Anton Goloborodko committed 0d87e83 Merge

merge back

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Files changed (2)


             filename, resolution)
     def saveByChromosomeHeatmap(self, filename, resolution=10000,
-                                includeTrans=False,
+                                includeTrans=True,
         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]


 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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