diff --git a/endian_swap.h b/endian_swap.h
index 4bd4f1b3..ff86f1cf 100644
--- a/endian_swap.h
+++ b/endian_swap.h
@@ -75,7 +75,7 @@ static inline uint64_t endianSwapU64(uint64_t u) {
template
static inline index_t endianSwapIndex(index_t u) {
if(sizeof(index_t) == 8) {
- return endianSwapU64(u);
+ return (index_t)endianSwapU64(u);
} else if(sizeof(index_t) == 4) {
return endianSwapU32(u);
} else {
diff --git a/evaluation/build_indexes.py b/evaluation/build_indexes.py
index 1f71c70e..ae3763cf 100755
--- a/evaluation/build_indexes.py
+++ b/evaluation/build_indexes.py
@@ -9,7 +9,7 @@ def build_indexes():
if not os.path.exists("indexes"):
os.mkdir("indexes")
os.chdir("indexes")
- aligners = ["HISAT2", "HISAT", "Bowtie", "STAR", "GSNAP"]
+ aligners = ["HISAT2", "HISAT", "Bowtie", "STAR", "GSNAP", "BWA"]
for genome in ["genome", "22", "22_20-21M"]:
for aligner in aligners:
if genome == "genome":
@@ -35,6 +35,8 @@ def build_indexes():
cmd = cmd + "; mkdir gtf; ../../aligners/bin/STAR --runMode genomeGenerate --genomeDir gtf --genomeFastaFiles ../../data/%s.fa --sjdbGTFfile ../../data/%s.gtf --sjdbOverhang 99 --runThreadN 4" % (genome, genome)
elif aligner == "GSNAP":
cmd = "../../aligners/bin/gmap_build -B ../../aligners/bin -D . -d %s ../../data/%s.fa" % (genome, genome)
+ elif aligner == "BWA":
+ cmd = "../../aligners/bin/bwa -p %s.fa ../../data/%s.fa" % (genome, genome)
else:
assert False
print >> sys.stderr, cmd
diff --git a/evaluation/get_data.py b/evaluation/get_data.py
index 33a9d5cd..3e49e953 100755
--- a/evaluation/get_data.py
+++ b/evaluation/get_data.py
@@ -74,7 +74,8 @@ def get_data(small = False):
else:
files = ["108M_RNA_wgEncodeCshlLongRnaSeq",
"62M_RNA_SRR353653",
- "80M_DNA_SRR345300"]
+ "80M_DNA_SRR345300",
+ "5M_DNA_NA12878D"]
for file in files:
if small and file.find("20M") != -1:
continue
diff --git a/evaluation/real/calculate_read_cost.py b/evaluation/real/calculate_read_cost.py
index 7c012e72..888c2b85 100755
--- a/evaluation/real/calculate_read_cost.py
+++ b/evaluation/real/calculate_read_cost.py
@@ -7,6 +7,8 @@
import re
from datetime import datetime, date, time
+MAX_EDIT = 51
+
"""
"""
def reverse_complement(seq):
@@ -448,7 +450,7 @@ def extract_reads_and_pairs(chr_dic, sam_filename, read_filename, pair_filename,
NM = XM + gap
if hisat2:
XM, NM = HISAT2_XM, HISAT2_NM
- if NM < 10:
+ if NM < MAX_EDIT:
print >> temp_read_file, "%s\t%d\t%s\t%s\t%s\tXM:i:%d\tNM:i:%d" % \
(read_id, flag, chr, pos, cigar_str, XM, NM)
@@ -522,9 +524,9 @@ def remove_redundant_junctions(junctions):
def read_stat(read_filename, gtf_junctions, chr_dic = None, debug = False):
- read_stat = [[0, 0, 0] for i in range(10)]
- temp_junctions = [set() for i in range(10)]
- temp_gtf_junctions = [set() for i in range(10)]
+ read_stat = [[0, 0, 0] for i in range(MAX_EDIT)]
+ temp_junctions = [set() for i in range(MAX_EDIT)]
+ temp_gtf_junctions = [set() for i in range(MAX_EDIT)]
alignment = []
prev_read_id = ""
@@ -592,10 +594,10 @@ def read_stat(read_filename, gtf_junctions, chr_dic = None, debug = False):
def pair_stat(pair_filename, gtf_junctions, chr_dic):
- pair_stat = [[0, 0, 0] for i in range(10)]
- dis_pair_stat = [0 for i in range(10)]
- temp_junctions = [set() for i in range(10)]
