STREL-976 Preserve softlinks in input ref paths

This change makes reference fasta file path cleaning consistent across all
applications and between reference and alignment files. In all cases, it
makes the lookup of samtools sidecar-style index files more reliable.

.travis.yml

@@ -1,7 +1,7 @@
 
 #
 # Using sudo-false/container-based tests for greater (linux) test responsiveness. This doesn't seem
-# to effect the queing time for OSX tests.
+# to effect the queueing time for OSX tests.
 #
 
 dist: trusty

CHANGELOG.md

@@ -1,3 +1,10 @@
+## v2.9.7 - 2018-08-14
+
+This is a minor bugfix update from v2.9.6.
+
+### Fixed
+- Preserve softlinks in input reference fasta file paths (STREL-976)
+
 ## v2.9.6 - 2018-07-17
 
 This is a minor bugfix update from v2.9.5.

src/c++/lib/applications/GetChromDepth/ChromDepthOptions.cpp

@@ -58,8 +58,8 @@ parseOptions(
     ChromDepthOptions& opt,
     std::string& errorMsg)
 {
-    if (checkStandardizeInputFile(opt.alignmentFilename, "alignment", errorMsg)) return true;
-    if (checkStandardizeInputFile(opt.referenceFilename, "reference fasta", errorMsg)) return true;
+    if (checkAndStandardizeRequiredInputFilePath(opt.alignmentFilename, "alignment", errorMsg)) return true;
+    if (checkAndStandardizeRequiredInputFilePath(opt.referenceFilename, "reference fasta", errorMsg)) return true;
 
     if (vm.count("chrom"))
     {

src/c++/lib/applications/GetRegionDepth/RegionDepthOptions.cpp

@@ -58,8 +58,8 @@ parseOptions(
     RegionDepthOptions& opt,
     std::string& errorMsg)
 {
-    if (checkStandardizeInputFile(opt.alignmentFilename, "alignment", errorMsg)) return true;
-    if (checkStandardizeInputFile(opt.referenceFilename, "reference fasta", errorMsg)) return true;
+    if (checkAndStandardizeRequiredInputFilePath(opt.alignmentFilename, "alignment", errorMsg)) return true;
+    if (checkAndStandardizeRequiredInputFilePath(opt.referenceFilename, "reference fasta", errorMsg)) return true;
 
     if (vm.count("region"))
     {

src/c++/lib/blt_util/compat_util.cpp

@@ -27,28 +27,6 @@
 #include <iostream>
 
 
-#ifdef _MSC_VER
-#include "compat_util_win32_realpath.c"
-#endif
-
-
-
-bool
-compat_realpath(std::string& path)
-{
-    errno=0;
-    const char* newpath(realpath(path.c_str(),nullptr));
-    if ((nullptr==newpath) || (errno!=0))
-    {
-        if (nullptr!=newpath) free((void*)newpath);
-        return false;
-    }
-    path = newpath;
-    free((void*)newpath);
-    return true;
-}
-
-
 
 double
 compat_round(const double x)

src/c++/lib/blt_util/compat_util.hh

@@ -42,9 +42,3 @@ compat_round(const double x);
 
 const char*
 compat_basename(const char* s);
-
-
-// gets canonical name of paths, but only when these refer to existing items
-// returns false on error.
-bool
-compat_realpath(std::string& path);

src/c++/lib/options/AlignmentFileOptionsParser.cpp

@@ -68,7 +68,7 @@ checkOptions(
         std::set<std::string> nameCheck;
         for (std::string& afile : opt.alignmentFilenames)
         {
-            if (checkStandardizeInputFile(afile,"alignment file",errorMsg)) break;
+            if (checkAndStandardizeRequiredInputFilePath(afile, "alignment file", errorMsg)) break;
             if (nameCheck.count(afile))
             {
                 std::ostringstream oss;

src/c++/lib/options/optionsUtil.cpp

@@ -26,7 +26,7 @@
 
 
 bool
-checkStandardizeInputFile(
+checkAndStandardizeRequiredInputFilePath(
     std::string& filename,
     const char* fileLabel,
     std::string& errorMsg)

src/c++/lib/options/optionsUtil.hh

@@ -22,13 +22,11 @@
 #include <string>
 
 
-/// check if input file exists and is usable as
-/// input, if so canonicalize the name
+/// Check if input path exists and is usable as input, if so, convert the input filename to an absolute path.
 ///
-/// In case of error return true and provide error
-/// message
+/// In case of error return true and provide error message
 bool
-checkStandardizeInputFile(
+checkAndStandardizeRequiredInputFilePath(
     std::string& filename,
     const char* fileLabel,
     std::string& errorMsg);

src/c++/lib/starling_common/starling_base_option_parser.cpp

@@ -21,6 +21,7 @@
 
 #include "blt_common/blt_arg_validate.hh"
 #include "blt_util/compat_util.hh"
+#include "options/optionsUtil.hh"
 #include "starling_common/Tier2OptionsParser.hh"
 
 #include "boost/filesystem.hpp"
@@ -169,13 +170,15 @@ finalize_starling_base_options(
         pinfo.usage("Must specify a fasta reference file");
     }
 
-    // canonicalize the reference sequence path:
-    /// TODO: replace this with the same thing from boost?
-    if (! compat_realpath(opt.referenceFilename))
+    // Convert reference sequence path to an absolute path. Just like for BAM/CRAM files, we want absolute but not
+    // canonical path in this case, because following softlinks to the canonical path will often cause us to miss the
+    // sidecar index file.
     {
-        std::ostringstream oss;
-        oss << "can't resolve reference path: " << opt.referenceFilename << "\n";
-        pinfo.usage(oss.str().c_str());
+        std::string errorMsg;
+        if (checkAndStandardizeRequiredInputFilePath(opt.referenceFilename, "reference fasta", errorMsg))
+        {
+            pinfo.usage(errorMsg.c_str());
+        }
     }
 
     // set analysis regions:
@@ -226,12 +229,15 @@ finalize_starling_base_options(
     {
         checkOptionalInputFile(pinfo, indelErrorModelFilename, "indel error models");
     }
-    /// tier2 options are not parsed by starling_base, but need to live up here for now,
-    /// so validate them together with the rest of starling_base
-    std::string errorMsg;
-    if (parseTier2Options(vm,opt.tier2,errorMsg))
+
+    // tier2 options are not parsed by starling_base, but need to live up here for now,
+    // so validate them together with the rest of starling_base
     {
-        pinfo.usage(errorMsg.c_str());
+        std::string errorMsg;
+        if (parseTier2Options(vm, opt.tier2, errorMsg))
+        {
+            pinfo.usage(errorMsg.c_str());
+        }
     }
 
     if (opt.useTier2Evidence)