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|
Description: switching from pcre3 to pcre2
This was tested by running pcreTest (in cpp/src/GsnapParseTest1.cc)
successfully. Yet I did not compile the other files.
Author: Pierre Gruet <pgt@debian.org>
Bug-Debian: https://bugs.debian.org/1000043
Forwarded: https://github.com/CampagneLaboratory/goby3/issues/9
Last-Update: 2021-11-26
--- a/cpp/src/GsnapParseTest1.cc
+++ b/cpp/src/GsnapParseTest1.cc
@@ -20,6 +20,7 @@
#if HAVE_CONFIG_H
#include <config.h>
#endif
+#include <string>
#include <sys/types.h>
#include <sys/stat.h>
@@ -29,11 +30,13 @@
#else
#include <unistd.h>
#endif
+#include <iostream>
#include "goby/C_Gsnap.h"
#include "goby/C_Alignments.h"
#include "goby/C_Reads.h"
-#include <pcrecpp.h>
+#define PCRE2_CODE_UNIT_WIDTH 8
+#include <pcre2.h>
using namespace std;
@@ -178,21 +181,53 @@
}
void pcreTest() {
- char *a = "s-reads:3.2..b:5.1,l_reads:3,c:3,d:5,a:0..b:2.8";
+ string a = string("s-reads:3.2..b:5.1,l_reads:3,c:3,d:5,a:0..b:2.8");
string temp1;
string da; string daClip; string daProb;
string temp2;
string std; string stdClip;
- pcrecpp::StringPiece input(a); // Wrap in a StringPiece
- pcrecpp::RE re("(([A-Za-z_\\-]+):(\\d+)\\.(\\d))|(([A-Za-z_\\-]+):(\\d))");
+ //Setting up pcre2.
+ pcre2_code *re;
+ string sPattern = string("(([A-Za-z_\\-]+):(\\d+)\\.(\\d))|(([A-Za-z_\\-]+):(\\d))");
+ PCRE2_SPTR pattern = (PCRE2_SPTR)(sPattern.c_str());
+ PCRE2_SPTR subject = (PCRE2_SPTR)(a.c_str());
+ int errornumber;
+ int rc;
+ PCRE2_SIZE erroroffset;
+ PCRE2_SIZE *ovector;
+ PCRE2_SIZE subject_length = (PCRE2_SIZE)(sPattern.length());
+ pcre2_match_data *match_data;
+ re = pcre2_compile(pattern, PCRE2_ZERO_TERMINATED, 0, &errornumber, &erroroffset, NULL);
+ match_data = pcre2_match_data_create_from_pattern(re, NULL);
+ PCRE2_SIZE start_offset = 0;
printf("pcre start\n");
- while (re.FindAndConsume(&input,
- &temp1,
- &da, &daClip, &daProb,
- &temp2,
- &std, &stdClip)) {
+ do {
+ rc = pcre2_match(re, subject, subject_length, start_offset, 0, match_data, NULL);
+
+ if (rc != PCRE2_ERROR_NOMATCH) {
+ char** sStore = new char*[7];
+ //Match succeeded. Converting strings to the needed types.
+ ovector = pcre2_get_ovector_pointer(match_data);
+ for (int i = 0 ; i < 7 ; i++) {
+ sStore[i] = new char[ovector[2 * i + 3] - ovector[2 * i + 2]];
+ sprintf(sStore[i1], "%.*s", (int)(ovector[2 * i + 3] - ovector[2 * i + 2]), (char*)(subject + ovector[2 * i + 2]));
+ }
+ temp1 = string(sStore[0]);
+ da = string(sStore[1]);
+ daClip = string(sStore[2]);
+ daProb = string(sStore[3]);
+ temp2 = string(sStore[4]);
+ std = string(sStore[5]);
+ stdClip = string(sStore[6]);
+ for (int i = 0 ; i < 7 ; i++) {
+ delete[] sStore[i];
+ }
+ delete[] sStore;
+ //Preparing next match.