- temp_gtf_junctions = [set() for i in range(10)]
+ pair_stat = [[0, 0, 0] for i in range(MAX_EDIT)]
+ dis_pair_stat = [0 for i in range(MAX_EDIT)]
+ temp_junctions = [set() for i in range(MAX_EDIT)]
+ temp_gtf_junctions = [set() for i in range(MAX_EDIT)]
alignment, dis_alignments = [], []
prev_read_id = ""
@@ -745,7 +747,7 @@ def write_analysis_data(sql_db, database_name, paired):
print >> database_file, "aligner\tuse_annotation\tend_type\tedit_distance\tmapped_reads\tjunction_reads\tgtf_junction_reads\tjunctions\tgtf_junctions\truntime"
for aligner in aligners:
- for edit_distance in range(10):
+ for edit_distance in range(MAX_EDIT):
sql_row = "SELECT aligner, use_annotation, end_type, edit_distance, mapped_reads, junction_reads, gtf_junction_reads, junctions, gtf_junctions, runtime FROM Mappings"
sql_row += " WHERE reads = '%s' and aligner = '%s' and edit_distance = %d and end_type = '%s' ORDER BY created DESC LIMIT 1" % (database_name, aligner, edit_distance, paired)
output = sql_execute(sql_db, sql_row)
@@ -786,7 +788,8 @@ def calculate_read_cost():
["star", "x2", "", ""],
["gsnap", "", "", ""],
["bowtie", "", "", ""],
- ["bowtie2", "", "", ""]
+ ["bowtie2", "", "", ""],
+ ["bwa", "", "", ""]
]
is_large_file = False
assert os.path.exists("1.fq")
@@ -794,11 +797,13 @@ def calculate_read_cost():
is_large_file = True
aligners = [
- ["hisat", "", "", ""],
- ["hisat2", "", "", ""],
+ # ["hisat", "", "", ""],
+ # ["hisat2", "", "", ""],
# ["hisat2", "", "snp", ""],
# ["hisat2", "", "tran", ""],
- ["hisat2", "x1", "snp_tran", ""],
+ ["hisat2", "x1", "snp", ""],
+ ["bwa", "mem", "", ""],
+ # ["bwa", "sw", "", ""],
# ["hisat", "", "", ""],
# ["star", "", "", ""],
# ["star", "x2", "", ""],
@@ -862,7 +867,12 @@ def get_aligner_version(aligner):
cmd_process = subprocess.Popen(cmd, stderr=subprocess.PIPE)
version = cmd_process.communicate()[1][:-1].split("\n")[0]
version = version.split()[2]
-
+ elif aligner == "bwa":
+ cmd = ["%s/bwa" % (aligner_bin_base)]
+ cmd_process = subprocess.Popen(cmd, stderr=subprocess.PIPE)
+ version = cmd_process.communicate()[1][:-1].split("\n")[2]
+ version = version.split()[1]
+
return version
index_base = "../../../../indexes"
@@ -878,6 +888,9 @@ def get_aligner_cmd(RNA, aligner, type, index_type, version, read1_fname, read2_
# cmd += ["-k", "5"]
# cmd += ["--score-min", "C,-18"]
+
+ # daehwan - for debugging purposes
+ # cmd += ["--score-min", "C,-50"]
if version != "":
version = int(version)
@@ -1037,17 +1050,29 @@ def get_aligner_cmd(RNA, aligner, type, index_type, version, read1_fname, read2_
read1_fname]
if paired:
cmd += [read2_fname]
+ elif aligner == "bwa":
+ cmd = ["%s/bwa" % (aligner_bin_base)]
+ if type in ["mem", "aln"]:
+ cmd += [type]
+ elif type == "sw":
+ cmd += ["bwa" + type]
+ if num_threads > 1:
+ cmd += ["-t", str(num_threads)]
+ cmd += ["%s/BWA%s/%s.fa" % (index_base, index_add, genome)]
+ cmd += [read1_fname]
+ if paired:
+ cmd += [read2_fname]
else:
assert False
return cmd
- init_time = {"hisat2" : 0.0, "hisat" : 0.0, "bowtie" : 0.0, "bowtie2" : 0.0, "star" : 0.0, "olego" : 0.0, "gsnap" : 0.0, "tophat2" : 0.0}
+ init_time = {"hisat2" : 0.0, "hisat" : 0.0, "bowtie" : 0.0, "bowtie2" : 0.0, "star" : 0.0, "olego" : 0.0, "gsnap" : 0.0, "tophat2" : 0.0, "bwa" : 0.0}
