Bugfix edge creation #46
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* Bug interval start before end (#35) * MS coverage log message * Meanshift refinement for shifts restricted to interval limits * Remove temporary logs * Bug cigar none (#37) * Check if mate mapped in refine discordant edges * Reinsert homology boundary adjustment comment * Plot default style (#38) * Plot style options * Amplified intervals output file bugfix and remove bedlist option * Add --out option to amplified_intervals.py * Add plotstyle option * Adjust small plot annotation text position * Plot default style (#39) * Plot style options * Amplified intervals output file bugfix and remove bedlist option * Add --out option to amplified_intervals.py * Add plotstyle option * Adjust small plot annotation text position * Plot default style, amplified_intervals commandline arguments (#40) * Plot style options * Amplified intervals output file bugfix and remove bedlist option * Add --out option to amplified_intervals.py * Add plotstyle option * Adjust small plot annotation text position * bugfixes to outfile writing (#36) * bugfixes to outfile writing * Update command line arguments GAIN and CNSIZE_MIN are command line args now * Make GAIN float, small bug fixes * Update README.md
Bugfixes, plot_style, amplified_intervals cleanup and citation.
virajbdeshpande
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Jun 12, 2019
* Bugfixes, plotstyle, amplified_interval.py (#43) * Bug interval start before end (#35) * MS coverage log message * Meanshift refinement for shifts restricted to interval limits * Remove temporary logs * Bug cigar none (#37) * Check if mate mapped in refine discordant edges * Reinsert homology boundary adjustment comment * Plot default style (#38) * Plot style options * Amplified intervals output file bugfix and remove bedlist option * Add --out option to amplified_intervals.py * Add plotstyle option * Adjust small plot annotation text position * Plot default style (#39) * Plot style options * Amplified intervals output file bugfix and remove bedlist option * Add --out option to amplified_intervals.py * Add plotstyle option * Adjust small plot annotation text position * Plot default style, amplified_intervals commandline arguments (#40) * Plot style options * Amplified intervals output file bugfix and remove bedlist option * Add --out option to amplified_intervals.py * Add plotstyle option * Adjust small plot annotation text position * bugfixes to outfile writing (#36) * bugfixes to outfile writing * Update command line arguments GAIN and CNSIZE_MIN are command line args now * Make GAIN float, small bug fixes * Update README.md * Bugfix selecting threshold for discordant edge creation * Correct description of UNCLUSTERED extendmode
virajbdeshpande
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Oct 22, 2020
* Bugfix edge creation (#46) * Bugfixes, plotstyle, amplified_interval.py (#43) * Bug interval start before end (#35) * MS coverage log message * Meanshift refinement for shifts restricted to interval limits * Remove temporary logs * Bug cigar none (#37) * Check if mate mapped in refine discordant edges * Reinsert homology boundary adjustment comment * Plot default style (#38) * Plot style options * Amplified intervals output file bugfix and remove bedlist option * Add --out option to amplified_intervals.py * Add plotstyle option * Adjust small plot annotation text position * Plot default style (#39) * Plot style options * Amplified intervals output file bugfix and remove bedlist option * Add --out option to amplified_intervals.py * Add plotstyle option * Adjust small plot annotation text position * Plot default style, amplified_intervals commandline arguments (#40) * Plot style options * Amplified intervals output file bugfix and remove bedlist option * Add --out option to amplified_intervals.py * Add plotstyle option * Adjust small plot annotation text position * bugfixes to outfile writing (#36) * bugfixes to outfile writing * Update command line arguments GAIN and CNSIZE_MIN are command line args now * Make GAIN float, small bug fixes * Update README.md * Bugfix selecting threshold for discordant edge creation * Correct description of UNCLUSTERED extendmode * Update dependencies for Ubuntu20.04 * Docker dependencies for 20.04, python2 versioning (#82) * Tweak README to include link for "development" data repo. * Force use of python2 * tweak update message * update entropy calculation, include support for missing MD tag * fix version check * fix version check * use jluebeck fork * update and fix dockerfile * better Dockerfile organization * use python2 to install mosek * update links for dockerhub * use python2 * README update Co-authored-by: Jens Luebeck <jluebeck@eng.ucsd.edu> Co-authored-by: Deshpande <vdeshpande@illumina.com>
virajbdeshpande
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Oct 27, 2020