+ start_offset = ovector[1];
+ }
if (da.length() > 0) {
cout << "da=" << da << " ";
@@ -203,7 +238,7 @@
cout << "stdClip=" << stdClip << endl;
}
- }
+ } while (rc != PCRE2_ERROR_NOMATCH);
printf("done\n");
}
--- a/cpp/src/goby/C_Alignments.cc
+++ b/cpp/src/goby/C_Alignments.cc
@@ -18,7 +18,8 @@
#include <string>
#include <iostream>
-#include <pcrecpp.h>
+#define PCRE2_CODE_UNIT_WIDTH 8
+#include <pcre2.h>
#include <stdio.h>
#include "Reads.h"
@@ -872,8 +873,21 @@
}
void applyCigar(CSamHelper *samHelper) {
- pcrecpp::RE re("([0-9]+)([SMID])");
- pcrecpp::StringPiece input(samHelper->cpp_cigar->c_str());
+ //Setting up pcre2.
+ pcre2_code *re;
+ string sPattern = string("([0-9]+)([SMID])");
+ PCRE2_SPTR pattern = (PCRE2_SPTR)(sPattern.c_str());
+ PCRE2_SPTR subject = (PCRE2_SPTR)(samHelper->cpp_cigar->c_str());
+ int errornumber;
+ int rc;
+ PCRE2_SIZE erroroffset;
+ PCRE2_SIZE *ovector;
+ PCRE2_SIZE subject_length = (PCRE2_SIZE)(sPattern.length());
+ pcre2_match_data *match_data;
+ re = pcre2_compile(pattern, PCRE2_ZERO_TERMINATED, 0, &errornumber, &erroroffset, NULL);
+ match_data = pcre2_match_data_create_from_pattern(re, NULL);
+ PCRE2_SIZE start_offset = 0;
+
debug (fprintf(stderr, ":: Applying cigar=%s\n", samHelper->cpp_cigar->c_str());)
int length;
char op;
@@ -883,7 +897,25 @@
samHelper->numInsertions = 0;
samHelper->numDeletions = 0;
samHelper->numMisMatches = 0;
- while (re.Consume(&input, &length, &op)) {
+
+ do {
+ rc = pcre2_match(re, subject, subject_length, start_offset, 0, match_data, NULL);
+
+ if (rc != PCRE2_ERROR_NOMATCH) {
+ //Match succeeded. Converting strings to the needed types.
+ ovector = pcre2_get_ovector_pointer(match_data);
+ char* sLength = new char[ovector[3] - ovector[2] + 1];
+ char* sOp = new char[ovector[5] - ovector[4] + 1];
+ sprintf(sLength, "%.*s", (int)(ovector[3] - ovector[2]), (char*)(subject + ovector[2]));
+ sprintf(sOp, "%.*s", (int)(ovector[5] - ovector[4]), (char*)(subject + ovector[4]));
+ length = stoi(string(sLength));
+ op = string(sOp)[0];
+ delete[] sLength;
+ delete[] sOp;
+ //Preparing next match.
+ start_offset = ovector[1];
+ }
+
switch(op) {
case 'S':
// Soft clipping
@@ -933,20 +965,48 @@
break;
}
startOfCigar = false;
- }
+ } while (rc != PCRE2_ERROR_NOMATCH);
}
void applyMd(CSamHelper *samHelper) {
// My RE is simplified from the SAM spec but performs the same task
// the major difference being mine would allow 5ACG where the current
// spec would require 5A0C0G0 (which mine will still work with just fine).
- pcrecpp::RE re("([0-9]+|[ACGTN]|\\^[ACGTN]+)");
- pcrecpp::StringPiece input(samHelper->cpp_md->c_str());
+
+ //Setting up pcre2.
