfer stable components from Manta windows port
v0.28.0
- MANTA-259 Support joint analysis of multiple diploid samples
- MANTA-260 Add per-sample filtration to separate QUAL and GQ filters for
diploid case
- MANTA-252 Add fast chrom median depth estimator (partally enables CRAM)
- MANTA-258 Add PL values to diploid output
v0.27.2
- MANTA-257 Fix rare failure condition for graph merge
- MANTA-255 include zlib in build, simplify win64 development
- MANTA-254 Fix handling of off-edge splicing in the RNA Jump Intron Aligner
- MANTA-253 improve alignment corner cases and debugging features
v0.27.1
- [#6] Fix assertion caused by filtered graph edges on bin boundaries.
- [#5] Improve robustness to filesystem delay (update ot pyflow v1.1.7)
v0.27.0
- MANTA-188/[#4] fix off-by-one position issues in some precise duplication
and inversion breakends
- MANTA-229 Add initial support for tumor-only analysis
v0.26.5
- Update pyflow to v1.1.6: fixes multithread bug introduced in v1.1.5.
Manta should be isolated from this issue in theory.
v0.26.4
- Update license to GPLv3
- Update to relicensed pyflow v1.1.5
- MANTA-244 Handle unstranded RNA data
- MANTA-239 Use RNA bam alignments for ref read scoring
- Fix core/memory auto-detect for OSX
v0.26.3
- Fix OSX build and demo run (req. update to boost 1.56)
- Update travis CI OSX build, static analyzer
v0.26.2
- MANTA-242 cleanup code portability and documentation:
-- Updated all build/installation and contributor guidelines
-- Updated Manta user guide
-- Added Travis CI configuration file for clang/gcc build and demo run
-- Minor code edits to clean compile on OS X 10.9, CentOS 5,6,7, Ubuntu
12.04 and 14.04
-- Updated demo: new dataset covers COSMIC HCC1954 variants, added test
to verify expected output from demo run.
v0.26.1
- Remove python reflection from run configuration process, fixes rare
config issue
- VCF output formatting: FileData corrected to FileDate
v0.26.0
- MANTA-224 improve short-fragment handling for RNA
- MANTA-235 kmer reference mask to accelerate RNA contig alignments
- MANTA-232 filter large SVs with no read pair support
- MANTA-236 expand conditions for large insertion search to normalize
BWA-mem/Isaac performance
- MANTA-231 expand scoring phase split read search around breakends to
find soft clipped ref and alt support.
- MANTA-234 remove discovery pair counts from scored output files
- MANTA-222 support bwa-mem '-M' split read format
- MANTA-218 filter spanning candidates without significant signal/noise
- MANTA-155 handle N's and lowqual bases during assembly
- MANTA-219 Build system improvements for auditing, visual studio support
- MANTA-217 Improve runtime for large min candidate size settings, creating
a high speed large-event mode.
v0.25.0
- RNA - parameter adjustments, additional vcf output, orientation fixes
- MANTA-187 treat split reads symmetrically to improve RNA fusion detection
-- detect split reads directly rather than via associated soft-clip sequence
-- exclude split reads from contributing to local assembly evidence
v0.24.0
- MANTA-213 FFPE runtime optimization:
-- Recognize new BAM format for fragments shorter than read length,
prevent these reads from triggering assembly.
-- Improve insert size distribution estimation by including fragments shorter
than read length.
-- Add new runtime instrumentation report for candidate generation
-- Add runtime summary to existing graph report
-- Reduce SW edit matrix size with short k-mer match bounds on ref seq
-- Improve graph noise filtration by testing specific region for evidence
signal threshold
-- Use adaptive noise rates in hypoth gen step: background read anomaly rate
is used to determine if signal is significant. Currently applies to small
assembly candidates only.
