From d3e74ae9942971d3f52a24422bc7cfadbfef7f70 Mon Sep 17 00:00:00 2001 From: kew24 Date: Wed, 6 Apr 2022 09:56:27 -0400 Subject: [PATCH 1/2] add headers for std::numeric_limits error --- .../src/graphcore/GraphCoordinates.cpp | 2 ++ 1 file changed, 2 insertions(+) diff --git a/ehunter/thirdparty/graph-tools-master-0cd9399/src/graphcore/GraphCoordinates.cpp b/ehunter/thirdparty/graph-tools-master-0cd9399/src/graphcore/GraphCoordinates.cpp index 2550eda..f90eddc 100644 --- a/ehunter/thirdparty/graph-tools-master-0cd9399/src/graphcore/GraphCoordinates.cpp +++ b/ehunter/thirdparty/graph-tools-master-0cd9399/src/graphcore/GraphCoordinates.cpp @@ -22,6 +22,8 @@ #include "graphutils/PairHashing.hh" #include +#include +#include namespace graphtools { From 67f83d6c132ba3f2dd8010a38592d1fcd3dab645 Mon Sep 17 00:00:00 2001 From: kew24 Date: Wed, 6 Apr 2022 09:58:16 -0400 Subject: [PATCH 2/2] expand index search, don't require .b/cram in name --- ehunter/io/ParameterLoading.cpp | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/ehunter/io/ParameterLoading.cpp b/ehunter/io/ParameterLoading.cpp index 6087605..2c11481 100644 --- a/ehunter/io/ParameterLoading.cpp +++ b/ehunter/io/ParameterLoading.cpp @@ -163,11 +163,11 @@ static void assertPathToExistingFile(const string& pathEncoding) static void assertIndexExists(const string& htsFilePath) { - const vector kPossibleIndexExtensions = { ".bai", ".csi", ".crai" }; + const vector kPossibleIndexExtensions = { ".bai", ".bam.bai", ".csi", ".bam.csi", ".cram.csi", ".crai", ".cram.crai" }; for (const string& indexExtension : kPossibleIndexExtensions) { - if (fs::exists(htsFilePath + indexExtension)) + if (fs::exists(htsFilePath.substr(0, htsFilePath.find_last_of(".")) + indexExtension)) { return; }