bbi.fetch with summary="sum" (#12)

* Sum aggregation mode * Missed a line * Test * Use higher zoom level in test * Actually do sum in test * Improve test * Whitespace
nvictus · Jun 12, 2020 · 0c3ebbf · 0c3ebbf
1 parent 6064b91
commit 0c3ebbf
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Showing 6 changed files with 18 additions and 1 deletion.
diff --git a/bbi/__init__.py b/bbi/__init__.py
@@ -15,4 +15,4 @@
 __all__ = ['is_bbi', 'is_bigwig', 'is_bigbed', 'info', 'zooms', 'chromsizes',
            'fetch', 'stackup', 'fetch_intervals']
 
-__version__ = '0.2.2'
+__version__ = '0.2.3'
diff --git a/bbi/cbbi.pxd b/bbi/cbbi.pxd
@@ -122,6 +122,7 @@ cdef extern from "bbiFile.h":
         bbiSumMin = 2
         bbiSumCoverage = 3
         bbiSumStandardDeviation = 4
+        bbiSumSum = 5
 
     cdef struct bbiSummary:
         bbiSummary *next

diff --git a/bbi/cbbi.pyx b/bbi/cbbi.pyx
@@ -78,6 +78,7 @@ cpdef dict BBI_SUMMARY_TYPES = {
     'min': bbiSumMin,
     'cov': bbiSumCoverage,
     'std': bbiSumStandardDeviation,
+    'sum': bbiSumSum,
 }
 
 
@@ -254,6 +255,7 @@ def info(str inFile):
             'std': sqrt(var_from_sums(summ.sumData,
                                       summ.sumSquares,
                                       summ.validCount)),
+            'sum': summ.sumData,
         }
     }
     bbiFileClose(&bbi)
@@ -731,6 +733,8 @@ cdef inline void array_query_summarized(
                         val = sqrt(var_from_sums(el.sumData,
                                                  el.sumSquares,
                                                  el.validCount))
+                    elif summaryType == bbiSumSum:
+                        val = el.sumData
                     else:
                         raise RuntimeError
                     out[i] = val

diff --git a/include/bbiFile.h b/include/bbiFile.h
@@ -200,6 +200,7 @@ enum bbiSummaryType
     bbiSumMin = 2,	/* Minimum value */
     bbiSumCoverage = 3,  /* Bases in region containing actual data. */
     bbiSumStandardDeviation = 4, /* Standard deviation in window. */
+    bbiSumSum = 5, /* Sum value */
     };
 
 enum bbiSummaryType bbiSummaryTypeFromString(char *string);

diff --git a/src/bbiRead.c b/src/bbiRead.c
@@ -280,6 +280,8 @@ else if (sameWord(string, "coverage") || sameWord(string, "dataCoverage"))
     return bbiSumCoverage;
 else if (sameWord(string, "std"))
     return bbiSumStandardDeviation;
+else if (sameWord(string, "sum"))
+    return bbiSumSum;
 else
     {
     errAbort("Unknown bbiSummaryType %s", string);
@@ -302,6 +304,8 @@ switch (type)
         return "coverage";
     case bbiSumStandardDeviation:
         return "std";
+    case bbiSumSum:
+        return "sum";
     default:
 	errAbort("Unknown bbiSummaryType %d", (int)type);
 	return NULL;
@@ -691,6 +695,9 @@ if (ret)
 		case bbiSumStandardDeviation:
 		    val = calcStdFromSums(el->sumData, el->sumSquares, el->validCount);
 		    break;
+		case bbiSumSum:
+		    val = el->sumData;
+		    break;
 		default:
 		    internalErr();
 		    val = 0.0;

diff --git a/tests/test_bbi.py b/tests/test_bbi.py
@@ -120,6 +120,10 @@ def test_fetch_summary_stats(path):
         path, 'chr21', 20000000, 20001000, bins=10, summary='max'
     ).max()
     assert np.isclose(vmax, np.max(values))
+    vsum = bbi.fetch(path, 'chr21', 20000000, 20001000, bins=100, summary='sum')
+    values_sum_every_ten = np.reshape(values, (-1, 10)).sum(axis=-1)
+    assert len(vsum) == len(values_sum_every_ten)
+    assert np.allclose(vsum, values_sum_every_ten)
 
     with pytest.raises(ValueError):
         bbi.fetch(path, 'chr21', 20000000, 20001000, bins=10, summary='foo')