From 9f580f07420ed384dc542e7661c30a67b0415023 Mon Sep 17 00:00:00 2001 From: Gaik Tamazian Date: Thu, 14 May 2015 17:45:51 +0300 Subject: [PATCH 1/4] Typo fixed --- src/utils/BamTools/src/api/internal/io/HostAddress_p.cpp | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/utils/BamTools/src/api/internal/io/HostAddress_p.cpp b/src/utils/BamTools/src/api/internal/io/HostAddress_p.cpp index 5c42c5b35..1b4e57dc2 100644 --- a/src/utils/BamTools/src/api/internal/io/HostAddress_p.cpp +++ b/src/utils/BamTools/src/api/internal/io/HostAddress_p.cpp @@ -263,7 +263,7 @@ bool HostAddress::operator<(const HostAddress& other) const { // if self is IPv4 if ( m_protocol == HostAddress::IPv4Protocol ) { if ( other.m_protocol == HostAddress::IPv4Protocol ) - return m_ip4Address < m_ip4Address; + return m_ip4Address < other.m_ip4Address; } // if self is IPv6 From 3c969b08c24797c6533cc36a7cb1249925c2e3ee Mon Sep 17 00:00:00 2001 From: Gaik Tamazian Date: Thu, 14 May 2015 17:56:34 +0300 Subject: [PATCH 2/4] Mapping quality variable made signed The mapping quality variables was made signed to handle correctly erroneous input. --- src/bedToBam/bedToBam.cpp | 2 +- src/bedpeToBam/bedpeToBam.cpp | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/src/bedToBam/bedToBam.cpp b/src/bedToBam/bedToBam.cpp index f7261286f..1287b07ae 100644 --- a/src/bedToBam/bedToBam.cpp +++ b/src/bedToBam/bedToBam.cpp @@ -53,7 +53,7 @@ int bedtobam_main(int argc, char* argv[]) { string bedFile = "stdin"; string genomeFile; - unsigned int mapQual = 255; + int mapQual = 255; bool haveBed = true; bool haveGenome = false; diff --git a/src/bedpeToBam/bedpeToBam.cpp b/src/bedpeToBam/bedpeToBam.cpp index 9a31081b8..4afa3cdce 100644 --- a/src/bedpeToBam/bedpeToBam.cpp +++ b/src/bedpeToBam/bedpeToBam.cpp @@ -54,7 +54,7 @@ int bedpetobam_main(int argc, char* argv[]) { string bedpeFile = "stdin"; string genomeFile; - unsigned int mapQual = 255; + int mapQual = 255; bool haveBedPE = true; bool haveGenome = false; From d6061de76a5b652ccd8d46943af4bb58a13087e2 Mon Sep 17 00:00:00 2001 From: Gaik Tamazian Date: Tue, 2 Jun 2015 11:57:40 +0300 Subject: [PATCH 3/4] Format specifier fixed --- src/split/splitBed.cpp | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/split/splitBed.cpp b/src/split/splitBed.cpp index ff0e440d3..4faa1c412 100644 --- a/src/split/splitBed.cpp +++ b/src/split/splitBed.cpp @@ -148,7 +148,7 @@ std::FILE* BedSplit::saveFileChunk(std::string& filename,size_t file_index) char tmp[10]; filename.assign(this->outfileprefix); - sprintf(tmp,"%05d",(file_index+1)); + sprintf(tmp,"%05zu",(file_index+1)); filename.append(".").append(tmp).append(".bed"); FILE* out = fopen(filename.c_str(),"w"); if(out==NULL) From 9d87d90bf63c64d1e65fc129c6b9fdb1d1c07b66 Mon Sep 17 00:00:00 2001 From: Gaik Tamazian Date: Sun, 17 May 2015 23:37:47 +0300 Subject: [PATCH 4/4] abs calls for long int fixed The `abs` function calls were replaced with `labs` for long int variables. --- src/fisher/kfunc.c | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/fisher/kfunc.c b/src/fisher/kfunc.c index 5c39d4973..baa60c273 100644 --- a/src/fisher/kfunc.c +++ b/src/fisher/kfunc.c @@ -243,7 +243,7 @@ double kt_fisher_exact(long long n11, long long n12, long long n21, long long n2 *two = left + right; if (*two > 1.) *two = 1.; // adjust left and right - if (abs((long) (i - n11)) < abs((long) (j - n11))) right = 1. - left + q; + if (labs((long) (i - n11)) < labs((long) (j - n11))) right = 1. - left + q; else left = 1.0 - right + q; *_left = left; *_right = right; return q;