Commits

Commits on Jun 24, 2024

ensure block names are all ASCII characters (#14 )
jgarthur
committedJun 24, 2024

Commits on Mar 31, 2024

update README with notes on conda (#13 )
jgarthur
committedMar 31, 2024
Merge pull request #12 from SUwonglab/ja/dependency_updates
jgarthur
committedMar 31, 2024
fix pmf_kernel_smooth for newer versions of numpy
jgarthur
committedMar 31, 2024
python-graph -> igraph; remove pysam version pinning
jgarthur
committedMar 31, 2024

Commits on Sep 15, 2023

Merge pull request #7 from SUwonglab/ja/high_split_library_support
jgarthur
committedSep 15, 2023

Commits on Feb 2, 2023

update README
jgarthur
committedFeb 2, 2023

Commits on Jan 18, 2022

add '-t highsplit' option for calling SVs on libraries with high numbers of split reads
jgarthur
committedJan 18, 2022
Merge pull request #6 from SUwonglab/ja/del_read_through
jgarthur
committedJan 18, 2022

Commits on Jan 13, 2022

readthrough alignments cannot be Del type DRPs
jgarthur
committedJan 13, 2022
minimum KDE bandwidth of 1 (#5 )
jgarthur
committedJan 13, 2022

Commits on Dec 14, 2021

minimum KDE bandwidth of 1
jgarthur
committedDec 14, 2021

Commits on Jan 29, 2019

remove use of has_unmapped_records (deprecated)
jgarthur
committedJan 29, 2019

Commits on Sep 12, 2018

fix possible issue when mate is unmapped but AlignedSegment.mrnm == -1
jgarthur
committedSep 12, 2018

Commits on Jul 10, 2018

updated version.py
Joey Arthur
committedJul 10, 2018

Commits on Jul 6, 2018

added max_sr_support and max_pe_support options to filter-merge
Joey Arthur
committedJul 6, 2018
added max/min_allele_fraction to filter criteria in filter-merge
Joey Arthur
committedJul 6, 2018
refactored option names for filter-merge to be more readable; added --min_sr_support and --min_pe_support options
Joey Arthur
committedJul 6, 2018
added --nocompoundhet option in filter-merge
Joey Arthur
committedJul 6, 2018

Commits on Jun 13, 2018

--noinsertions option in filter-merge now includes complex SVs with insertions
Joey Arthur
committedJun 13, 2018

Commits on Jun 12, 2018

Commits on Jun 8, 2018

error message in filter_output.py; reorder VCF INFO tags; EVENT_SPAN in all VCF entries; move HCN FORMAT tag to HAPLOID_CN (only affects duplications); update VCF header
Joey Arthur
committedJun 8, 2018

Commits on May 19, 2018

update example output to reflect the id format from 08e7982
Joey Arthur
committedMay 19, 2018
minor change to -f option error message
Joey Arthur
committedMay 19, 2018
move reference and gap files to required arguments
Joey Arthur
committedMay 19, 2018
rename MAF tag in VCF to AF (just allele freq, not 'minor')
Joey Arthur
committedMay 19, 2018

Commits on Mar 24, 2018

added remaining tags to VCF out, so it now shows the same information as arcsv_out.tab; changed SV id format to use underscores instead of commas for VCF compatibility
Joey Arthur
committedMar 24, 2018

Commits on Mar 23, 2018

merge vcf output into sv_output()
Joey Arthur
committedMar 23, 2018

Commits on Mar 21, 2018

add AF tag to VCF header
Joey Arthur
committedMar 21, 2018
allow haploid-only calling with -f ""; output allele fraction as AF tag in VCF
Joey Arthur
committedMar 21, 2018
Merge branch 'readthrough'
Joey Arthur
committedMar 21, 2018

Commits on Mar 3, 2018

update example output
Joey Arthur
committedMar 3, 2018
update example output
Joey Arthur
committedMar 3, 2018

Commits on Mar 2, 2018

fix minor bug in compute_likelihood -- should only effect hanging read likelihood around duplications
Joey Arthur
committedMar 2, 2018