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pindel: fixing compilation issues for gcc5+ (#28387)

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snehring 2022-05-17 02:45:08 -05:00 committed by GitHub
parent 446cbf4b5a
commit d566330a33
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GPG Key ID: 4AEE18F83AFDEB23
2 changed files with 110 additions and 18 deletions
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100
var/spack/repos/builtin/packages/pindel/gcc-5-compat.patch Normal file
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@ -0,0 +1,100 @@
diff --git a/src/bddata.cpp b/src/bddata.cpp
index 7820084..270f242 100644
--- a/src/bddata.cpp
+++ b/src/bddata.cpp
@@ -2,6 +2,12 @@
#include <fstream>
#include "bddata.h"
+// return the 'absolute value' of the difference between two unsigned ints
+inline unsigned int unsigned_abs_sub(unsigned int a, unsigned int b)
+{
+ return(a>b)?a-b:b-a;
+}
+
BDData::BDData() : m_currentWindow( &g_dummyChromosome, 0, 0 )
{
m_breakDancerMask = NULL;
@@ -114,7 +120,7 @@ void BDData::loadBDFile(const std::string& filename) {
firstPos += g_SpacerBeforeAfter; // ??? ask Kai
secondPos += g_SpacerBeforeAfter;
- if (firstChrName == secondChrName && secondChrName != "" && abs(firstPos - secondPos) < 500)
+ if (firstChrName == secondChrName && secondChrName != "" && unsigned_abs_sub(firstPos, secondPos) < 500)
continue;
if ( firstChrName!="" && secondChrName!="") {
BreakDancerCoordinate firstBDCoordinate( firstChrName, firstPos );
@@ -162,10 +168,10 @@ void SortRPByChrPos(std::vector <RP_READ> & Reads_RP) { // no interchromosome RP
}*/
bool RecipicalOverlap(RP_READ & first, RP_READ & second) {
int distance = 1000;
- if (abs(first.PosA - first.PosA1) > distance) return false;
- if (abs(first.PosB - first.PosB1) > distance) return false;
- if (abs(second.PosA - second.PosA1) > distance) return false;
- if (abs(second.PosB - second.PosB1) > distance) return false;
+ if (unsigned_abs_sub(first.PosA, first.PosA1) > distance) return false;
+ if (unsigned_abs_sub(first.PosB, first.PosB1) > distance) return false;
+ if (unsigned_abs_sub(second.PosA, second.PosA1) > distance) return false;
+ if (unsigned_abs_sub(second.PosB, second.PosB1) > distance) return false;
float cutoff = 0.9;
unsigned FirstPosA = (first.PosA + first.PosA1)/2;
@@ -377,7 +383,7 @@ void ModifyRP(std::vector <RP_READ> & Reads_RP) {
Reads_RP[first].PosB = Reads_RP[first].PosB + Reads_RP[first].ReadLength;
Reads_RP[first].PosB1 = Reads_RP[first].PosB1 + Reads_RP[first].ReadLength;
}
- if (Reads_RP[first].ChrNameA == Reads_RP[first].ChrNameB && abs(Reads_RP[first].PosA - Reads_RP[first].PosB) < 500) Reads_RP[first].Visited = true;
+ if (Reads_RP[first].ChrNameA == Reads_RP[first].ChrNameB && unsigned_abs_sub(Reads_RP[first].PosA, Reads_RP[first].PosB) < 500) Reads_RP[first].Visited = true;
//std::cout << "Final: " << Reads_RP[first].ChrNameA << " " << Reads_RP[first].DA << " " << Reads_RP[first].PosA << "\t" << Reads_RP[first].ChrNameB << " " << Reads_RP[first].DB << " " << Reads_RP[first].PosB << std::endl;
}
}
diff --git a/src/genotyping.cpp b/src/genotyping.cpp
index 58e2978..d258734 100644
--- a/src/genotyping.cpp
+++ b/src/genotyping.cpp
@@ -35,6 +35,11 @@
#include <algorithm>
#include <math.h>
+// return the 'absolute value' of the difference between two unsigned ints
+inline unsigned int unsigned_abs_sub(unsigned int a, unsigned int b)
+{
+ return(a>b)?a-b:b-a;
+}
void doGenotyping (ControlState & CurrentState, UserDefinedSettings* userSettings ) {
const int SV_Genotype_Cutoff = 1000;
@@ -124,7 +129,7 @@ void doGenotyping (ControlState & CurrentState, UserDefinedSettings* userSetting
