fix the spamming warning due to the missing reads from split read bas…

…ecalling
hasindu2008 · Aug 9, 2024 · 1935adb · 1935adb
1 parent 3c03d2d
commit 1935adb
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Showing 4 changed files with 31 additions and 5 deletions.
diff --git a/src/f5c.c b/src/f5c.c
@@ -247,6 +247,7 @@ core_t* init_core(const char* bamfilename, const char* fastafile,
  STDERR("Error in loading SLOW5 index for %s\n",slow5file);
  exit(EXIT_FAILURE);
  }
+ slow5_set_skip_rid();
 
  if(drna_detect(core->sf)) {
  opt.flag |= F5C_RNA;

diff --git a/src/f5cio.c b/src/f5cio.c
@@ -433,9 +433,10 @@ void read_slow5_single(core_t* core, db_t* db, int i){
 
 
  if(record==NULL || len <0){ //todo : should we free if len<0
- db->bad_fast5_file++;
+ //db->bad_fast5_file++;
+ __sync_fetch_and_add(&db->bad_fast5_file,1);
  if (core->opt.flag & F5C_SKIP_UNREADABLE) {
- WARNING("Slow5 record for read [%s] is unavailable/unreadable and will be skipped", qname.c_str());
+ //WARNING("Slow5 record for read [%s] is unavailable/unreadable and will be skipped", qname.c_str());
  db->sig[i]->nsample = 0;
  db->sig[i]->rawptr = NULL;
  } else {

diff --git a/src/meth_main.c b/src/meth_main.c
@@ -826,7 +826,17 @@ int meth_main(int argc, char* argv[], int8_t mode) {
  if(core->qc_fail_reads + core->failed_calibration_reads + core->failed_alignment_reads > core->total_reads/2){
  WARNING("%ld out of %ld reads failed. Double check --pore and --rna options.",(long)core->qc_fail_reads + core->failed_calibration_reads + core->failed_alignment_reads,(long)core->total_reads);
  }
-
+ if(core->bad_fast5_file > core->total_reads/10.0){
+ WARNING("%ld out of %ld reads missing in FAST5/SLOW5.",(long)core->bad_fast5_file,(long)core->total_reads);
+ }
+ if(core->qc_fail_reads + core->failed_calibration_reads + core->failed_alignment_reads + core->bad_fast5_file >= core->total_reads){
+ ERROR("all %ld out of %ld reads failed. Check the input files.",(long)core->total_reads,(long)core->total_reads);
+ exit(EXIT_FAILURE);
+ }
+ if(core->total_reads==0){
+ ERROR("%s","0 reads processed. Check the input files.");
+ exit(EXIT_FAILURE);
+ }
  //free the core data structure
  free_core(core,opt);
 

diff --git a/src/resquiggle.c b/src/resquiggle.c
@@ -95,6 +95,7 @@ core_t* init_core_rsq(opt_t opt, const char *slow5file, double realtime0) {
  STDERR("Error in loading SLOW5 index for %s\n",slow5file);
  exit(EXIT_FAILURE);
  }
+ slow5_set_skip_rid();
  if(drna_detect(core->sf)) {
  core->opt.flag |= F5C_RNA;
  opt.flag |= F5C_RNA;
@@ -483,9 +484,10 @@ static void read_slow5_single(core_t* core, db_t* db, int i){
  MALLOC_CHK(db->sig[i]);
 
  if(record==NULL || len <0){ //todo : should we free if len<0
- db->bad_fast5_file++;
+ __sync_fetch_and_add(&db->bad_fast5_file,1);
+ //db->bad_fast5_file++;
  if (core->opt.flag & F5C_SKIP_UNREADABLE) {
- WARNING("Slow5 record for read [%s] is unavailable/unreadable and will be skipped", db->read_id[i]);
+ //WARNING("Slow5 record for read [%s] is unavailable/unreadable and will be skipped", db->read_id[i]);
  db->sig[i]->nsample = 0;
  db->sig[i]->rawptr = NULL;
  } else {
@@ -785,9 +787,21 @@ int resquiggle_main(int argc, char **argv) {
 
  fprintf(stderr,"\n");
 
+ //todo duplicate code from meth_main.c - can be modularised
  if(core->qc_fail_reads + core->failed_calibration_reads + core->failed_alignment_reads > core->total_reads/2){
  WARNING("%ld out of %ld reads failed. Double check --pore and --rna options.",(long)core->qc_fail_reads + core->failed_calibration_reads + core->failed_alignment_reads,(long)core->total_reads);
  }
+ if(core->bad_fast5_file > core->total_reads/10.0){
+ WARNING("%ld out of %ld reads missing in SLOW5.",(long)core->bad_fast5_file,(long)core->total_reads);
+ }
+ if(core->qc_fail_reads + core->failed_calibration_reads + core->failed_alignment_reads + core->bad_fast5_file >= core->total_reads){
+ ERROR("all %ld out of %ld reads failed. Check the input files.",(long)core->total_reads,(long)core->total_reads);
+ exit(EXIT_FAILURE);
+ }
+ if(core->total_reads==0){
+ ERROR("%s","0 reads processed. Check the input files.");
+ exit(EXIT_FAILURE);
+ }
 
  kseq_destroy(seq);
  gzclose(fp);