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r199: renamed pre.ovlp.bin to pre.ec.bin

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Also updated the Makefile dependencies
This commit is contained in:
Heng Li
2020-04-05 13:45:50 -04:00
parent 0f1994fc1f
commit 46f83e152d
3 changed files with 44 additions and 13 deletions
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CommandLines.h
+1 -1
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@@ -3,7 +3,7 @@
#include <pthread.h>
#define HA_VERSION "0.3.0-dirty-r198"
#define HA_VERSION "0.3.0-dirty-r199"
#define VERBOSE 0
Makefile
+32
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@@ -31,3 +31,35 @@ depend:
(LC_ALL=C; export LC_ALL; makedepend -Y -- $(CPPFLAGS) $(DFLAGS) -- *.cpp)
# DO NOT DELETE
Assembly.o: Assembly.h CommandLines.h Process_Read.h Overlaps.h kvec.h kdq.h
Assembly.o: Hash_Table.h htab.h POA.h Correct.h Levenshtein_distance.h
Assembly.o: Output.h
CommandLines.o: CommandLines.h ketopt.h
Correct.o: Correct.h Hash_Table.h htab.h Process_Read.h Overlaps.h kvec.h
Correct.o: kdq.h CommandLines.h Levenshtein_distance.h POA.h Assembly.h
Hash_Table.o: Hash_Table.h htab.h Process_Read.h Overlaps.h kvec.h kdq.h
Hash_Table.o: CommandLines.h Correct.h Levenshtein_distance.h POA.h ksort.h
Levenshtein_distance.o: Levenshtein_distance.h
Output.o: Output.h CommandLines.h
Overlaps.o: Overlaps.h kvec.h kdq.h ksort.h Process_Read.h CommandLines.h
Overlaps.o: Hash_Table.h htab.h Correct.h Levenshtein_distance.h POA.h
Overlaps.o: Purge_Dups.h
POA.o: POA.h Hash_Table.h htab.h Process_Read.h Overlaps.h kvec.h kdq.h
POA.o: CommandLines.h Correct.h Levenshtein_distance.h
Process_Read.o: Process_Read.h Overlaps.h kvec.h kdq.h CommandLines.h
Purge_Dups.o: ksort.h Purge_Dups.h kvec.h kdq.h Overlaps.h Hash_Table.h
Purge_Dups.o: htab.h Process_Read.h CommandLines.h Correct.h
Purge_Dups.o: Levenshtein_distance.h POA.h
Trio.o: khashl.h kthread.h Process_Read.h Overlaps.h kvec.h kdq.h
Trio.o: CommandLines.h htab.h
anchor.o: htab.h Process_Read.h Overlaps.h kvec.h kdq.h CommandLines.h
anchor.o: ksort.h Hash_Table.h
hist.o: htab.h Process_Read.h Overlaps.h kvec.h kdq.h CommandLines.h
htab.o: kthread.h khashl.h kseq.h ksort.h htab.h Process_Read.h Overlaps.h
htab.o: kvec.h kdq.h CommandLines.h
kthread.o: kthread.h
main.o: CommandLines.h Process_Read.h Overlaps.h kvec.h kdq.h Assembly.h
main.o: Levenshtein_distance.h htab.h
sketch.o: kvec.h htab.h Process_Read.h Overlaps.h kdq.h CommandLines.h
sys.o: htab.h Process_Read.h Overlaps.h kvec.h kdq.h CommandLines.h
Overlaps.cpp
+11 -12
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@@ -13688,26 +13688,25 @@ void write_ma_hit_ts(ma_hit_t_alloc* x, long long n_read, char* read_file_name)
fprintf(stderr, "ma_hit_ts has been written.\n");
}
void write_all_data_to_disk(ma_hit_t_alloc* sources, ma_hit_t_alloc* reverse_sources,
All_reads *RNF, char* output_file_name)
void write_all_data_to_disk(ma_hit_t_alloc* sources, ma_hit_t_alloc* reverse_sources, All_reads *RNF, char* output_file_name)
{
char* gfa_name = (char*)malloc(strlen(output_file_name)+25);
sprintf(gfa_name, "%s.ovlp", output_file_name);
write_All_reads(RNF, gfa_name);
sprintf(gfa_name, "%s.ovlp.source", output_file_name);
write_ma_hit_ts(sources, RNF->total_reads, gfa_name);
char* gfa_name = (char*)malloc(strlen(output_file_name)+25);
sprintf(gfa_name, "%s.ec", output_file_name);
write_All_reads(RNF, gfa_name);
sprintf(gfa_name, "%s.ovlp.reverse", output_file_name);
write_ma_hit_ts(reverse_sources, RNF->total_reads, gfa_name);
sprintf(gfa_name, "%s.ovlp.source", output_file_name);
write_ma_hit_ts(sources, RNF->total_reads, gfa_name);
free(gfa_name);
sprintf(gfa_name, "%s.ovlp.reverse", output_file_name);
write_ma_hit_ts(reverse_sources, RNF->total_reads, gfa_name);
free(gfa_name);
}
int load_all_data_from_disk(ma_hit_t_alloc **sources, ma_hit_t_alloc **reverse_sources, char* output_file_name)
{
char* gfa_name = (char*)malloc(strlen(output_file_name)+25);
sprintf(gfa_name, "%s.ovlp", output_file_name);
sprintf(gfa_name, "%s.ec", output_file_name);
if (!load_All_reads(&R_INF, gfa_name)) {
free(gfa_name);
return 0;