// step 4 for each variant, do genotyping
for (unsigned SV_index =0; SV_index < AllSV4Genotyping.size(); SV_index++) {
// step 4.1 if type == DEL, GenotypeDel
- if (AllSV4Genotyping[SV_index].ChrA == AllSV4Genotyping[SV_index].ChrB && abs(AllSV4Genotyping[SV_index].PosA - AllSV4Genotyping[SV_index].PosB) < SV_Genotype_Cutoff) {
+ if (AllSV4Genotyping[SV_index].ChrA == AllSV4Genotyping[SV_index].ChrB && unsigned_abs_sub(AllSV4Genotyping[SV_index].PosA, AllSV4Genotyping[SV_index].PosB) < SV_Genotype_Cutoff) {
std::cout << "Skip One SV " << OneSV.Type << " " << OneSV.ChrA << " " << OneSV.PosA << " "
<< OneSV.CI_A << " " << OneSV.ChrB << " " << OneSV.PosB << " "
<< OneSV.CI_B << std::endl;
diff --git a/src/pindel.cpp b/src/pindel.cpp
index 7d8b3a5..c137ce7 100644
--- a/src/pindel.cpp
+++ b/src/pindel.cpp
@@ -123,6 +123,11 @@ std::vector<Parameter *> parameters;
UserDefinedSettings* userSettings;
+// return the 'absolute value' of the difference between two unsigned ints
+inline unsigned int unsigned_abs_sub(unsigned int a, unsigned int b)
+{
+ return(a>b)?a-b:b-a;
+}
// #########################################################
@@ -1557,7 +1562,7 @@ void MergeInterChr(ControlState& currentState, UserDefinedSettings *usersettings
for (unsigned index_b = index_a; index_b < All.size(); index_b++) {
if (index_a == index_b) continue;
if (All[index_a].FirstChrName == All[index_b].FirstChrName && All[index_a].SecondChrName == All[index_b].SecondChrName) {
- if (abs(All[index_a].FirstPos - All[index_b].FirstPos) < 10 && abs(All[index_a].SecondPos - All[index_b].SecondPos) < 10 && All[index_a].NumSupport + All[index_b].NumSupport >= cutoff) {
+ if (unsigned_abs_sub(All[index_a].FirstPos, All[index_b].FirstPos) < 10 && unsigned_abs_sub(All[index_a].SecondPos, All[index_b].SecondPos) < 10 && All[index_a].NumSupport + All[index_b].NumSupport >= cutoff) {
INToutputfile << "chr\t" << All[index_a].FirstChrName << "\tpos\t" << unsigned((All[index_a].FirstPos + All[index_b].FirstPos) / 2) << "\tchr\t" << All[index_a].SecondChrName << "\tpos\t"
<< unsigned((All[index_a].SecondPos + All[index_b].SecondPos) / 2) << "\tseq\t" << All[index_a].InsertedSequence << "\tsupport\t" << All[index_a].NumSupport + All[index_b].NumSupport << "\tINFOR\t"

28
var/spack/repos/builtin/packages/pindel/package.py
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@ -21,26 +21,18 @@ class Pindel(MakefilePackage):
version('0.2.5', sha256='9908940d090eff23d940c3b6f2f6b3fc2bb1fd3b7a2d553cc81eed240a23fd9f')
depends_on('htslib@1.7:')
#
# This Makefile2 stuff is due to the original installer,
# The author wants to run make twice, the first
# time generates a Makefile.local then returns "false"
# User is then suppose to run make again and the
# package will compile. This is an attempt to
# stay as close to the original installer as possible
#
# GCC > 4.8 seems to dislike calling abs on an unsigned integer
# replace ambiguous calls to abs() on the difference between two
# unsigned ints with a one line funtion that returns the 'absolute
# value' of the difference between two unsigned ints.
patch('gcc-5-compat.patch', when='@0.2.5b8%gcc@5:')
build_directory = 'src'
def edit(self, spec, prefix):
copy('Makefile', 'Makefile2')
myedit = FileFilter('Makefile2')
myedit.filter('-include Makefile.local', '#removed include')
myedit.filter('@false', '#removed autofailure')
def build(self, spec, prefix):
make("Makefile.local", "-f",
"Makefile2",
"HTSLIB=%s" % spec['htslib'].prefix)
make("HTSLIB=%s" % spec['htslib'].prefix)
filter_file('include ../Makefile.local', '', 'src/Makefile')
filter_file('Makefile.local', '', 'src/Makefile')
def install(self, spec, prefix):
mkdirp(prefix.bin)