diff --git a/docs/src/Tutorial_03_Low_Level.ipynb b/docs/src/Tutorial_03_Low_Level.ipynb index 1e655de60..709daef06 100644 --- a/docs/src/Tutorial_03_Low_Level.ipynb +++ b/docs/src/Tutorial_03_Low_Level.ipynb @@ -124,6 +124,7 @@ "outputs": [], "source": [ "lane, tile, cycle, channel = (1, 1101, 15, 0)\n", + "extraction_metrics.rebuild_index(true)\n", "extraction_metric = extraction_metrics.get_metric(lane, tile, cycle)\n", "intensity = extraction_metric.max_intensity (channel)" ] diff --git a/docs/src/changes.md b/docs/src/changes.md index 9a2f4fee6..bee28d7a7 100644 --- a/docs/src/changes.md +++ b/docs/src/changes.md @@ -1,4 +1,11 @@ -# Changes {#changes} +# Changes {#changes} + +## v1.2.1 + +| Date | Description | +|------------|--------------------------------------------------------| +| 2023-01-30 | Fix bug in core.py with newer versions of NumPy | +| 2023-01-30 | Fix bug in tutorial 03 low level missing rebuild_index | ## v1.2.0 @@ -6,597 +13,567 @@ |------------|------------------------------------------------------------| | 2022-10-21 | Add missing read-level and run-level cluster count metrics | - ## v1.1.28 -Date | Description ----------- | ----------- -2022-09-26 | Ensure Python wheels support ARM M1 with universal2 - +| Date | Description | +|------------|-----------------------------------------------------| +| 2022-09-26 | Ensure Python wheels support ARM M1 with universal2 | ## v1.1.27 -Date | Description ----------- | ----------- -2022-08-23 | Fix issue where wheels cannot be updated - +| Date | Description | +|------------|------------------------------------------| +| 2022-08-23 | Fix issue where wheels cannot be updated | ## v1.1.26 -Date | Description ----------- | ----------- -2022-08-09 | Support parsing error metrics v6 -2022-08-09 | Fix potential bugs when parsing Q-metrics -2022-08-13 | Issue-282: Support universal build for M1 mac -2022-08-13 | Issue-282: Remove support for Python 3.5 (not working on Mac M1) -2022-08-13 | Issue-282: Update Windows Agent to 2019 from 2016 (2016 discontinued) -2022-07-18 | Fix InterOp Python Wheels do not run on Mac OS X High Sierra 10.13 since v1.1.24 +| Date | Description | +|------------|----------------------------------------------------------------------------------| +| 2022-08-09 | Support parsing error metrics v6 | +| 2022-08-09 | Fix potential bugs when parsing Q-metrics | +| 2022-08-13 | Issue-282: Support universal build for M1 mac | +| 2022-08-13 | Issue-282: Remove support for Python 3.5 (not working on Mac M1) | +| 2022-08-13 | Issue-282: Update Windows Agent to 2019 from 2016 (2016 discontinued) | +| 2022-07-18 | Fix InterOp Python Wheels do not run on Mac OS X High Sierra 10.13 since v1.1.24 | ## v1.1.25 -Date | Description ----------- | ----------- -2022-06-25 | Add test for .NET standard artifacts -2022-06-16 | Deploy .NET Standard Nuget package on public repo using Github Actions -2022-06-16 | Deploy C++ applications on public repo using Github Actions -2022-06-15 | IPA-10585: Add github action support for deploying docs +| Date | Description | +|------------|------------------------------------------------------------------------| +| 2022-06-25 | Add test for .NET standard artifacts | +| 2022-06-16 | Deploy .NET Standard Nuget package on public repo using Github Actions | +| 2022-06-16 | Deploy C++ applications on public repo using Github Actions | +| 2022-06-15 | IPA-10585: Add github action support for deploying docs | ## v1.1.24 -Date | Description ----------- | ----------- -2022-03-14 | Add support for Python 3.10 for Linux, Windows and Mac OSX -2022-06-07 | Add support for Github Actions - + Date | Description +------------|------------------------------------------------------------ + 2022-03-14 | Add support for Python 3.10 for Linux, Windows and Mac OSX + 2022-06-07 | Add support for Github Actions ## v1.1.23 -Date | Description ----------- | ----------- -2021-4-08 | Issue-262: Fix bugs with index tables in core.py - + Date | Description +-----------|-------------------------------------------------- + 2021-4-08 | Issue-262: Fix bugs with index tables in core.py ## v1.1.22 -Date | Description ----------- | ----------- -2021-03-24 | Issue-259: Add simple functions with doc test examples - + Date | Description +------------|-------------------------------------------------------- + 2021-03-24 | Issue-259: Add simple functions with doc test examples ## v1.1.21 -Date | Description ----------- | ----------- -2021-01-20 | Fix linux Python wheel deploy - + Date | Description +------------|------------------------------- + 2021-01-20 | Fix linux Python wheel deploy ## v1.1.20 -Date | Description ----------- | ----------- -2021-01-27 | Issue-250: Improve cluster count precision -2021-01-05 | Fix documentation deployment + Date | Description +------------|-------------------------------------------- + 2021-01-27 | Issue-250: Improve cluster count precision + 2021-01-05 | Fix documentation deployment ## v1.1.19 -Date | Description ----------- | ----------- -2021-01-05 | Fix broken deployment of docs and failing tests on deployment - + Date | Description +------------|--------------------------------------------------------------- + 2021-01-05 | Fix broken deployment of docs and failing tests on deployment ## v1.1.18 -Date | Description ----------- | ----------- -2021-01-04 | Issue-245: Support Python 3.9 - + Date | Description +------------|------------------------------- + 2021-01-04 | Issue-245: Support Python 3.9 ## v1.1.17 -Date | Description ----------- | ----------- -2020-12-05 | Downgrade Mac image to Xcode 7.3 to support older Macs -2020-12-04 | Travis reports error when it cannot find a wheel to update on non-Python builds - + Date | Description +------------|--------------------------------------------------------------------------------- + 