if not is_large_file:
if desktop:
- init_time = {"hisat2" : 3.0, "hisat" : 3.0, "bowtie" : 1.3, "bowtie2" : 1.9, "star" : 27.0, "gsnap" : 12}
+ init_time = {"hisat2" : 3.0, "hisat" : 3.0, "bowtie" : 1.3, "bowtie2" : 1.9, "star" : 27.0, "gsnap" : 1, "bwa" : 1.3}
else:
- init_time = {"hisat2" : 9.5, "hisat" : 9.5, "bowtie" : 3.3, "bowtie2" : 4.1, "star" : 1.7, "gsnap" : 0.1}
+ init_time = {"hisat2" : 9.5, "hisat" : 9.5, "bowtie" : 3.3, "bowtie2" : 4.1, "star" : 1.7, "gsnap" : 0.1, "bwa" : 3.3}
init_time["tophat2"] = 0.0
for aligner, type, index_type, version in aligners:
@@ -1077,7 +1102,7 @@ def get_aligner_cmd(RNA, aligner, type, index_type, version, read1_fname, read2_
start_time = datetime.now()
if verbose:
print >> sys.stderr, start_time, "\t", " ".join(dummy_cmd)
- if aligner in ["hisat2", "hisat", "bowtie", "bowtie2", "gsnap"]:
+ if aligner in ["hisat2", "hisat", "bowtie", "bowtie2", "gsnap", "bwa"]:
proc = subprocess.Popen(dummy_cmd, stdout=open("/dev/null", "w"), stderr=subprocess.PIPE)
else:
proc = subprocess.Popen(dummy_cmd, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
@@ -1105,7 +1130,7 @@ def get_aligner_cmd(RNA, aligner, type, index_type, version, read1_fname, read2_
start_time = datetime.now()
if verbose:
print >> sys.stderr, start_time, "\t", " ".join(aligner_cmd)
- if aligner in ["hisat2", "hisat", "bowtie", "bowtie2", "gsnap"]:
+ if aligner in ["hisat2", "hisat", "bowtie", "bowtie2", "gsnap", "bwa"]:
proc = subprocess.Popen(aligner_cmd, stdout=open(out_fname, "w"), stderr=subprocess.PIPE)
else:
proc = subprocess.Popen(aligner_cmd, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
diff --git a/evaluation/tests/parallel/bowtie2/bowtie2.xcodeproj/project.pbxproj b/evaluation/tests/parallel/bowtie2/bowtie2.xcodeproj/project.pbxproj
new file mode 100644
index 00000000..1b3ebfb8
--- /dev/null
+++ b/evaluation/tests/parallel/bowtie2/bowtie2.xcodeproj/project.pbxproj
@@ -0,0 +1,557 @@
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diff --git a/evaluation/tests/parallel/bowtie2/bowtie2.xcodeproj/project.xcworkspace/contents.xcworkspacedata b/evaluation/tests/parallel/bowtie2/bowtie2.xcodeproj/project.xcworkspace/contents.xcworkspacedata
new file mode 100644
index 00000000..2a2a8ccc
--- /dev/null
+++ b/evaluation/tests/parallel/bowtie2/bowtie2.xcodeproj/project.xcworkspace/contents.xcworkspacedata
@@ -0,0 +1,7 @@
+
+
+
+
+
diff --git a/evaluation/tests/parallel/bowtie2/bowtie2.xcodeproj/project.xcworkspace/xcuserdata/infphilo.xcuserdatad/UserInterfaceState.xcuserstate b/evaluation/tests/parallel/bowtie2/bowtie2.xcodeproj/project.xcworkspace/xcuserdata/infphilo.xcuserdatad/UserInterfaceState.xcuserstate
new file mode 100644
index 00000000..239218c6
Binary files /dev/null and b/evaluation/tests/parallel/bowtie2/bowtie2.xcodeproj/project.xcworkspace/xcuserdata/infphilo.xcuserdatad/UserInterfaceState.xcuserstate differ
diff --git a/evaluation/tests/parallel/bowtie2/bowtie2.xcodeproj/xcuserdata/infphilo.xcuserdatad/xcschemes/xcschememanagement.plist b/evaluation/tests/parallel/bowtie2/bowtie2.xcodeproj/xcuserdata/infphilo.xcuserdatad/xcschemes/xcschememanagement.plist
new file mode 100644
index 00000000..957bfbda
