profile: early quick when no target detected

CHANGELOG.md

@@ -4,6 +4,7 @@
 
 - `kmcp profile`:
  - fix log of "xx% (yy/zz) reads matched", the numerator should be the number of matched reads instead of reads belonging to references.
+ - early quick when no target detected.
 
 ### v0.9.3 - 2023-07-16
 

docs/tutorial/profiling/index.md

@@ -44,9 +44,14 @@ Mapping and removing mapped reads:
 
  index=~/ws/db/bowtie2/chm13v2.0
 
+ # paired-end reads
  bowtie2 --threads 32 -x $index -1 in_1.fq.gz -2 in_2.fq.gz \
   | samtools fastq -f 4 -o sample.fq.gz -
 
+ # unpaired reads
+ bowtie2 --threads 32 -x $index -U in.fq.gz \
+  | samtools fastq -f 4 | pigz -c > sample.fq.gz
+
 ### Step 3. Searching
 
 **Reads can be searched against multiple databases which can be built with different parameters**,

kmcp/cmd/profile.go

@@ -1100,6 +1100,12 @@ Examples:
 
  if opt.Verbose || opt.Log2File {
  log.Infof(" number of estimated references: %d", len(profile))
+ }
+ if len(profile) == 0 {
+ log.Warningf(" no target found, please adjust parameters")
+ return
+ }
+ if opt.Verbose || opt.Log2File {
  if len(profile) >= 1000 && !noAmbCorr {
  log.Warningf(" too many candidates detected, the next stage would be very slow")
  log.Warningf(" the flag --no-amb-corr is recommended to disable ambiguous reads correction which has very little effect on the results")
@@ -1887,6 +1893,12 @@ Examples:
 
  if opt.Verbose || opt.Log2File {
  log.Infof(" number of estimated references: %d", len(profile2))
+ }
+ if len(profile) == 0 {
+ log.Warningf(" no target found, please adjust parameters")
+ return
+ }
+ if opt.Verbose || opt.Log2File {
  log.Infof(" elapsed time: %s", time.Since(timeStart1))
  log.Info()
  }
@@ -2559,6 +2571,12 @@ Examples:
 
  if opt.Verbose || opt.Log2File {
  log.Infof(" number of estimated references: %d", len(targets))
+ }
+ if len(profile) == 0 {
+ log.Warningf(" no target found, please adjust parameters")
+ return
+ }
+ if opt.Verbose || opt.Log2File {
  log.Infof(" elapsed time: %s", time.Since(timeStart1))
  log.Info()
  if total > 0 {