Add exact summaries and zoom table fetcher

nvictus · Feb 17, 2024 · 67a8931 · 67a8931
1 parent e5e4a90
commit 67a8931
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Showing 3 changed files with 230 additions and 73 deletions.
diff --git a/bbi/_bbi.py b/bbi/_bbi.py
@@ -25,7 +25,7 @@ def chromsizes(inFile):
 
     Returns
     -------
-    OrderedDict (str -> int)
+    dict[str, int]
 
     """
     with cbbi.open(inFile) as f:
@@ -44,7 +44,7 @@ def zooms(inFile):
 
     Returns
     -------
-    list of int
+    list[int]
 
     """
     with cbbi.open(inFile) as f:
@@ -70,26 +70,38 @@ def info(inFile):
 
 
 @documented_by(cbbi.BBIFile.fetch)
-def fetch(inFile, chrom, start, end, bins=-1, missing=0.0, oob=np.nan, summary="mean"):
+def fetch(
+    inFile,
+    chrom,
+    start,
+    end,
+    bins=-1,
+    missing=0.0,
+    oob=np.nan,
+    summary="mean",
+    exact=False,
+):
     with cbbi.open(inFile) as f:
-        return f.fetch(chrom, start, end, bins, missing, oob, summary)
+        return f.fetch(chrom, start, end, bins, missing, oob, summary, exact)
 
 
 @documented_by(cbbi.BBIFile.stackup)
 def stackup(
-    inFile, chroms, starts, ends, bins=-1, missing=0.0, oob=np.nan, summary="mean"
+    inFile,
+    chroms,
+    starts,
+    ends,
+    bins=-1,
+    missing=0.0,
+    oob=np.nan,
+    summary="mean",
+    exact=False,
 ):
     with cbbi.open(inFile) as f:
-        return f.stackup(chroms, starts, ends, bins, missing, oob, summary)
+        return f.stackup(chroms, starts, ends, bins, missing, oob, summary, exact)
 
 
 @documented_by(cbbi.BBIFile.fetch_intervals)
-def fetch_intervals(
-    inFile,
-    chrom,
-    start,
-    end,
-    iterator=True
-):
+def fetch_intervals(inFile, chrom, start, end, iterator=True):
     with cbbi.open(inFile) as f:
         return f.fetch_intervals(chrom, start, end, iterator)
diff --git a/bbi/cbbi.pxd b/bbi/cbbi.pxd
@@ -256,7 +256,7 @@ cdef extern from "bigWig.h":
         int start,
         int end,
         bbiSummaryType summaryType,
-        double defaultVal);
+        double defaultVal)
     boolean bigWigSummaryArray(
         bbiFile *bwf,
         char *chrom,
@@ -312,15 +312,15 @@ cdef extern from "bigBed.h":
         bits32 start,
         bits32 end,
         int summarySize,
-        bbiSummaryElement *summary);
+        bbiSummaryElement *summary)
     char *bbiCachedChromLookup(
         bbiFile *bbi,
         int chromId,
         int lastChromId,
         char *chromBuf,
         int chromBufSize)
     char *bigBedAutoSqlText(bbiFile *bbi)
-    asObject *bigBedAs(bbiFile *bbi);
+    asObject *bigBedAs(bbiFile *bbi)
     asObject *bigBedAsOrDefault(bbiFile *bbi)
     asObject *bigBedFileAsObjOrDefault(char *fileName)