--- /dev/null
+++ b/evaluation/tests/parallel/bowtie2/bowtie2.xcodeproj/xcuserdata/infphilo.xcuserdatad/xcschemes/xcschememanagement.plist
@@ -0,0 +1,22 @@
+
+
+
+
+ SchemeUserState
+
+ bowtie2-buildlx.xcscheme
+
+ orderHint
+ 0
+
+
+ SuppressBuildableAutocreation
+
+ E8E6B3FA1C24B8F500C9D7F1
+
+ primary
+
+
+
+
+
diff --git a/gbwt_graph.h b/gbwt_graph.h
index cc708702..3d8623a8 100644
--- a/gbwt_graph.h
+++ b/gbwt_graph.h
@@ -134,11 +134,11 @@ class RefGraph {
cerr << "Could not open file for writing a reference graph: \"" << fname << "\"" << endl;
throw 1;
}
- writeIndex(rg_file, nodes.size(), bigEndian);
+ writeIndex(rg_file, (index_t)nodes.size(), bigEndian);
for(index_t i = 0; i < nodes.size(); i++) {
nodes[i].write(rg_file, bigEndian);
}
- writeIndex(rg_file, edges.size(), bigEndian);
+ writeIndex(rg_file, (index_t)edges.size(), bigEndian);
for(index_t i = 0; i < edges.size(); i++) {
edges[i].write(rg_file, bigEndian);
}
@@ -260,7 +260,7 @@ class RefGraph {
index_t size() const {
if(id == (index_t)INDEX_MAX) return 0;
- return add_ids.size() + 1;
+ return (index_t)add_ids.size() + 1;
}
index_t getID(index_t i) const {
if(i == 0) return id;
@@ -354,7 +354,7 @@ RefGraph::RefGraph(const SString& s,
assert_gt(nthreads, 0);
assert_gt(szs.size(), 0);
- index_t jlen = s.length();
+ index_t jlen = (index_t)s.length();
#ifndef NDEBUG
debug = (jlen <= 20);
@@ -461,8 +461,8 @@ RefGraph::RefGraph(const SString& s,
#endif
}
- if((size_t)nthreads > tmp_szs.size()) {
- nthreads = tmp_szs.size();
+ if(nthreads > (int)tmp_szs.size()) {
+ nthreads = (int)tmp_szs.size();
}
assert_gt(nthreads, 0);
AutoArray threads(nthreads);
@@ -515,8 +515,8 @@ RefGraph::RefGraph(const SString& s,
cerr << "Could not open file for reading a reference graph: \"" << rg_fname << "\"" << endl;
throw 1;
}
- index_t curr_num_nodes = nodes.size();
- ASSERT_ONLY(index_t curr_num_edges = edges.size());
+ index_t curr_num_nodes = (index_t)nodes.size();
+ ASSERT_ONLY(index_t curr_num_edges = (index_t)edges.size());
ASSERT_ONLY(index_t num_spanning_edges = 0);
// Read nodes to be connected to last nodes in a previous thread
if(i > 0) {
@@ -590,22 +590,22 @@ RefGraph::RefGraph(const SString& s,
for(size_t i = 0; i < s.length(); i++) {
nodes.expand();
nodes.back().label = "ACGT"[(int)s[i]];
- nodes.back().value = i;
+ nodes.back().value = (index_t)i;
assert_geq(nodes.size(), 2);
edges.expand();
- edges.back().from = nodes.size() - 2;
- edges.back().to = nodes.size() - 1;
+ edges.back().from = (index_t)nodes.size() - 2;
+ edges.back().to = (index_t)nodes.size() - 1;
}
// Create tail node
nodes.expand();
nodes.back().label = 'Z';
- nodes.back().value = s.length();
- lastNode = nodes.size() - 1;
+ nodes.back().value = (index_t)s.length();
+ lastNode = (index_t)nodes.size() - 1;
edges.expand();
- edges.back().from = nodes.size() - 2;
- edges.back().to = nodes.size() - 1;
+ edges.back().from = (index_t)nodes.size() - 2;
+ edges.back().to = (index_t)nodes.size() - 1;
// Create nodes and edges for SNPs
for(size_t i = 0; i < alts.size(); i++) {
@@ -620,9 +620,9 @@ RefGraph::RefGraph(const SString& s,
nodes.back().value = alt.pos;
edges.expand();
edges.back().from = alt.pos;
- edges.back().to = nodes.size() - 1;