2020-12-05 | Downgrade Mac image to Xcode 7.3 to support older Macs + 2020-12-04 | Travis reports error when it cannot find a wheel to update on non-Python builds ## v1.1.16 -Date | Description ----------- | ----------- -2020-11-30 | Issue-241: Write out outliers to GNUPlot file - + Date | Description +------------|----------------------------------------------- + 2020-11-30 | Issue-241: Write out outliers to GNUPlot file ## v1.1.15 -Date | Description ----------- | ----------- -2020-11-13 | Issue-229: Support % loading concentration -2020-11-13 | Issue-229: Fix Python binding for read_metrics_from_buffer - + Date | Description +------------|------------------------------------------------------------ + 2020-11-13 | Issue-229: Support % loading concentration + 2020-11-13 | Issue-229: Fix Python binding for read_metrics_from_buffer ## v1.1.14 -Date | Description ----------- | ----------- -2020-11-09 | Travis deployment broke with a warning. The fix broke it further - + Date | Description +------------|------------------------------------------------------------------ + 2020-11-09 | Travis deployment broke with a warning. The fix broke it further ## v1.1.13 -Date | Description ----------- | ----------- -2020-11-06 | Issue-322: Update RunParameters.xml parsing to support iSeq and NextSeq2k - + Date | Description +------------|--------------------------------------------------------------------------- + 2020-11-06 | Issue-322: Update RunParameters.xml parsing to support iSeq and NextSeq2k ## v1.1.12 -Date | Description ----------- | ----------- -2020-08-25 | Issue-228: Update RunInfo.xml support for NextSeq2k -2020-08-25 | Issue-228: Add blue/green channel name support -2020-08-25 | Issue-228: Add reverse complement support -2020-08-25 | Issue-228: Fix memory corruption in RunInfo.xml parsing - + Date | Description +------------|--------------------------------------------------------- + 2020-08-25 | Issue-228: Update RunInfo.xml support for NextSeq2k + 2020-08-25 | Issue-228: Add blue/green channel name support + 2020-08-25 | Issue-228: Add reverse complement support + 2020-08-25 | Issue-228: Fix memory corruption in RunInfo.xml parsing ## v1.1.11 -Date | Description ----------- | ----------- -2020-08-10 | Issue-223: Add missing v5 error metric file format - + Date | Description +------------|---------------------------------------------------- + 2020-08-10 | Issue-223: Add missing v5 error metric file format ## v1.1.10 -Date | Description ----------- | ----------- -2020-04-17 | Issue-216: Fix bug where surface list is not updated on read -2020-04-17 | Add unit test for NextSeq1k2k run info - + Date | Description +------------|-------------------------------------------------------------- + 2020-04-17 | Issue-216: Fix bug where surface list is not updated on read + 2020-04-17 | Add unit test for NextSeq1k2k run info ## v1.1.9 -Date | Description ----------- | ----------- -2020-04-07 | Remove Python 3.4 build from Windows -2020-04-06 | Support more recent versions of CMake -2020-04-06 | Fix bugs in format of Image and EmpiricalPhasing in dumptext (Issue-206) -2020-04-04 | Add % Occupied to run summary -2020-04-04 | Switch C# library from .Net Core to .Net Standard -2020-04-04 | Support iSeq % Occupancy (Issue-193) -2020-04-03 | Add support for Python 3.8 (Issue-205) - - + Date | Description +------------|-------------------------------------------------------------------------- + 2020-04-07 | Remove Python 3.4 build from Windows + 2020-04-06 | Support more recent versions of CMake + 2020-04-06 | Fix bugs in format of Image and EmpiricalPhasing in dumptext (Issue-206) + 2020-04-04 | Add % Occupied to run summary + 2020-04-04 | Switch C# library from .Net Core to .Net Standard + 2020-04-04 | Support iSeq % Occupancy (Issue-193) + 2020-04-03 | Add support for Python 3.8 (Issue-205) ## v1.1.8 -Date | Description ----------- | ----------- -2018-12-05 | Fix for Python 3.7 on Mac OSX wheel deployment - + Date | Description +------------|------------------------------------------------ + 2018-12-05 | Fix for Python 3.7 on Mac OSX wheel deployment ## v1.1.7 -Date | Description ----------- | ----------- -2018-11-11 | Improve Python documentation expounding upon the run module -2018-11-10 | Add auto generation of documentation -2018-10-03 | Fix MacOSX build - + Date | Description +------------|------------------------------------------------------------- + 2018-11-11 | Improve Python documentation expounding upon the run module + 2018-11-10 | Add auto generation of documentation + 2018-10-03 | Fix MacOSX build ## v1.1.6 -Date | Description ----------- | ----------- -2018-10-03 | New version of delocate broke MacOSX, need updated setuptools - + Date | Description +------------|--------------------------------------------------------------- + 2018-10-03 | New version of delocate broke MacOSX, need updated setuptools ## v1.1.5 -Date | Description ----------- | ----------- -2018-07-22 | Add Python 3.7 support -2018-06-28 | Future proof throw specification -2018-06-27 | Fix bug in example example_populate_qmetricset.pp -2018-05-07 | Fix C++ Linking bug with inconsistent macros -2018-05-07 | Add percent PF -2018-05-07 | Add support for iSeq -2018-03-18 | Add Linux and Windows .NET Core builds - + Date | Description +------------|--------------------------------------------------- + 2018-07-22 | Add Python 3.7 support + 2018-06-28 | Future proof throw specification + 2018-06-27 | Fix bug in example example_populate_qmetricset.pp + 2018-05-07 | Fix C++ Linking bug with inconsistent macros + 2018-05-07 | Add percent PF + 2018-05-07 | Add support for iSeq + 2018-03-18 | Add Linux and Windows .NET Core builds ## v1.1.4 -Date | Description ----------- | ----------- -2018-02-06 | Warn GNU