f863c012ea39c498eaf4cff84f85f92fef210c5f
jcasper
  Mon May 13 00:51:57 2019 -0700
Initial commit of Hi-C display support via .hic files, refs #18842

diff --git src/hg/lib/straw/straw.h src/hg/lib/straw/straw.h
new file mode 100644
index 0000000..fbc202b
--- /dev/null
+++ src/hg/lib/straw/straw.h
@@ -0,0 +1,62 @@
+/*
+  The straw library (straw.cpp, straw.h) is used with permission of the Aiden
+  Lab at the Broad Institute.  It is included below, along with modifications
+  to work in the environment of the UCSC Genome Browser, under the following
+  license:
+
+  The MIT License (MIT)
+ 
+  Copyright (c) 2011-2016 Broad Institute, Aiden Lab
+ 
+ Permission is hereby granted, free of charge, to any person obtaining a copy
+ of this software and associated documentation files (the "Software"), to deal
+ in the Software without restriction, including without limitation the rights
+ to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+ copies of the Software, and to permit persons to whom the Software is
+ furnished to do so, subject to the following conditions:
+ 
+ The above copyright notice and this permission notice shall be included in
+ all copies or substantial portions of the Software.
+ 
+ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+ IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+ FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+ AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+ LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+ OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+ THE SOFTWARE.
+*/
+#ifndef STRAW_H
+#define STRAW_H
+
+#include <fstream>
+#include <set>
+#include <vector>
+
+// pointer structure for reading blocks or matrices, holds the size and position 
+struct indexEntry {
+  int size;
+  long position;
+};
+
+// sparse matrix entry
+struct contactRecord {
+  int binX;
+  int binY;
+  float counts;
+};
+
+bool readMagicString(std::ifstream& fin);
+long readHeader(std::istream& fin, std::string chr1, std::string chr2, int &c1pos1, int &c1pos2, int &c2pos1, int &c2pos2, int &chr1ind, int &chr2ind);
+void readFooter(std::istream& fin, long master, int c1, int c2, std::string norm, std::string unit, int resolution, long &myFilePos, indexEntry &c1NormEntry, indexEntry &c2NormEntry);
+bool readMatrixZoomData(std::istream& fin, std::string myunit, int mybinsize, int &myBlockBinCount, int &myBlockColumnCount);
+void readMatrix(std::istream& fin, int myFilePosition, std::string unit, int resolution, int &myBlockBinCount, int &myBlockColumnCount);
+std::set<int> getBlockNumbersForRegionFromBinPosition(int* regionIndices, int blockBinCount, int blockColumnCount, bool intra);
+std::vector<contactRecord> readBlock(std::istream& fin, int blockNumber);
+std::vector<double> readNormalizationVector(std::istream& fin, indexEntry entry);
+void straw(std::string norm, std::string fname, int binsize, std::string chr1loc, std::string chr2loc, std::string unit, std::vector<int>& xActual, std::vector<int>& yActual, std::vector<float>& counts);
+
+extern "C" char* Cstraw (char *norm, char *fname, int binsize, char *chr1loc, char *chr2loc, char *unit, int **xActual, int **yActual, double **counts, int *numRecords);
+
+extern "C" char *CstrawHeader (char *filename, char **genome, char ***chromNames, int *nChroms, char ***bpResolutions, int *nBpRes, char ***fragResolutions, int *nFragRes);
+#endif