-- Collapse redundant assembly candidates for small indels to single copy
v0.23.1
- MANTA-206 Disable remote read search in T/N analysis
- MANTA-195 Improve filtration of short fragments in FFPE samples
v0.23.0
- MANTA-200 Add filter for overlapping diploid calls which can't be explained
as two haplotypes.
- MANTA-199 Fix low-frequency fragment/breakpoint mismatch (primarily
an issue when large numbers of short ref contigs were used)
- Add CRAM support for individual tools - still need a quick chrom depth estimator
for full workflow CRAM support
- c++11 update
- MANTA-185 remove transloc calls with neg position (from circular genome)
- [mantadev] #1 Fix SA split read breakpoint position
- MANTA-183 handle paired/single read mixture in input alignments
- MANTA-182 submit config on cmdline
v0.22.0
- MANTA-181 fix assembler path and coverage issues
- MANTA-177 filter redundant partial insertions
- MANTA-142 improve contig alignment for large events
- MANTA-160 add pseudo-coloring to assembly, and improve multi-pass
read/contig association
- MANTA-170 improve pair allele support accuracy
- MANTA-139 add shadow and chimera reads into pair counts
v0.21.0
- MANTA-167 semi-mapped som pair correction
- MANTA-156 filter out assm poison reads
- MANTA-161 make assembly robust to seed k-mer selection
- MANTA-164 batch retrieve assembly mate reads
- MANTA-158 improve small indel contig alignment specificity
- MANTA-146 use MAPQ0 mate reads in assembly
- MANTA-48 use shadow reads for split scoring
- MANTA-157 improve shadow read filter
- MANTA-153 fix diploid prior
- MANTA-150 fix SV scoring size cutoff
- MANTA-148 check bam records for region errors
- RNA: rna-scoring
v0.20.1
- Lower default min candidate size to 8
v0.20.0
- MANTA-136 turn on conservative large insertion calling
- MANTA-126 multi-junction SV scoring
- MANTA-131 improve large somatic sv specificity with expanded
supporting evidence search
- RNA: track candidate orientation
v0.19.0
- MANTA-127 RG based insert stats (default off) 
- MANTA-128 Improved pair orientation estimation and error checks
- RNA: Improve fusion specificity
- MANTA-125 add experimental large insertion calling (default off)
- MANTA-125 add tier2 permissive split score to reduce small somatic
FP deletions
- MANTA-125 add tier2 chimera rate to reduce somatic FP calls 
v0.18.0
- MANTA-125 modify pair weight for small SVs
- MANTA-120 Improve stability of SV scoring as a function of read length
v0.17.0
- Filter SA split read segments by MAPQ value
- MANTA-116 better handle BWA-mem SA split-reads for inversions
- MANTA-118 static libstdc++ for gcc 4.5+
v0.16.0
- MANTA-117 add somatic quality score
- fix SA tag parsing
- MANTA-27 accept bam/fasta filenames with spaces
v0.15.0
- MANTA-108 combine clip/semi-aligned evidence detection, don't detect
overlapping reads as assembly evidence
- MANTA-98 make fewer bam scans during scoring
- MANTA-106 add high depth limit to candgen and assembler
- MANTA-75 Better match reads to SV candidates to improve
runtime and lower repeat observations (part 2)
- MANTA-105 filter poorly supported candidates to reduce per-edge compute time
- MANTA-103 fix issue in RNA and WES modes introduced by MANTA-99
v0.14.0
- MANTA-102 filter calls with high MQ0 fraction
- MANTA-99 add high-depth graph filter to improve FFPE runtime
- MANTA-100 allow for neighboring variants during assembly
- MANTA-83 sort vcfs in bam chrom order
- MANTA-96 Keep matching read pairs after candidate generation
read buffer fills
- MANTA-89 Use semi-mapped read pairs to improve germline/somatic
classification.