* Bugfix edge creation (#46) * Bugfixes, plotstyle, amplified_interval.py (#43) * Bug interval start before end (#35) * MS coverage log message * Meanshift refinement for shifts restricted to interval limits * Remove temporary logs * Bug cigar none (#37) * Check if mate mapped in refine discordant edges * Reinsert homology boundary adjustment comment * Plot default style (#38) * Plot style options * Amplified intervals output file bugfix and remove bedlist option * Add --out option to amplified_intervals.py * Add plotstyle option * Adjust small plot annotation text position * Plot default style (#39) * Plot style options * Amplified intervals output file bugfix and remove bedlist option * Add --out option to amplified_intervals.py * Add plotstyle option * Adjust small plot annotation text position * Plot default style, amplified_intervals commandline arguments (#40) * Plot style options * Amplified intervals output file bugfix and remove bedlist option * Add --out option to amplified_intervals.py * Add plotstyle option * Adjust small plot annotation text position * bugfixes to outfile writing (#36) * bugfixes to outfile writing * Update command line arguments GAIN and CNSIZE_MIN are command line args now * Make GAIN float, small bug fixes * Update README.md * Bugfix selecting threshold for discordant edge creation * Correct description of UNCLUSTERED extendmode * Update dependencies for Ubuntu20.04 * Tweak README to include link for "development" data repo. * Force use of python2 * tweak update message * update entropy calculation, include support for missing MD tag * fix version check * fix version check * use jluebeck fork * update and fix dockerfile * better Dockerfile organization * use python2 to install mosek * update links for dockerhub * use python2 * Docker dependencies for 20.04, python2 versioning (#82) * Tweak README to include link for "development" data repo. * Force use of python2 * tweak update message * update entropy calculation, include support for missing MD tag * fix version check * fix version check * use jluebeck fork * update and fix dockerfile * better Dockerfile organization * use python2 to install mosek * update links for dockerhub * use python2 * README update * critical bugfix * update shebang to use /usr/bin/env python2 * Small fix Co-authored-by: Jens Luebeck <jluebeck@eng.ucsd.edu> Co-authored-by: Deshpande <vdeshpande@illumina.com>
virajbdeshpande
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Sep 14, 2022
* Bugfix edge creation (#46) * Bugfixes, plotstyle, amplified_interval.py (#43) * Bug interval start before end (#35) * MS coverage log message * Meanshift refinement for shifts restricted to interval limits * Remove temporary logs * Bug cigar none (#37) * Check if mate mapped in refine discordant edges * Reinsert homology boundary adjustment comment * Plot default style (#38) * Plot style options * Amplified intervals output file bugfix and remove bedlist option * Add --out option to amplified_intervals.py * Add plotstyle option * Adjust small plot annotation text position * Plot default style (#39) * Plot style options * Amplified intervals output file bugfix and remove bedlist option * Add --out option to amplified_intervals.py * Add plotstyle option * Adjust small plot annotation text position * Plot default style, amplified_intervals commandline arguments (#40) * Plot style options * Amplified intervals output file bugfix and remove bedlist option * Add --out option to amplified_intervals.py * Add plotstyle option * Adjust small plot annotation text position * bugfixes to outfile writing (#36) * bugfixes to outfile writing * Update command line arguments GAIN and CNSIZE_MIN are command line args now * Make GAIN float, small bug fixes * Update README.md * Bugfix selecting threshold for discordant edge creation * Correct description of UNCLUSTERED extendmode * Update dependencies for Ubuntu20.04 * Tweak README to include link for "development" data repo. * Force use of python2 * tweak update message * update entropy calculation, include support for missing MD tag * fix version check * fix version check * use jluebeck fork * update and fix dockerfile * better Dockerfile organization * use python2 to install mosek * update links for dockerhub * use python2 * critical bugfix * update shebang to use /usr/bin/env python2 * Update README.md * v1.2 revision 2 initial * pair support min * add insert_sdevs arg * only use cstats if the pair support is the same * bugfix to cstats update * add --no_cstats * bugfix to --no_cstats * bugfix to --no_cstats * Update documentation for v1.2_r2 * update pip2 in dockerfile * add curl to docker image * add libcurl-dev-gnutls * add python-dev * set pysam version to pip2 compatible * update README info about pysam * Updated everted cutoff to max_insert * Update README.md Update link to pip2 download * mm10 test update * make mm10 testing repo available * initial addition of python3 compatibility * update documentation * Updates to logging, amplicon sorting, merge window size * arg description update and shebang * bugfix to visualization issue * integer division fix python3 * improve meanshift debug logging * update docker and documentation * test bugfix for small chrom meanshift * bugfix for small chromosome * test bugfix for small segments * bugfix * improve cstats logging and comparisons * update to amplified_intervals large seed threshold * clean up docker reqs * version 1.3_r1 release * Update README.md * clean up prints and logging * bugfix to sorting for python3 * bugfix to sorting for python3 * update data repo link * Add nf-core/circdna info to README. * do not use previous cstats if NaN is present * update readme and logging * test GRCh38_viral mode * update for GRCh38_viral * update for GRCh38_viral * update for GRCh38_viral * update for GRCh38_viral * Update README.md Co-authored-by: Viraj Deshpande <virajbdeshpande@gmail.com>
virajbdeshpande
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Nov 5, 2023