compiler versions less than 4.8 -2018-01-31 | Fix for the MinGW build -2018-01-28 | Add Imaging Table example in Python -2018-01-26 | Fix missing version.h in C++ install -2018-01-26 | Fix missing apps on Windows - + Date | Description +------------|------------------------------------------ + 2018-02-06 | Warn GNU compiler versions less than 4.8 + 2018-01-31 | Fix for the MinGW build + 2018-01-28 | Add Imaging Table example in Python + 2018-01-26 | Fix missing version.h in C++ install + 2018-01-26 | Fix missing apps on Windows ## v1.1.3 -Date | Description ----------- | ----------- -2018-01-15 | Distribute Python packages to PyPI - + Date | Description +------------|------------------------------------ + 2018-01-15 | Distribute Python packages to PyPI ## v1.1.2 -Date | Description ----------- | ----------- -2017-12-19 | Fix missing NuGet Package is created for Windows -2017-11-09 | IPA-7159: Fix bug for BaseSpace read_interop_from_buffer on per-cycle InterOp files -2017-11-09 | Update Linux build script - + Date | Description +------------|------------------------------------------------------------------------------------- + 2017-12-19 | Fix missing NuGet Package is created for Windows + 2017-11-09 | IPA-7159: Fix bug for BaseSpace read_interop_from_buffer on per-cycle InterOp files + 2017-11-09 | Update Linux build script ## v1.1.1 -Date | Description ----------- | ----------- -2017-10-24 | Update windows build script + Date | Description +------------|----------------------------- + 2017-10-24 | Update windows build script ## v1.1.0 -Date | Description ----------- | ----------- -2017-10-16 | Add Jupyter Notebook Python Example for the SAV Indexing Tab -2017-10-16 | Add CentOS7 docker build image -2017-10-13 | Add percent occupied to imaging and analysis tabs -2017-10-13 | IPA-7068: Fix q-metric reorder issue -2017-09-28 | Add flowcell validation logic to RunInfo.xml parsing -2017-09-22 | Added additional documentation for index summary -2017-08-29 | Improve run info validation -2017-08-29 | Update build scripts with various bug fixes -2017-08-29 | IPA-6789: Create NuGet build test -2017-08-25 | IPA-6646: Fix extraction_metric nan logic -2017-07-31 | IPA-6641: Audit lookup table usage to reduce memory -2017-07-31 | Fix bug that caused SAV 2.3.4 to crash when tile metrics was missing or empty -2017-07-21 | Native shared libraries are now copied to bin folder for NuGet packages on Linux (non-Windows systems) -2017-07-11 | IPA-6535: Error rate should report NaN for no data -2017-07-10 | Simplify build scripts, add nuget package and additional MSVC libraries -2017-06-27 | IPA-6640: Fix issues with summary app and phasing reporting -2017-06-12 | IPA-6290: Create .NET Core build for InterOp -2017-06-05 | IPA-6597: Enable hash map for visual studio -2017-06-02 | Bug fix for VS2017 warning as error -2017-05-31 | IPA-6541: Fix index sequence order for BaseSpace -2017-05-25 | IPA-6540: Make tile list validation less catastrophic and own exception + Date | Description +------------|-------------------------------------------------------------------------------------------------------- + 2017-10-16 | Add Jupyter Notebook Python Example for the SAV Indexing Tab + 2017-10-16 | Add CentOS7 docker build image + 2017-10-13 | Add percent occupied to imaging and analysis tabs + 2017-10-13 | IPA-7068: Fix q-metric reorder issue + 2017-09-28 | Add flowcell validation logic to RunInfo.xml parsing + 2017-09-22 | Added additional documentation for index summary + 2017-08-29 | Improve run info validation + 2017-08-29 | Update build scripts with various bug fixes + 2017-08-29 | IPA-6789: Create NuGet build test + 2017-08-25 | IPA-6646: Fix extraction_metric nan logic + 2017-07-31 | IPA-6641: Audit lookup table usage to reduce memory + 2017-07-31 | Fix bug that caused SAV 2.3.4 to crash when tile metrics was missing or empty + 2017-07-21 | Native shared libraries are now copied to bin folder for NuGet packages on Linux (non-Windows systems) + 2017-07-11 | IPA-6535: Error rate should report NaN for no data + 2017-07-10 | Simplify build scripts, add nuget package and additional MSVC libraries + 2017-06-27 | IPA-6640: Fix issues with summary app and phasing reporting + 2017-06-12 | IPA-6290: Create .NET Core build for InterOp + 2017-06-05 | IPA-6597: Enable hash map for visual studio + 2017-06-02 | Bug fix for VS2017 warning as error + 2017-05-31 | IPA-6541: Fix index sequence order for BaseSpace + 2017-05-25 | IPA-6540: Make tile list validation less catastrophic and own exception ## v1.0.25 -Date | Description ----------- | ----------- -2017-05-08 | IPA-6419: Filter metric list by empty metric values -2017-05-05 | Refactor plot-by-lane, cycle and flowcell to use reflection-like enums -2017-04-28 | IPA-6413: Add C# exception unit tests -2017-04-26 | Fix bug in list filename by moving clear -2017-04-25 | Fixes for the regression tests -2017-04-20 | Add feature to list all InterOp filenames -2017-04-14 | IPA-6353: Handle Legacy RunInfo rewrite -2017-03-28 | IPA-5052: All lanes on Indexing Tab - + Date | Description +------------|------------------------------------------------------------------------ + 2017-05-08 | IPA-6419: Filter metric list by empty metric values + 2017-05-05 | Refactor plot-by-lane, cycle and flowcell to use reflection-like enums + 2017-04-28 | IPA-6413: Add C# exception unit tests + 2017-04-26 | Fix bug in list filename by moving clear + 2017-04-25 | Fixes for the regression tests + 2017-04-20 | Add feature to list all InterOp filenames + 2017-04-14 | IPA-6353: Handle Legacy RunInfo rewrite + 2017-03-28 | IPA-5052: All lanes on Indexing Tab ## v1.0.24 -Date | Description ----------- | ----------- -2017-05-05 | Remove Python library from module dependencies + Date | Description +------------|------------------------------------------------ + 2017-05-05 | Remove Python library from module dependencies ## v1.0.23 -Date | Description ----------- | ----------- -2017-04-15 | Handle legacy HiSeq RunInfo rewrite -2017-04-14 | Fix deployment in Travis and Appveyor -2017-04-13 | Ensure empty metrics consistently produce empty plots + Date | Description +------------|------------------------------------------------------- + 2017-04-15 | Handle legacy HiSeq RunInfo rewrite + 2017-04-14 | Fix deployment in Travis and Appveyor + 2017-04-13 | Ensure empty metrics consistently produce empty plots ## v1.0.22 -Date | Description ----------- | ----------- -2017-04-13 | Create a ManyLinux build of InterOp and InterOp Python + Date | Description +------------|-------------------------------------------------------- + 2017-04-13 | Create a ManyLinux build of InterOp and InterOp Python ## v1.0.21 -Date | Description ----------- | ----------- -2017-04-11 | Fix missing dependencies in Python and create more portable build + Date | Description +------------|------------------------------------------------------------------- + 2017-04-11 | Fix missing dependencies in Python and create more portable build ## v1.0.20 -Date | Description ----------- | ----------- -2017-04-07 | More portable Python build + Date | Description +------------|---------------------------- + 2017-04-07 | More portable Python build ## v1.0.19 -Date | Description ----------- | ----------- -2017-04-02 | Added Python 3 support + Date | Description +------------|------------------------ + 2017-04-02 | Added Python 3 support ## v1.0.18 -Date | Description ----------- | ----------- -2017-03-16 | Add Swig Python binding to InterOp Library -2017-03-15 | IPA-6285: IPA-6285: Support CSV writing of summary + Date | Description +------------|---------------------------------------------------- + 2017-03-16 | Add Swig Python binding to InterOp Library + 2017-03-15 | IPA-6285: IPA-6285: Support CSV writing of summary ## v1.0.17 -Date | Description ----------- | ----------- -2017-03-13 | Update documents to clarify calculations -2017-03-02 | IPA-6235: Add is_pair_end to run_info -2017-03-02 | IPA-6233: Release new non-polymorphic template function interface -2017-02-24 | IPA-6189: Fixed compute_buffer_size to handle mutli record format tile -2017-02-20 | IPA-6178: Fix another bug in flowcell loading from collapsed-q -2017-02-20 | IPA-6057: Simplify polymorphic functions -2017-02-18 | IPA-6167: Fix bug in by cycle and flowcell plots for BaseSpace Collapsed Q Metrics -2017-02-16 | IPA-6059: Fix windows regression tests -2017-02-16 | IPA-6050: Add parse enum to SWIG binding -2017-02-16 | IPA-6165: Add summary example -2017-02-16 | IPA-6027: Support RunInfo writing -2017-02-01 | IPA-6066: Threaded performance test for reading -2017-01-24 | Update documentation, fixes for compressed q-metrics + Date | Description +------------|------------------------------------------------------------------------------------ + 2017-03-13 | Update documents to clarify calculations + 2017-03-02 | IPA-6235: Add is_pair_end to run_info + 2017-03-02 | IPA-6233: Release new non-polymorphic template function interface + 2017-02-24 | IPA-6189: Fixed compute_buffer_size to handle mutli record format tile + 2017-02-20 | IPA-6178: Fix another bug in flowcell loading from collapsed-q + 2017-02-20 | IPA-6057: Simplify polymorphic functions + 2017-02-18 | IPA-6167: Fix bug in by cycle and flowcell plots for BaseSpace Collapsed Q Metrics + 2017-02-16 | IPA-6059: Fix windows regression tests + 2017-02-16 | IPA-6050: Add parse enum to SWIG binding + 2017-02-16 | IPA-6165: Add summary example + 2017-02-16 | IPA-6027: Support RunInfo writing + 2017-02-01 | IPA-6066: Threaded performance test for reading + 2017-01-24 | Update documentation, fixes for compressed q-metrics ## v1.0.16 -Date | Description ----------- | ----------- -2017-01-19 | Fixed bugs in dumptext and dumpbin and update new phasing tests -2017-01-17 | Ensure empirical phasing loads with tile -2017-01-16 | NovaSeq changes + Date | Description +------------|----------------------------------------------------------------- + 2017-01-19 | Fixed bugs in dumptext and dumpbin and update new phasing tests + 2017-01-17 | Ensure empirical phasing loads with tile + 2017-01-16 | NovaSeq changes ## v1.0.15 -Date | Description ----------- | ----------- -2017-01-04 | Update summary app to support levels of verbosity -2017-01-03 | Fixes to documentation and text writing + Date | Description +------------|--------------------------------------------------- + 2017-01-04 | Update summary app to support levels of verbosity + 2017-01-03 | Fixes to documentation and text writing ## v1.0.14 -Date | Description ----------- | ----------- -2016-12-21 | Replace interop2csv with dumptext -2016-12-20 | IPA-5923: Fix bug in legacy q-metric binning -2016-12-19 | Removes the coverity run from the build matrix for every pull request -2016-12-16 | IPA-5885: Ensure error summary matches requirements -2016-12-14 | Enhance C# version information -2016-12-14 | Clean up unused enum types -2016-12-12 | IPA-5153: Ensure Summary tab calculations are consistent with Docs -2016-12-09 | IPA-5883: Fix possible memory issue in MSVC12 -2016-12-08 | IPA-4674: Add support for absolute naming convention -2016-12-07 | IPA-5869: Add section filtering -2016-12-06 | IPA-5734: Synchronize master -2016-12-02 | Add Google Analytics tracking to documentation -2016-12-08 | Added admonition to avoid using MSVC 12 (2013) with C# bindings -2016-12-08 | Added support for absolute tile naming -2016-12-08 | Added ability to do section filtering -2016-12-05 | Added regression tests for imaging -2016-12-05 | Added unit tests for format coverage -2016-11-17 | Improved performance of InterOp calculations