Bug fix for NovaSeqX 25B flow cells and QByLane (#365)

* Bug fix for NovaSeqX 25B flow cells and certain plotting logic using QByLane

* Ensure proper uint64 support

* Try to fix windows warnings

* Fix another warning

* Try more fixes

* Add more fixes

* Fix swig

* Fix bug in test

* Fix bug in test

Author: ezralanglois

docs/src/changes.md

@@ -1,5 +1,12 @@
 # Changes {#changes}
 
+## v1.7.0
+
+| Date       | Description                                                                  |
+|------------|------------------------------------------------------------------------------|
+| 2025-11-19 | Add support for QMetrics v8 and v9 as well as QByLane v8 and v9              |
+| 2025-11-19 | Bug fix for NovaSeqX 25B flow cells and certain plotting logic using QByLane |
+
 ## v1.6.0
 
 | Date       | Description                                                            |

interop/model/metrics/q_by_lane_metric.h

@@ -26,7 +26,7 @@ namespace illumina { namespace interop { namespace model { namespace metrics
             /** Unique type code for metric */
             TYPE = constants::QByLane,
             /** Latest version of the InterOp format */
-            LATEST_VERSION = 6
+            LATEST_VERSION = 9
         };
         /** Define the base type */
         typedef constants::base_lane_t base_t;

interop/model/metrics/q_collapsed_metric.h

@@ -105,10 +105,10 @@ namespace illumina { namespace interop { namespace model { namespace metrics {
         q_collapsed_metric(const uint_t lane,
                            const uint_t tile,
                            const uint_t cycle,
-                           const uint_t q20,
-                           const uint_t q30,
-                           const uint_t total,
-                           const uint_t median_qscore) :
+                           const uint64_t q20,
+                           const uint64_t q30,
+                           const uint64_t total,
+                           const uint64_t median_qscore) :
                 metric_base::base_cycle_metric(lane, tile, cycle),
                 m_q20(q20),
                 m_q30(q30),
@@ -135,31 +135,31 @@ namespace illumina { namespace interop { namespace model { namespace metrics {
          *
          * @return number of q20 clusters
          */
-        uint_t q20()const
+        uint64_t q20()const
         {
             return m_q20;
         }
         /** Number of Q30 clusters
          *
          * @return number of q30 clusters
          */
-        uint_t q30()const
+        uint64_t q30()const
         {
             return m_q30;
         }
         /** Total number of q-scored clusters
          *
          * @return total number of q-scored clusters
          */
-        uint_t total()const
+        uint64_t total()const
         {
             return m_total;
         }
         /** Median q-score for tile
          *
          * @return median q-score
          */
-        uint_t median_qscore()const
+        uint64_t median_qscore()const
         {
             return m_median_qscore;
         }
@@ -261,10 +261,10 @@ namespace illumina { namespace interop { namespace model { namespace metrics {
         static const char* suffix(){return "2030";}
 
     private:
-        uint_t m_q20;
-        uint_t m_q30;
-        uint_t m_total;
-        uint_t m_median_qscore;
+        uint64_t m_q20;
+        uint64_t m_q30;
+        uint64_t m_total;
+        uint64_t m_median_qscore;
         ulong_t m_cumulative_q20;
         ulong_t m_cumulative_q30;
         ulong_t m_cumulative_total;

interop/model/metrics/q_metric.h

@@ -266,16 +266,16 @@ namespace illumina { namespace interop { namespace model { namespace metrics
         typedef header_type::qscore_bin_vector_type qscore_bin_vector_type;
         /** Defines a vector of unsigned 32-bit ints
          */
-        typedef std::vector< ::uint32_t > uint32_vector;
+        typedef std::vector< ::uint64_t > uint32_vector;
         /** Defines a vector of unsigned 32-bit ints (TODO: remove this def)
          */
-        typedef std::vector< ::uint32_t > uint_vector;
+        typedef std::vector< ::uint64_t > uint_vector;
         /** Defines a vector of unsigned 64-bit ints
         */
         typedef std::vector< ::uint64_t > uint64_vector;
         /** Define a uint pointer to a uint array
          */
-        typedef ::uint32_t *uint_pointer_t;
+        typedef ::uint64_t *uint_pointer_t;
     public:
         /** Constructor
          */
@@ -358,7 +358,7 @@ namespace illumina { namespace interop { namespace model { namespace metrics
          *
          * @return q-score value of the histogram
          */
-        uint_t qscore_hist(const size_t n) const INTEROP_THROW_SPEC((model::index_out_of_bounds_exception))
+        uint64_t qscore_hist(const size_t n) const INTEROP_THROW_SPEC((model::index_out_of_bounds_exception))
         {
             INTEROP_BOUNDS_CHECK(n, m_qscore_hist.size(), "Index out of bounds");
             return m_qscore_hist[n];
@@ -386,9 +386,9 @@ namespace illumina { namespace interop { namespace model { namespace metrics
          *
          * @return q-score histogram sum
          */
-        uint_t sum_qscore() const
+        uint64_t sum_qscore() const
         {
-            return std::accumulate(m_qscore_hist.begin(), m_qscore_hist.end(), 0);
+            return std::accumulate(m_qscore_hist.begin(), m_qscore_hist.end(), uint64_t(0));
         }
 
