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Anton Goloborodko committed 0d87e83 Merge

merge back

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Files changed (2)

src/hiclib/fragmentHiC.py

             filename, resolution)
 
     def saveByChromosomeHeatmap(self, filename, resolution=10000,
-                                includeTrans=False,
+                                includeTrans=True,
                                 countDiagonalReads="Once"):
         """
         Saves chromosome by chromosome heatmaps to h5dict.
                 p2 = p2[args]
 
             for chrom2 in xrange(chrom, self.genome.chrmCount):
+                if (includeTrans == False) and (chrom2 != chrom):
+                    continue
                 start = np.searchsorted(c2, chrom2, "left")
                 end = np.searchsorted(c2, chrom2, "right")
                 cur1 = p1[start:end]

src/hiclib/highResBinnedData.py

 and for HDD storage it supports both sparse and dense matrix logic.
 In fact, sparse logic with HDF5-based storage in memory is already good (default settings).
 
+.. note::
+    This class loads data, saved by saveByChromosomeHeatmap method of fragmentHiC.
+    It is not designed to load heatmaps saved by "saveHeatmap" class, because those
+    can fit in memory, and should be analyzed by a more powerful binnedData class.
+
+
+
+
+
 Class structure
 ---------------
 
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