+ pcre2_code *re;
+ string sPattern = string("([0-9]+|[ACGTN]|\\^[ACGTN]+)");
+ PCRE2_SPTR pattern = (PCRE2_SPTR)(sPattern.c_str());
+ PCRE2_SPTR subject = (PCRE2_SPTR)(samHelper->cpp_md->c_str());
+ int errornumber;
+ int rc;
+ PCRE2_SIZE erroroffset;
+ PCRE2_SIZE *ovector;
+ PCRE2_SIZE subject_length = (PCRE2_SIZE)(sPattern.length());
+ pcre2_match_data *match_data;
+ re = pcre2_compile(pattern, PCRE2_ZERO_TERMINATED, 0, &errornumber, &erroroffset, NULL);
+ match_data = pcre2_match_data_create_from_pattern(re, NULL);
+ PCRE2_SIZE start_offset = 0;
+
debug (fprintf(stderr, ":: Applying md=%s\n", samHelper->cpp_md->c_str());)
string mdPart;
int position = samHelper->numLeftClipped;
int i;
- while (re.Consume(&input, &mdPart)) {
+
+ do {
+ rc = pcre2_match(re, subject, subject_length, start_offset, 0, match_data, NULL);
+
+ if (rc != PCRE2_ERROR_NOMATCH) {
+ //Match succeeded.
+ ovector = pcre2_get_ovector_pointer(match_data);
+ char* sMdPart = new char[ovector[3] - ovector[2] + 1];
+ sprintf(sMdPart, "%.*s", (int)(ovector[3] - ovector[2]), (char*)(subject + ovector[2]));
+ mdPart = string(sMdPart);
+ delete[] sMdPart;
+ //Preparing next match.
+ start_offset = ovector[1];
+ }
+
if (isdigit(mdPart[0])) {
int length = atoi(mdPart.c_str());
position += length;
@@ -962,7 +1022,7 @@
samHelper->numMisMatches++;
}
}
- }
+ } while (rc != PCRE2_ERROR_NOMATCH);
}
void samHelper_constructRefAndQuery(CSamHelper *samHelper) {
--- a/cpp/src/goby/C_Gsnap.cc
+++ b/cpp/src/goby/C_Gsnap.cc
@@ -27,7 +27,8 @@
#include "C_Gsnap_structs.h"
#include "C_Alignments.h"
#include "hash.h"
-#include "pcrecpp.h"
+#define PCRE2_CODE_UNIT_WIDTH 8
+#include <pcre2.h>
/*
* TODO: Make sure the fields I moved from segment to alignment really
@@ -44,10 +45,6 @@
using namespace std;
-using pcrecpp::StringPiece;
-using pcrecpp::RE;
-using pcrecpp::RE_Options;
-
#undef C_GSNAP_DEBUG
#ifdef C_GSNAP_DEBUG
#define debug(x) x
@@ -359,13 +356,47 @@
string temp2;
string std; string stdClip;
- pcrecpp::StringPiece input(a); // Wrap in a StringPiece
- pcrecpp::RE re("(([A-Za-z_\\-]+):(\\d+)\\.(\\d+))|(([A-Za-z_\\-]+):(\\d+))");
+ //Setting up pcre2.
+ pcre2_code *re;
+ string sPattern = string("(([A-Za-z_\\-]+):(\\d+)\\.(\\d+))|(([A-Za-z_\\-]+):(\\d+))");
+ PCRE2_SPTR pattern = (PCRE2_SPTR)(sPattern.c_str());
+ PCRE2_SPTR subject = (PCRE2_SPTR)(a);
+ int errornumber;
+ int rc;
+ PCRE2_SIZE erroroffset;
+ PCRE2_SIZE *ovector;
+ PCRE2_SIZE subject_length = (PCRE2_SIZE)(sPattern.length());
+ pcre2_match_data *match_data;
+ re = pcre2_compile(pattern, PCRE2_ZERO_TERMINATED, 0, &errornumber, &erroroffset, NULL);
+ match_data = pcre2_match_data_create_from_pattern(re, NULL);
+ PCRE2_SIZE start_offset = 0;
+
+ do {
+ rc = pcre2_match(re, subject, subject_length, start_offset, 0, match_data, NULL);
+
+ if (rc != PCRE2_ERROR_NOMATCH) {
+ char** sStore = new char*[7];
+ //Match succeeded. Converting strings to the needed types.