         /** Sum the cumulative q-score histogram
@@ -416,10 +416,10 @@ namespace illumina { namespace interop { namespace model { namespace metrics
          * @param bins q-score histogram bins
          * @return total of clusters over the given q-score
          */
-        uint_t total_over_qscore(const uint_t qscore,
+        uint64_t total_over_qscore(const uint_t qscore,
                                  const qscore_bin_vector_type &bins) const
         {
-            uint_t total_count = 0;
+            uint64_t total_count = 0;
             for (size_t i = 0; i < bins.size(); i++)
             {
                 if (bins[i].value() >= qscore)
@@ -439,11 +439,11 @@ namespace illumina { namespace interop { namespace model { namespace metrics
          * @param qscore_index index of the q-score (for unbinned 29 is Q30)
          * @return total of clusters over the given q-score
          */
-        uint_t total_over_qscore(const size_t qscore_index) const
+        uint64_t total_over_qscore(const size_t qscore_index) const
         {
-            uint_t total_count = 0;
+            uint64_t total_count = 0;
             if(qscore_index <= m_qscore_hist.size())
-                total_count = std::accumulate(m_qscore_hist.begin() + qscore_index, m_qscore_hist.end(), 0);
+                total_count = std::accumulate(m_qscore_hist.begin() + qscore_index, m_qscore_hist.end(), uint64_t(0));
             return total_count;
         }
 
@@ -482,7 +482,7 @@ namespace illumina { namespace interop { namespace model { namespace metrics
         {
             const float total = static_cast<float>(sum_qscore());
             if (total == 0.0f) return std::numeric_limits<float>::quiet_NaN();
-            const uint_t total_count = total_over_qscore(qscore_index);
+            const uint64_t total_count = total_over_qscore(qscore_index);
             return 100 * total_count / total;
         }
 
@@ -548,7 +548,7 @@ namespace illumina { namespace interop { namespace model { namespace metrics
         {
             const float total = static_cast<float>(sum_qscore());
             if (total == 0.0f) return std::numeric_limits<float>::quiet_NaN();
-            const uint_t total_count = total_over_qscore(qscore_index, bins);
+            const uint64_t total_count = total_over_qscore(qscore_index, bins);
             return 100.0f * total_count / total;
         }
 
@@ -584,12 +584,12 @@ namespace illumina { namespace interop { namespace model { namespace metrics
          * @param bins header bins
          * @return median q-score
          */
-        uint_t median(const qscore_bin_vector_type &bins = qscore_bin_vector_type()) const
+        uint64_t median(const qscore_bin_vector_type &bins = qscore_bin_vector_type()) const
         {
-            const uint_t total = sum_qscore();
-            const uint_t position = total % 2 == 0 ? total / 2 + 1 : (total + 1) / 2;
+            const uint64_t total = sum_qscore();
+            const uint64_t position = total % 2 == 0 ? total / 2 + 1 : (total + 1) / 2;
             uint_t i = 0;
-            uint_t sum = 0;
+            uint64_t sum = 0;
             for (; i < m_qscore_hist.size(); i++)
             {
                 sum += m_qscore_hist[i];
@@ -600,7 +600,7 @@ namespace illumina { namespace interop { namespace model { namespace metrics
                     break;
                 }
             }
-            return std::numeric_limits<uint_t>::max();
+            return std::numeric_limits<uint64_t>::max();
         }
 
         /** Check if the cumulative histogram has not been populated
@@ -665,7 +665,7 @@ namespace illumina { namespace interop { namespace model { namespace metrics
          * @deprecated Will be removed in 1.1.x (use qscore_hist instead)
          * @return q-score value of the histogram
          */
-        uint_t qscoreHist(const size_t n) const
+        uint64_t qscoreHist(const size_t n) const
         {
             INTEROP_ASSERT(n < m_qscore_hist.size());
             return m_qscore_hist[n];

src/ext/python/core.py

@@ -775,12 +775,6 @@ def read(run, valid_to_load=None, requires=None, search_paths=None, **extra):
     ...
     interop.py_interop_run.xml_file_not_found_exception: cannot open file some/non/existing/run_folder_name/RunInfo.xml
 
-    Read from a None object
-    >>> metrics = read(None)
-    Traceback (most recent call last):
-    ...
-    ValueError: invalid null reference in method 'run_metrics_read', argument 2 of type 'std::string const &'
-
     :param run: string path including name of run folder (or run_metrics object)
     :param valid_to_load: list of strings containing InterOp metric names (Default: None, load everything)
     :param requires: list of required metric (Default: None, check nothing)

src/ext/swig/table.i

@@ -16,6 +16,12 @@
 %import "src/ext/swig/metrics.i"
 %import "src/ext/swig/run_metrics.i"
 
+%ignore operator<<;
+%ignore operator>>;
+%ignore *::operator<<;
+%ignore *::operator>>;
+%ignore illumina::interop::model::table::operator<<;
+%ignore illumina::interop::model::table::operator>>;
 
 // Ensure all the modules import the shared namespace
 %pragma(csharp) moduleimports=%{

src/interop/logic/metric/q_metric.cpp

@@ -198,10 +198,10 @@ namespace illumina { namespace interop { namespace logic { namespace metric
         collapsed.set_version(model::metrics::q_collapsed_metric::LATEST_VERSION);
         for(const_iterator beg = metric_set.begin(), end = metric_set.end();beg != end;++beg)
         {
-            const uint_t q20 = beg->total_over_qscore(q20_idx);
-            const uint_t q30 = beg->total_over_qscore(q30_idx);
-            const uint_t total = beg->sum_qscore();
-            const uint_t median = beg->median(metric_set.get_bins());
+            const uint64_t q20 = beg->total_over_qscore(q20_idx);
+            const uint64_t q30 = beg->total_over_qscore(q30_idx);
+            const uint64_t total = beg->sum_qscore();
+            const uint64_t median = beg->median(metric_set.get_bins());
             collapsed.insert(model::metrics::q_collapsed_metric(beg->lane(),
                                                                 beg->tile(),
                                                                 beg->cycle(),