Changes

v1.1.23

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

v1.1.21

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

v1.1.19

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

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

v1.1.16

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

v1.1.14

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

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

v1.1.11

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

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)

v1.1.8

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

v1.1.6

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

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

v1.1.3

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

v1.1.1

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

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

v1.0.24

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

v1.0.22

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

v1.0.20

Date Description
2017-04-07 More portable Python build

v1.0.19

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

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

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

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

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

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

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

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

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

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

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

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

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

v1.0.5

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

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

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

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