+ edges.back().to = (index_t)nodes.size() - 1;
edges.expand();
- edges.back().from = nodes.size() - 1;
+ edges.back().from = (index_t)nodes.size() - 1;
edges.back().to = alt.pos + 2;
}
else if(alt.type == ALT_SNP_DEL) {
@@ -641,11 +641,11 @@ RefGraph::RefGraph(const SString& s,
nodes.back().label = ch;
nodes.back().value = (index_t)INDEX_MAX;
edges.expand();
- edges.back().from = (j == 0 ? alt.pos : nodes.size() - 2);
- edges.back().to = nodes.size() - 1;
+ edges.back().from = (j == 0 ? alt.pos : (index_t)nodes.size() - 2);
+ edges.back().to = (index_t)nodes.size() - 1;
}
edges.expand();
- edges.back().from = nodes.size() - 1;
+ edges.back().from = (index_t)nodes.size() - 1;
edges.back().to = alt.pos + 1;
} else if(alt.type == ALT_SPLICESITE) {
if(alt.excluded) continue;
@@ -689,7 +689,7 @@ pair RefGraph::findEdges(const EList& edges, in
assert_gt(edges.size(), 0);
// Find lower bound
- index_t low = 0, high = edges.size() - 1;
+ index_t low = 0, high = (index_t)edges.size() - 1;
index_t temp;
while(low < high) {
index_t mid = low + (high - low) / 2;
@@ -714,7 +714,7 @@ pair RefGraph::findEdges(const EList& edges, in
}
// Find upper bound
- high = edges.size() - 1;
+ high = (index_t)edges.size() - 1;
while(low < high)
{
index_t mid = low + (high - low + 1) / 2;
@@ -740,7 +740,7 @@ void RefGraph::buildGraph_worker(void* vp) {
RefGraph& refGraph = *(threadParam->refGraph);
const SString& s = *(threadParam->s);
- index_t jlen = s.length();
+ index_t jlen = (index_t)s.length();
const EList >& alts = *(threadParam->alts);
@@ -763,12 +763,12 @@ void RefGraph::buildGraph_worker(void* vp) {
index_t& num_nodes = threadParam->num_nodes;
index_t& num_edges = threadParam->num_edges;
- index_t szs_idx = 0, szs_idx_end = tmp_szs.size();
+ index_t szs_idx = 0, szs_idx_end = (index_t)tmp_szs.size();
if(threadParam->thread_id != 0) {
- szs_idx = (tmp_szs.size() / nthreads) * thread_id;
+ szs_idx = (index_t)((tmp_szs.size() / nthreads) * thread_id);
}
if(thread_id + 1 < nthreads) {
- szs_idx_end = (tmp_szs.size() / nthreads) * (thread_id + 1);
+ szs_idx_end = (index_t)((tmp_szs.size() / nthreads) * (thread_id + 1));
}
index_t curr_pos = 0;
@@ -794,22 +794,22 @@ void RefGraph::buildGraph_worker(void* vp) {
for(size_t i = curr_pos; i < curr_pos + curr_len; i++) {
nodes.expand();
nodes.back().label = "ACGT"[(int)s[i]];
- nodes.back().value = i;
+ nodes.back().value = (index_t)i;
assert_geq(nodes.size(), 2);
edges.expand();
- edges.back().from = nodes.size() - 2;
- edges.back().to = nodes.size() - 1;
+ edges.back().from = (index_t)nodes.size() - 2;
+ edges.back().to = (index_t)nodes.size() - 1;
}
// Create tail node
nodes.expand();
nodes.back().label = 'Z';
- nodes.back().value = s.length();
- lastNode = nodes.size() - 1;
+ nodes.back().value = (index_t)s.length();
+ lastNode = (index_t)nodes.size() - 1;
edges.expand();
- edges.back().from = nodes.size() - 2;
- edges.back().to = nodes.size() - 1;
- ASSERT_ONLY(index_t backbone_nodes = nodes.size());
+ edges.back().from = (index_t)nodes.size() - 2;
+ edges.back().to = (index_t)nodes.size() - 1;
+ ASSERT_ONLY(index_t backbone_nodes = (index_t)nodes.size());
// Create nodes and edges for SNPs
for(; alt_idx < alts.size(); alt_idx++) {