for C++11 enabled version -2016-11-14 | Added version to Windows DLLs -2016-11-14 | Added regression tests for indexing -2016-11-09 | Added unit tests for clearing logic -2016-11-07 | Added regression tests for analysis plots -2016-11-01 | Improved performance of InterOp loading -2016-10-26 | Added path class to handle RTA output filenames -2016-09-22 | Added regression tests for summary - + Date | Description +------------|------------------------------------------------------------------------ + 2016-12-21 | Replace interop2csv with dumptext + 2016-12-20 | IPA-5923: Fix bug in legacy q-metric binning + 2016-12-19 | Removes the coverity run from the build matrix for every pull request + 2016-12-16 | IPA-5885: Ensure error summary matches requirements + 2016-12-14 | Enhance C# version information + 2016-12-14 | Clean up unused enum types + 2016-12-12 | IPA-5153: Ensure Summary tab calculations are consistent with Docs + 2016-12-09 | IPA-5883: Fix possible memory issue in MSVC12 + 2016-12-08 | IPA-4674: Add support for absolute naming convention + 2016-12-07 | IPA-5869: Add section filtering + 2016-12-06 | IPA-5734: Synchronize master + 2016-12-02 | Add Google Analytics tracking to documentation + 2016-12-08 | Added admonition to avoid using MSVC 12 (2013) with C# bindings + 2016-12-08 | Added support for absolute tile naming + 2016-12-08 | Added ability to do section filtering + 2016-12-05 | Added regression tests for imaging + 2016-12-05 | Added unit tests for format coverage + 2016-11-17 | Improved performance of InterOp calculations for C++11 enabled version + 2016-11-14 | Added version to Windows DLLs + 2016-11-14 | Added regression tests for indexing + 2016-11-09 | Added unit tests for clearing logic + 2016-11-07 | Added regression tests for analysis plots + 2016-11-01 | Improved performance of InterOp loading + 2016-10-26 | Added path class to handle RTA output filenames + 2016-09-22 | Added regression tests for summary ## v1.0.13 -Date | Description ----------- | ----------- -2016-11-30 | Removed Win32 build testing - this is not supported -2016-11-28 | IPA-5830: Fix tile naming bug for on demand datasets -2016-10-19 | Remove time from imaging table -2016-09-27 | IPA-5213: Create per surface summary model/logic/app - + Date | Description +------------|------------------------------------------------------ + 2016-11-30 | Removed Win32 build testing - this is not supported + 2016-11-28 | IPA-5830: Fix tile naming bug for on demand datasets + 2016-10-19 | Remove time from imaging table + 2016-09-27 | IPA-5213: Create per surface summary model/logic/app ## v1.0.12 -Date | Description ----------- | ----------- -2016-09-26 | IPA-5210: Create CSV parsable summary output -2016-09-23 | IPA-5194: Create nuspec package file -2016-09-17 | Refactor individual metric unit tests -2016-09-17 | Refactor metric stream tests -2016-09-14 | Reorganized code into own stat util file -2016-09-14 | Fixes error rate at a specific cycle when tiles are at different cycles -2016-09-14 | Add version information for zip archives -2016-09-14 | IPA-5070: Add optional flag to skip median for summary -2016-09-13 | Ensure ANSI build is being tested - + Date | Description +------------|------------------------------------------------------------------------- + 2016-09-26 | IPA-5210: Create CSV parsable summary output + 2016-09-23 | IPA-5194: Create nuspec package file + 2016-09-17 | Refactor individual metric unit tests + 2016-09-17 | Refactor metric stream tests + 2016-09-14 | Reorganized code into own stat util file + 2016-09-14 | Fixes error rate at a specific cycle when tiles are at different cycles + 2016-09-14 | Add version information for zip archives + 2016-09-14 | IPA-5070: Add optional flag to skip median for summary + 2016-09-13 | Ensure ANSI build is being tested ## v1.0.11 -Date | Description ----------- | ----------- -2016-09-12 | Fixed bug in q-score heatmap and q-score clearing -2016-09-12 | Added summary regression test, fixed regression test framework, fixed runParameters reading -2016-09-09 | Added sentinel for missing values in the heatmap type plots -2016-09-09 | Fixed invalid pointer deference and double free in MSVC -2016-09-08 | Added sentinel for missing values in the imaging table -2016-09-08 | Fixed potential problem found by coverity -2016-09-07 | IPA-5101: Fix MSVC bug in vector type loading (Master) -2016-09-02 | Added buffered reader to improve loading speed -2016-09-01 | Bug fix for SWIG in on-demand loading + Date | Description +------------|--------------------------------------------------------------------------------------------- + 2016-09-12 | Fixed bug in q-score heatmap and q-score clearing + 2016-09-12 | Added summary regression test, fixed regression test framework, fixed runParameters reading + 2016-09-09 | Added sentinel for missing values in the heatmap type plots + 2016-09-09 | Fixed invalid pointer deference and double free in MSVC + 2016-09-08 | Added sentinel for missing values in the imaging table + 2016-09-08 | Fixed potential problem found by coverity + 2016-09-07 | IPA-5101: Fix MSVC bug in vector type loading (Master) + 2016-09-02 | Added buffered reader to improve loading speed + 2016-09-01 | Bug fix for SWIG in on-demand loading ## v1.0.10 -Date | Description ----------- | ----------- -2016-09-01 | Bug fix clearing the summary stat prior to setting it -2016-09-01 | Fixed a bug in QMetrics V6 Unbinned, added unit test and C# example -2016-08-31 | IPA-5069: Flush out on demand loading further for each tab -2016-08-30 | Various minor fixes to get public working with Clang3.4 and MSVC12 -2016-08-30 | Bug fix to RunInfo section validation -2016-08-30 | IPA-5069: Support on demand loading for SAV (Part 1) -2016-08-26 | IPA-5028: Add RunInfo and InterOp validation + Date | Description +------------|--------------------------------------------------------------------- + 2016-09-01 | Bug fix clearing the summary stat prior to setting it + 2016-09-01 | Fixed a bug in QMetrics V6 Unbinned, added unit test and C# example + 2016-08-31 | IPA-5069: Flush out on demand loading further for each tab + 2016-08-30 | Various minor fixes to get public working with Clang3.4 and MSVC12 + 2016-08-30 | Bug fix to RunInfo section validation + 2016-08-30 | IPA-5069: Support on demand loading for SAV (Part 1) + 2016-08-26 | IPA-5028: Add RunInfo and InterOp validation ## v1.0.9 -Date | Description ----------- | ----------- -2016-08-26 | Refactor CSharp code into additional library -2016-08-26 | IPA-5028: Add RunInfo and InterOp validation -2016-08-19 | Fix sorting in imaging table -2016-08-18 | Cleanup code -2016-08-17 | Fix the read ID -2016-08-16 | IPA-5009: Add sorting to imaging table -2016-08-16 | IPA-5007: Fix combo boxes on analysis tab -2016-08-16 | Fix msvc warning and some script differences -2016-08-15 | Add clear function to run metrics -2016-08-15 | IPA-4799: Create Internal Coverity Build -2016-08-11 | Refactor unit tests to make more flexible for regression testing -2016-08-08 | IPA-4922: Move logic code from header to cpp -2016-08-05 | IPA-4827: Make run info parsing more robust -2016-08-03 | Refactor code and add test build script -2016-08-02 | Add big object support for unit tests -2016-08-02 | Clean buffers in the heatmap and flowcell -2016-08-02 | Update travis-ci to GCC-5 -2016-07-28 | Added float array backing to heat map -2016-07-25 | IPA-4752: Replace InterOp 1.x Code with InterOp 2.x Code - Imaging Tab -2016-07-22 | Fix camel case -2016-07-22 | IPA-4751: Integrated InterOp2.x with Analysis Tab -2016-07-22 | Github Issue 74: Compiler warning as error unsigned/signed comp -2016-07-21 | Bug fixes for flowcell chart and more recent versions of GCC -2016-07-17 | Added coverity online scan and fixed some issues found + Date | Description +------------|------------------------------------------------------------------------ + 2016-08-26 | Refactor CSharp code into additional library + 2016-08-26 | IPA-5028: Add RunInfo and InterOp validation + 2016-08-19 | Fix sorting in imaging table + 2016-08-18 | Cleanup code + 2016-08-17 | Fix the read ID + 2016-08-16 | IPA-5009: Add sorting to imaging table + 2016-08-16 | IPA-5007: Fix combo boxes on analysis tab + 2016-08-16 | Fix msvc warning and some script differences + 2016-08-15 | Add clear function to run metrics + 2016-08-15 | IPA-4799: Create Internal Coverity Build + 2016-08-11 | Refactor unit tests to make more flexible for regression testing + 2016-08-08 | IPA-4922: Move logic code from header to cpp + 2016-08-05 | IPA-4827: Make run info parsing more robust + 2016-08-03 | Refactor code and add test build script + 2016-08-02 | Add big object support for unit tests + 2016-08-02 | Clean buffers in the heatmap and flowcell + 2016-08-02 | Update travis-ci to GCC-5 + 2016-07-28 | Added float array backing to heat map + 2016-07-25 | IPA-4752: Replace InterOp 1.x Code with InterOp 2.x Code - Imaging Tab + 2016-07-22 | Fix camel case + 2016-07-22 | IPA-4751: Integrated InterOp2.x with Analysis Tab + 2016-07-22 | Github Issue 74: Compiler warning as error unsigned/signed comp + 2016-07-21 | Bug fixes for flowcell chart and more recent versions of GCC + 2016-07-17 | Added coverity online scan and fixed some issues found ## v1.0.8 -Commit | Description -------- | ----------- -b74024d | Added support for paths with spaces in the build system -d76117a | Remove support for 32-bit builds -27c1942 | IPA-4778: Fixed issues found by coverity -ad8cac0 | Updated the documentation + Commit | Description +---------|--------------------------------------------------------- + b74024d | Added support for paths with spaces in the build system + d76117a | Remove support for 32-bit builds + 27c1942 | IPA-4778: Fixed issues found by coverity + ad8cac0 | Updated the documentation ## v1.0.7 -Commit | Description -------- | ----------- -2d8480c | Fixed C# binding and filter_option validation -32daedd | Added package target to CMake build script -36ca197 | Add command line parser and update plotting apps -6cc52c2 | Continue refactoring SWIG C# binding and fix exceptions -5e01ff3 | Update tolerances to properly handle floating-point differences due to rounding -5e85cf0 | IPA-4608: Ensure cumulative q-metrics does not overflow -c60caa9 | IPA-4598: Regression test for imaging table -616e6e8 | IPA-4695: Setup framework to reuse unit test code for regression testing -839191c | Quick floor -> round bug fix for indexing plot y-max value -8fa8cfe | Test for larger CollapsedQ size -cbe3540 | IPA-4505: Fixed writing to buffer -76521e3 | IPA-4505: Fix summary tab, index tab and bs q-metrics -03867f0 | IPA-4598: Added imaging metrics and precision of numbers reported -8f5cf70 | IPA-4505: Fix empty PlotQC -fd5e265 | IPA-4505: Replace median, fixed missing percent aligned and fixed collapsed q-metrics -e2d1c80 | IPA-4505: Tile convention checking -e841107 | IPA-4598: Bind imaging logic to C# and test -37e6e21 | IPA-4505: Fix channel order in by cycle -23f1dca | IPA-4505: Fixed by cycle and q-bin index -987d02c | IPA-4595: Add index out of bounds checking to metrics -18e0ef7 | IPA-4505: Fix q-score median -d815021 | IPA-4595: Map plot metric types to input types -01f08c6 | IPA-4497: Fix camel case in metric_format -9cce9b9 | IPA-4486: Refactor code to use INTEROP_TUPLEX -37899c9 | IPA-4493: Replace q-metrics with collapsed q-metrics in logic -cb999ae | IPA-4485: Simplify mapping between constant types -333909f | IPA-4419: Add collapsed q-score logic -68d1b6a | IPA-4286: Add collapsed qscore metrics -2c82c4a | IPA-4292: Add imaging model and logic -c5aad38 | IPA-4292: Refactor to prepare code for imaging model and logic -d9e5a83 | IPA-4290: Add index summary logic -050a9ee | IPA-4447: Add index summary model -fc5d190 | IPA-4408: Plot sample QC for indexing tab -f05a2a3 | IPA-4406: Plot Logic - flowcell map -4eb6568 | IPA-4407: Plot Logic - plot q-score histogram -9706b24 | IPA-4404: Add plot logic - plot by lane -56bb897 | IPA-4384: Prototype PlotDataByCycle to build initial framework -9c8e8d8 | IPA-4384: Model for plot by cycle prototype (Part 1) -6c1fbc5 | IPA-4382: Refactor code to make naming more consistent -9a45340 | IPA-4383: Add filter options to support plot logic -b11e736 | IPA-4382: Create reflection-like interface for enums to support plot logic -d9deeea | IPA-4246: Add search for non Out interop files -3f2f2bf | Reorganize modules in doxygen -202d6ef | IPA-4146: Add summary logic and application -6c5a30d | IPA-4146: Added metric and channel logic and more statistics -735cda2 | IPA-4146: Refactor of the metric set - + Commit | Description +---------|--------------------------------------------------------------------------------------- + 2d8480c | Fixed C# binding and filter_option validation + 32daedd | Added package target to CMake build script + 36ca197 | Add command line parser and update plotting apps + 6cc52c2 | Continue refactoring SWIG C# binding and fix exceptions + 5e01ff3 | Update tolerances to properly handle floating-point differences due to rounding + 5e85cf0 | IPA-4608: Ensure cumulative q-metrics does not overflow + c60caa9 | IPA-4598: Regression test for imaging table + 616e6e8 | IPA-4695: Setup framework to reuse unit test code for regression testing + 839191c | Quick floor -> round bug fix for indexing plot y-max value + 8fa8cfe | Test for larger CollapsedQ size + cbe3540 | IPA-4505: Fixed writing to buffer + 76521e3 | IPA-4505: Fix summary tab, index tab and bs q-metrics + 03867f0 | IPA-4598: Added imaging metrics and precision of numbers reported + 8f5cf70 | IPA-4505: Fix empty PlotQC + fd5e265 | IPA-4505: Replace median, fixed missing percent aligned and fixed collapsed q-metrics + e2d1c80 | IPA-4505: Tile convention checking + e841107 | IPA-4598: Bind imaging logic to C# and test + 37e6e21 | IPA-4505: Fix channel order in by cycle + 23f1dca | IPA-4505: Fixed by cycle and q-bin index + 987d02c | IPA-4595: Add index out of bounds checking to metrics + 18e0ef7 | IPA-4505: Fix q-score median + d815021 | IPA-4595: Map plot metric types to input types + 01f08c6 | IPA-4497: Fix camel case in metric_format + 9cce9b9 | IPA-4486: Refactor code to use INTEROP_TUPLEX + 37899c9 | IPA-4493: Replace q-metrics with collapsed q-metrics in logic + cb999ae | IPA-4485: Simplify mapping between constant types + 333909f | IPA-4419: Add collapsed q-score logic + 68d1b6a | IPA-4286: Add collapsed qscore metrics + 2c82c4a | IPA-4292: Add imaging model and logic + c5aad38 | IPA-4292: Refactor to prepare code for imaging model and logic + d9e5a83 | IPA-4290: Add index summary logic + 050a9ee | IPA-4447: Add index summary model + fc5d190 | IPA-4408: Plot sample QC for indexing tab + f05a2a3 | IPA-4406: Plot Logic - flowcell map + 4eb6568 | IPA-4407: Plot Logic - plot q-score histogram + 9706b24 | IPA-4404: Add plot logic - plot by lane + 56bb897 | IPA-4384: Prototype PlotDataByCycle to build initial framework + 9c8e8d8 | IPA-4384: Model for plot by cycle prototype (Part 1) + 6c1fbc5 | IPA-4382: Refactor code to make naming more consistent + 9a45340 | IPA-4383: Add filter options to support plot logic + b11e736 | IPA-4382: Create reflection-like interface for enums to support plot logic + d9deeea | IPA-4246: Add search for non Out interop files + 3f2f2bf | Reorganize modules in doxygen + 202d6ef | IPA-4146: Add summary logic and application + 6c5a30d | IPA-4146: Added metric and channel logic and more statistics + 735cda2 | IPA-4146: Refactor of the metric set + ## v1.0.6 -Commit | Description -------- | ----------- -57be79c | Update all cycle states and bug fix for legacy q-metrics -0b4304a | Refactor to remove and mark deprecated code -647cc9e | Add utility for creating unit tests -9d82333 | Add search for non Out interop files + Commit | Description +---------|---------------------------------------------------------- + 57be79c | Update all cycle states and bug fix for legacy q-metrics + 0b4304a | Refactor to remove and mark deprecated code + 647cc9e | Add utility for creating unit tests + 9d82333 | Add search for non Out interop files ## v1.0.5 -Commit | Description -------- | ----------- -7380f29 | Bug fixes for q-metrics and compilation error on Mac OSX + Commit | Description +---------|---------------------------------------------------------- + 7380f29 | Bug fixes for q-metrics and compilation error on Mac OSX ## v1.0.4 -Commit | Description -------- | ----------- -50e8e2a | Update documentation -50e8e2a | Update documentation -0b22102 | Added summary tests -13f1fb4 | Added summary logic -339a914 | Added summary model -aca0152 | Added run metrics -6516098 | Added metric and channel logic as well as more statistics functions -221028a | Added parsers for RunInfo.xml and RunParameters.xml -5a7ca8f | Remove legacy error metric fields + Commit | Description +---------|--------------------------------------------------------------------- + 50e8e2a | Update documentation + 50e8e2a | Update documentation + 0b22102 | Added summary tests + 13f1fb4 | Added summary logic + 339a914 | Added summary model + aca0152 | Added run metrics + 6516098 | Added metric and channel logic as well as more statistics functions + 221028a | Added parsers for RunInfo.xml and RunParameters.xml + 5a7ca8f | Remove legacy error metric fields ## v1.0.3 -Commit | Description -------- | ----------- -5bf14ca | Fix for reading multiple reads with tile metrics -2cef41a | Fixing