+ ovector = pcre2_get_ovector_pointer(match_data);
+ for (int i = 0 ; i < 7 ; i++) {
+ sStore[i] = new char[ovector[2 * i + 3] - ovector[2 * i + 2]];
+ sprintf(sStore[i1], "%.*s", (int)(ovector[2 * i + 3] - ovector[2 * i + 2]), (char*)(subject + ovector[2 * i + 2]));
+ }
+ temp1 = string(sStore[0]);
+ da = string(sStore[1]);
+ daClip = string(sStore[2]);
+ daProb = string(sStore[3]);
+ temp2 = string(sStore[4]);
+ std = string(sStore[5]);
+ stdClip = string(sStore[6]);
+ for (int i = 0 ; i < 7 ; i++) {
+ delete[] sStore[i];
+ }
+ delete[] sStore;
+ //Preparing next match.
+ start_offset = ovector[1];
+ }
- while (re.FindAndConsume(&input, &temp1,
- &da, &daClip, &daProb,
- &temp2,
- &std, &stdClip)) {
if (da.length() > 0) {
if (da.length() > 12 && da.substr(0, 12) == "splice_dist_") {
// Remove the _1, _2 suffix
@@ -382,7 +413,7 @@
keys.push_back(std);
result[std] = stdClip;
}
- }
+ } while (rc != PCRE2_ERROR_NOMATCH);
}
return pair<vector<string>,
LIBGOBY_HASH_MAP<string, string> >(keys, result);
--- a/cpp/configure.ac
+++ b/cpp/configure.ac
@@ -63,9 +63,9 @@
# use pkg-config to make sure that protobuf is available
# see http://code.google.com/p/protobuf/
PKG_CHECK_MODULES([PROTOBUF], [protobuf >= 2.4.1])
-# use pkg-config to make sure that PCRE is available
+# use pkg-config to make sure that PCRE2 is available
# see http://www.pcre.org/
-PKG_CHECK_MODULES([LIBPCRECPP], [libpcrecpp >= 8.10])
+PKG_CHECK_MODULES([LIBPCRE2], [libpcre2-8 >= 10.39])
AC_CONFIG_FILES([Makefile src/Makefile goby.pc])
AC_OUTPUT
--- a/cpp/goby.pc.in
+++ b/cpp/goby.pc.in
@@ -6,5 +6,5 @@
Name: Goby
Description: API for reading binary data files created using the Goby next-gen data management framework
Version: @VERSION@
-Libs: -L${libdir} -lgoby @PROTOBUF_LIBS@ @LIBPCRECPP_LIBS@
-Cflags: -I${includedir} @PROTOBUF_CFLAGS@ @LIBPCRECPP_CFLAGS@
+Libs: -L${libdir} -lgoby @PROTOBUF_LIBS@ @LIBPCRE2_LIBS@
+Cflags: -I${includedir} @PROTOBUF_CFLAGS@ @LIBPCRE2_CFLAGS@
--- a/cpp/src/Makefile.am
+++ b/cpp/src/Makefile.am
@@ -22,10 +22,10 @@
BUILT_SOURCES = goby.timestamp
-AM_CXXFLAGS = @PROTOBUF_CFLAGS@ @LIBPCRECPP_CFLAGS@ ${BOOST_CPPFLAGS}
-AM_CFLAGS = @PROTOBUF_CFLAGS@ @LIBPCRECPP_CFLAGS@ ${BOOST_CPPFLAGS}
+AM_CXXFLAGS = @PROTOBUF_CFLAGS@ @LIBPCRE2_CFLAGS@ ${BOOST_CPPFLAGS}
+AM_CFLAGS = @PROTOBUF_CFLAGS@ @LIBPCRE2_CFLAGS@ ${BOOST_CPPFLAGS}
-libgoby_la_LIBADD = @PROTOBUF_LIBS@ @LIBPCRECPP_LIBS@
+libgoby_la_LIBADD = @PROTOBUF_LIBS@ @LIBPCRE2_LIBS@
libgoby_la_LDFLAGS = -version-info @version_info@ -export-dynamic # -no-undefined
libgoby_la_SOURCES = \
goby/ICBFileInputStream.cc \
|