const ALT& alt = alts[alt_idx];
@@ -825,10 +825,10 @@ void RefGraph::buildGraph_worker(void* vp) {
nodes.back().value = alt.pos;
edges.expand();
edges.back().from = alt.pos - curr_pos;
- edges.back().to = nodes.size() - 1;
+ edges.back().to = (index_t)nodes.size() - 1;
assert_lt(edges.back().from, backbone_nodes);
edges.expand();
- edges.back().from = nodes.size() - 1;
+ edges.back().from = (index_t)nodes.size() - 1;
edges.back().to = alt.pos - curr_pos + 2;
assert_lt(edges.back().to, backbone_nodes);
} else if(alt.type == ALT_SNP_DEL) {
@@ -848,11 +848,11 @@ void RefGraph::buildGraph_worker(void* vp) {
nodes.back().label = ch;
nodes.back().value = (index_t)INDEX_MAX;
edges.expand();
- edges.back().from = (j == 0 ? alt.pos - curr_pos : nodes.size() - 2);
- edges.back().to = nodes.size() - 1;
+ edges.back().from = (j == 0 ? alt.pos - curr_pos : (index_t)nodes.size() - 2);
+ edges.back().to = (index_t)nodes.size() - 1;
}
edges.expand();
- edges.back().from = nodes.size() - 1;
+ edges.back().from = (index_t)nodes.size() - 1;
edges.back().to = alt.pos - curr_pos + 1;
} else if(alt.type == ALT_SPLICESITE) {
if(alt.excluded) continue;
@@ -891,7 +891,7 @@ void RefGraph::buildGraph_worker(void* vp) {
}
// Identify head
- index_t head_node = nodes.size();
+ index_t head_node = (index_t)nodes.size();
for(index_t i = 0; i < nodes.size(); i++) {
if(nodes[i].label == 'Y') {
head_node = i;
@@ -934,7 +934,7 @@ void RefGraph::buildGraph_worker(void* vp) {
// Connect head nodes with tail nodes in the previous automaton
index_t num_head_nodes = 0;
- index_t tmp_num_edges = edges.size();
+ index_t tmp_num_edges = (index_t)edges.size();
if(head_off) {
EList nodes_to_head;
for(index_t i = 0; i < tmp_num_edges; i++) {
@@ -956,7 +956,7 @@ void RefGraph::buildGraph_worker(void* vp) {
if(nodes_to_head.size() > 0) {
assert_gt(thread_id, 0);
assert_eq(prev_tail_nodes.size(), 0);
- writeIndex(rg_out_file, nodes_to_head.size(), bigEndian);
+ writeIndex(rg_out_file, (index_t)nodes_to_head.size(), bigEndian);
for(index_t i = 0; i < nodes_to_head.size(); i++) {
writeIndex(rg_out_file, nodes_to_head[i], bigEndian);
}
@@ -979,7 +979,7 @@ void RefGraph::buildGraph_worker(void* vp) {
}
// Write nodes and edges
- index_t tmp_num_nodes = nodes.size();
+ index_t tmp_num_nodes = (index_t)nodes.size();
assert_gt(tmp_num_nodes, 2);
if(head_off) tmp_num_nodes--;
if(tail_off) tmp_num_nodes--;
@@ -992,7 +992,7 @@ void RefGraph::buildGraph_worker(void* vp) {
ASSERT_ONLY(num_nodes_written++);
}
assert_eq(tmp_num_nodes, num_nodes_written);
- tmp_num_edges = edges.size();
+ tmp_num_edges = (index_t)edges.size();
assert_gt(tmp_num_edges, num_head_nodes + prev_tail_nodes.size());
if(head_off) tmp_num_edges -= num_head_nodes;
if(tail_off) tmp_num_edges -= prev_tail_nodes.size();
@@ -1015,7 +1015,7 @@ void RefGraph::buildGraph_worker(void* vp) {
}
if(nthreads > 1 && thread_id + 1 < (index_t)nthreads && prev_tail_nodes.size() > 0) {
- writeIndex(rg_out_file, prev_tail_nodes.size(), bigEndian);
+ writeIndex(rg_out_file, (index_t)prev_tail_nodes.size(), bigEndian);
for(index_t i = 0; i < prev_tail_nodes.size(); i++) {
writeIndex(rg_out_file, prev_tail_nodes[i], bigEndian);
}
@@ -1086,7 +1086,7 @@ void RefGraph::reverseDeterminize(EList |