tile metric phasing/prephasing scale to match SAV -a11a3e1 | Fixed tile_number_for_lane -29905ea | Fixed clear for all metric sets -9af35c4 | Added simple statistical functions: mean and variance -2f04b3f | Added C# performance test -d8b79b0 | Added example program for simulating InterOps at a specific cycle + Commit | Description +---------|------------------------------------------------------------------- + 5bf14ca | Fix for reading multiple reads with tile metrics + 2cef41a | Fixing tile metric phasing/prephasing scale to match SAV + a11a3e1 | Fixed tile_number_for_lane + 29905ea | Fixed clear for all metric sets + 9af35c4 | Added simple statistical functions: mean and variance + 2f04b3f | Added C# performance test + d8b79b0 | Added example program for simulating InterOps at a specific cycle ## v1.0.2 -Commit | Description -------- | ----------- -27a7eab | Fixed unclear error message when InterOp is empty -7f93166 | Improvements to the documentation website theme -ade1187 | Ensure CMake configure script throws error of system does not support 32-bit float -096c817 | Made CMake configure script more robust to missing dependencies -498efc3 | Ensure proper cast to record_size_t -286c66c | Added header size calculation -06f567d | Added record size calculation -d35f6bf | Added new filename function without assuming directory -fc94e9f | Added links to Issues on webpage -08f579c | Updated documentation and build script building and deployment + Commit | Description +---------|------------------------------------------------------------------------------------ + 27a7eab | Fixed unclear error message when InterOp is empty + 7f93166 | Improvements to the documentation website theme + ade1187 | Ensure CMake configure script throws error of system does not support 32-bit float + 096c817 | Made CMake configure script more robust to missing dependencies + 498efc3 | Ensure proper cast to record_size_t + 286c66c | Added header size calculation + 06f567d | Added record size calculation + d35f6bf | Added new filename function without assuming directory + fc94e9f | Added links to Issues on webpage + 08f579c | Updated documentation and build script building and deployment ## v1.0.1 -Commit | Description -------- | ----------- -450b7e6 | Bundle RapidXML and update deployment scripts -b9cc4b0 | Add change log -f74a702 | Deploy binaries for Windows/Linux/OSX and major compilers - - | Ensure only Mono .Net 4.x compiler is used - - | Ensure only SWIG 3.x or later is used -3958559 | Setup Appveyor build script -f063b81 | Setup TravisCI build script -586f9d1 | Build C# examples by default -553856c | Updated documentation -03522ff | Fixed build issues -78881f4 | Disable C# examples when swig is disabled -b70f775 | Clean up documentation -216ea62 | Ensure C# compiler matches C++ 32/64-bit -6871246 | Switch to bootstrap theme for documentation + Commit | Description +---------|----------------------------------------------------------- + 450b7e6 | Bundle RapidXML and update deployment scripts + b9cc4b0 | Add change log + f74a702 | Deploy binaries for Windows/Linux/OSX and major compilers + - | Ensure only Mono .Net 4.x compiler is used + - | Ensure only SWIG 3.x or later is used + 3958559 | Setup Appveyor build script + f063b81 | Setup TravisCI build script + 586f9d1 | Build C# examples by default + 553856c | Updated documentation + 03522ff | Fixed build issues + 78881f4 | Disable C# examples when swig is disabled + b70f775 | Clean up documentation + 216ea62 | Ensure C# compiler matches C++ 32/64-bit + 6871246 | Switch to bootstrap theme for documentation diff --git a/src/ext/python/core.py b/src/ext/python/core.py index d23691bf5..7303e2efa 100644 --- a/src/ext/python/core.py +++ b/src/ext/python/core.py @@ -181,7 +181,7 @@ def summarize(summary_object, column_list, extra_row=None): if len(data) == 0: return np.asarray([]) _str_types = ('Index1', 'Index2', 'Sample Id', 'Project Name') - return np.asarray(data, dtype=extra_cols+[(col, dtype if col not in _str_types else np.object) for col in header]) + return np.asarray(data, dtype=extra_cols+[(col, dtype if col not in _str_types else np.dtype(object)) for col in header]) def index_summary_columns(level='Lane', ret_dict=False): diff --git a/src/ext/swig/exceptions/exceptions_impl.i b/src/ext/swig/exceptions/exceptions_impl.i index ef6ca7b8e..3c418778d 100644 --- a/src/ext/swig/exceptions/exceptions_impl.i +++ b/src/ext/swig/exceptions/exceptions_impl.i @@ -1,10 +1,6 @@ %include "std_except.i" %include "exception.i" -namespace std{ - %std_exception_map(bad_alloc, SWIG_MemoryError); -} - #if defined(SWIGCSHARP) namespace std { @@ -31,6 +27,10 @@ namespace std { virtual const char* what() const throw(); }; } +#else +namespace std{ + %std_exception_map(bad_alloc, SWIG_MemoryError); +} #endif %{ #include "interop/io/stream_exceptions.h" diff --git a/src/tests/interop/metrics/inc/error_metrics_test.h b/src/tests/interop/metrics/inc/error_metrics_test.h index cdadfef32..ffaae0961 100644 --- a/src/tests/interop/metrics/inc/error_metrics_test.h +++ b/src/tests/interop/metrics/inc/error_metrics_test.h @@ -194,7 +194,6 @@ namespace illumina { namespace interop { namespace unittest const float kAverageError100 = 26.0f; const float kAverageErrorAfter = 36.0f; - float sum = 0.0f; const size_t cycle_count = run_info.total_cycles(); for (size_t cycle = 1; cycle <= cycle_count; ++cycle) { @@ -209,12 +208,10 @@ namespace illumina { namespace interop { namespace unittest else if( cycle_within_read <= 35 ) { metrics.insert(metric_t(7, 1114, cycle_id, kAverageError35, kMissingValue)); - sum += kAverageError35; } else if( cycle_within_read <= 50 ) { metrics.insert(metric_t(7, 1114, cycle_id, kAverageError50, kMissingValue)); - sum += kAverageError35; } else if( cycle_within_read <= 75 ) {