032653c06fe43263c625613a538389fc2425976b
jcasper
  Tue Jul 16 17:16:51 2024 -0700
Updated hic straw library adapted for UCSC, with a udc-enabled curl substitute.  refs #33225

diff --git src/hg/lib/straw/new_straw.h src/hg/lib/straw/new_straw.h
index 45c65c6..53bb6a5 100644
--- src/hg/lib/straw/new_straw.h
+++ src/hg/lib/straw/new_straw.h
@@ -1,112 +1,127 @@
 /*
   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>
 #include <map>
 
 // pointer structure for reading blocks or matrices, holds the size and position
 struct indexEntry {
     int64_t size;
     int64_t position;
 };
 
 // sparse matrixType entry
 struct contactRecord {
   int32_t binX;
   int32_t binY;
   float counts;
 };
 
 // chromosome
 struct chromosome {
     std::string name;
     int32_t index;
     int64_t length;
 };
 
 // this is for creating a stream from a byte array for ease of use
 // see https://stackoverflow.com/questions/41141175/how-to-implement-seekg-seekpos-on-an-in-memory-buffer
 struct membuf : std::streambuf {
     membuf(char *begin, int32_t l) {
         setg(begin, begin, begin + l);
     }
 };
 
 struct memstream : virtual membuf, std::istream {
     memstream(char *begin, int32_t l) :
             membuf(begin, l),
             std::istream(static_cast<std::streambuf*>(this)) {
     }
 
     std::istream::pos_type seekpos(std::istream::pos_type sp, std::ios_base::openmode which) override {
         return seekoff(sp - std::istream::pos_type(std::istream::off_type(0)), std::ios_base::beg, which);
     }
 
     std::istream::pos_type seekoff(std::istream::off_type off,
                                     std::ios_base::seekdir dir,
                                     std::ios_base::openmode which = std::ios_base::in) override {
         if (dir == std::ios_base::cur)
             gbump(off);
         else if (dir == std::ios_base::end)
             setg(eback(), egptr() + off, egptr());
         else if (dir == std::ios_base::beg)
             setg(eback(), eback() + off, egptr());
         return gptr() - eback();
     }
 };
 
 // for holding data from URL call
 struct MemoryStruct {
     char *memory;
     size_t size;
 };
 
 std::map<int32_t, indexEntry>
 readMatrixZoomData(std::istream &fin, const std::string &myunit, int32_t mybinsize, float &mySumCounts,
                    int32_t &myBlockBinCount,
                    int32_t &myBlockColumnCount, bool &found);
 
 std::map<int32_t, indexEntry>
 readMatrix(std::istream &fin, int32_t myFilePosition, std::string unit, int32_t resolution, float &mySumCounts,
            int32_t &myBlockBinCount, int32_t &myBlockColumnCount);
 
 std::vector<double> readNormalizationVector(std::istream &fin, indexEntry entry);
 
 std::vector<contactRecord>
 straw(const std::string& matrixType, const std::string& norm, const std::string& fname, const std::string& chr1loc,
       const std::string& chr2loc, const std::string &unit, int32_t binsize);
 
 std::vector<std::vector<float>>
 strawAsMatrix(const std::string &matrixType, const std::string &norm, const std::string &fileName,
               const std::string &chr1loc, const std::string &chr2loc, const std::string &unit, int32_t binsize);
 
 int64_t getNumRecordsForFile(const std::string& filename, int32_t binsize, bool interOnly);
 
 int64_t getNumRecordsForChromosomes(const std::string& filename, int32_t binsize, bool interOnly);
 
+/* Added at UCSC */
+void getHeaderFields(const std::string &filename, std::string &genome, std::vector<std::string> &chromNames,
+        std::vector<int> &chromSizes, std::vector<int> &bpResolutions, std::vector<int> &fragResolutions,
+        std::vector<std::string> &attributes);
+/* Fill in the provided fields with information from the header of the hic file in the supplied filename.
+ * fragResolutions is left empty for now, as we're not making use of it. */
+
+class strawException : public std::runtime_error {
+/* Simple exception wrapper class */
+    public:
+    strawException(const std::string& error):
+        std::runtime_error(error) {
+    }
+};
+
 #endif