- MANTA-92 Add edge runtime performance log
- MANTA-75 Better match reads to SV candidates to improve
runtime and lower repeat observations
- MANTA-85 Increase uniformity of tags in vcf output
v0.13.2
- First complete pass at installation and user guide
v0.13.1
- MANTA-81 Fix small indel somatic false negatives introduced
in MANTA-63
- MANTA-80 Additional workflow options: run subsections of the
genome, finer task parallelization control and merge multiple
input BAMs per sample.
v0.13.0
- MANTA-63 Incorporate read-pair evidence into small SVs/indels
- MANTA-77 Fix assertion for rna-seq test
- MANTA-17 Include semi-aligned reads in discovery and scoring
- MANTA-69 Update score/write filter to account for CIGAR and SA-read
candidates, and new uniform candidate scheme for self-edges.
- MANTA-70 Correct filters to allow for small inversion and tandem dup
detection 
- MANTA-68 SVLEN not set correctly for non-deletions
- MANTA-64 Improve candidate generation for small regions
- MANTA-43 allow manta installation to be relocated
- MANTA-55 compile python code as part of build/install
v0.12.1
- MANTA-58 fix issue with breakends near contig boundaries
- MANTA-61 add markdown-based user guide to build
- MANTA-30 initial integration of known variant tracing framework
v0.12
- MANTA-20 incorporate split-reads into quality score
- MANTA-42 SV finder mismatches various read pair / sv-candidate combinations
- MANTA-53 Enable --rescore option in runWorkflow.py
- MANTA-40 Don't call splicing-events in RNA-seq as deletions
- MANTA-20 include split read counts for short reads
- MANTA-44 Fix Rhodobacter analysis
v0.11
- Adjust all vcf output to pass vcf-validator
- MANTA-20 fix split read breakpoint location
v0.10.1
- Fix low-frequency assertion due to unexpected alignment pattern
v0.10
- MANTA-20 Limit split read counts to those uniquely supporting each allele,
where P(allele|read)>0.999
- MANTA-20 Add likelihood based QUAL,GQ scores to diploid output, adjust
thresholds of somatic output to incorporate ref pairs and split reads.
- MANTA-41 Fails when chrom name not in [a-zA-z0-9_-]+
- MANTA-25 Partial support for BWA-MEM SA split reads
- MANTA-36 Segfault on RNA-Seq BAM input
- MANTA-20 Combined reference spanning read and split read evidence per variant
- MANTA-20 Diploid vcf output for non-tumor sample, diploid genotype inference score still todo
- MANTA-39 prevent crash on large CIGAR deletions
- MANTA-20 split read evidence counts for all large spanning SVs
v0.9
- MANTA-20 preliminary work on this branch allows assembly skip and control of min indel candidate size and min indel score size
- MANTA-33 reduce SV graph ram requirement to ~1/3 of its previous value, increase all post-merge task memory requests.
- MANTA-17 merged shadow reads into assembly and adjusted assembly parameters. Large (50+ base) insertion sensitivity improves by ~.35-.4 as a result.
- Improvements to vcf output and cmake build.
v0.8
- MANTA-28 Add prototype discovery/local-assembly of small events down to 10 bases 
- MANTA-24 Better handle very high depth and chimeric noise complexity based
on BWA-mem FFPE examples
- MANTA-26 Extend fragment stats to provide estimate of full fragment size
distribution
- Large event assembly fixes
- MANTA-23 enable use of pre-existing depth and stats files (for sparse bams)
v0.7
- Add assembly of large-event breakends and basepair resolution SV reporting
- MANTA-19 Correctly parse large deletion reads from Isaac and incorporate this into discovery
v0.6
- Fix sensitivity problems caused by unexpected proper pair bit settings, fix several self-edge issues. Detect intrachrom variants down to ~2kb.
v0.5
- Expand POC calls to include intrachromosomal variants down to ~5kb.
- Minor modifications to method based on FFPE testing.
v0.4
- POC somatic transloc output
v0.3
- POC translation of graph into candidate transloc vcf
v0.2
- working proof of concept denoised sv locus graph
v0.1
- initial prototype code tag