* Bugfix edge creation (#46) * Bugfixes, plotstyle, amplified_interval.py (#43) * Bug interval start before end (#35) * MS coverage log message * Meanshift refinement for shifts restricted to interval limits * Remove temporary logs * Bug cigar none (#37) * Check if mate mapped in refine discordant edges * Reinsert homology boundary adjustment comment * Plot default style (#38) * Plot style options * Amplified intervals output file bugfix and remove bedlist option * Add --out option to amplified_intervals.py * Add plotstyle option * Adjust small plot annotation text position * Plot default style (#39) * Plot style options * Amplified intervals output file bugfix and remove bedlist option * Add --out option to amplified_intervals.py * Add plotstyle option * Adjust small plot annotation text position * Plot default style, amplified_intervals commandline arguments (#40) * Plot style options * Amplified intervals output file bugfix and remove bedlist option * Add --out option to amplified_intervals.py * Add plotstyle option * Adjust small plot annotation text position * bugfixes to outfile writing (#36) * bugfixes to outfile writing * Update command line arguments GAIN and CNSIZE_MIN are command line args now * Make GAIN float, small bug fixes * Update README.md * Bugfix selecting threshold for discordant edge creation * Correct description of UNCLUSTERED extendmode * Update dependencies for Ubuntu20.04 * Tweak README to include link for "development" data repo. * Force use of python2 * tweak update message * update entropy calculation, include support for missing MD tag * fix version check * fix version check * use jluebeck fork * update and fix dockerfile * better Dockerfile organization * use python2 to install mosek * update links for dockerhub * use python2 * critical bugfix * update shebang to use /usr/bin/env python2 * Update README.md * v1.2 revision 2 initial * pair support min * add insert_sdevs arg * only use cstats if the pair support is the same * bugfix to cstats update * add --no_cstats * bugfix to --no_cstats * bugfix to --no_cstats * Update documentation for v1.2_r2 * update pip2 in dockerfile * add curl to docker image * add libcurl-dev-gnutls * add python-dev * set pysam version to pip2 compatible * update README info about pysam * Updated everted cutoff to max_insert * Update README.md Update link to pip2 download * mm10 test update * make mm10 testing repo available * initial addition of python3 compatibility * update documentation * Updates to logging, amplicon sorting, merge window size * arg description update and shebang * bugfix to visualization issue * integer division fix python3 * improve meanshift debug logging * update docker and documentation * test bugfix for small chrom meanshift * bugfix for small chromosome * test bugfix for small segments * bugfix * improve cstats logging and comparisons * update to amplified_intervals large seed threshold * clean up docker reqs * version 1.3_r1 release * Update README.md * clean up prints and logging * bugfix to sorting for python3 * bugfix to sorting for python3 * update data repo link * Add nf-core/circdna info to README. * do not use previous cstats if NaN is present * update readme and logging * test GRCh38_viral mode * update for GRCh38_viral * update for GRCh38_viral * update for GRCh38_viral * update for GRCh38_viral * Update README.md * version 1.3.r2 * version 1.3.r2 * fix liblzma-dev docker version error * add cstats_only to downsample.py * speedup for coverage.stats lookup * tweak downsample.py logging * add random seed control to downsample.py * add editable pdf text objects (type 42) * Update run_aa_script.sh * Proposal of universal Mosek interface * version 1.3.r3 * version 1.3.r3 bugfix to mosek version checking * version 1.3.r3 Tweak logging * version 1.3.r3 update readme * version 1.3.r3 update readme and cocker * typo in docker requirements * Update README.md * Update README.md * prevent empty cstats line issue * add mosek license test * version 1.3.r4 * version 1.3.r4 re-add is_unmapped filter to interval_coverage. * update logging * version 1.3.r4 version 1.3.r4 re-add is_unmapped filter to interval_coverage. * update logging * version 1.3.r5 * version 1.3.r5 * Update README * reduce logging spam from fonttools * Update README.md * minor optimizations Don't write the .out files for each segment and don't create a new graph when not needed * Update README.md * update README.md formatting * update README * Update README * Update some urls to AmpliconSuite github org * Update README.md * remove a debug print * move print to logging debug * warn if seeds file doesn't appear to be from AmpliconSuite-pipeline * Update installation instructions * Update README * development checkpoint * development checkpoint * development checkpoint * development checkpoint * version 1.3.r6 * version 1.3.r6 development checkpoint development checkpoint development checkpoint version 1.3.r6 * Update docs v1.3.r6 version 1.3.r6 * Update docs * Update docs * add version and datetime header to graph/cycles files * Create LICENSE The LICENSE info from the header of AmpliconArchitect.py is reproduced in a dedicated file. * add back interval .out files without problematic colon in filename * add ability to extract SV VCF read counts extract from 'DR' format field * handle undefined fields in VCF * improve warning logging * SV VCF read-count downsample rescaling bugfix * Update README.md * allow '.' in filter field for passing * Update README.md --------- Co-authored-by: Viraj Deshpande <virajbdeshpande@gmail.com> Co-authored-by: aszekMosek <michal.adamaszek@mosek.com>
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There was a bug in how AA inferred the threshold on number of reads required for creating a discordant edge. This commit fixes this bug.