do not throw error if input paired end files are empty when doing --detect-adapter.

Author: cihga39871

CHANGELOG.md

@@ -5,6 +5,10 @@
 - Feature: multiple primer trimming.
 - Feature: UMI trimming.
 
+## v4.1.2
+
+- Fix: do not throw error if input paired end files are empty when doing `--detect-adapter`.
+
 ## v4.1.1
 
 - Fix: `-z NUM -Z NUM` error when length to trim < 0.

Project.toml

@@ -1,7 +1,7 @@
 name = "Atria"
 uuid = "226cbef3-b485-431c-85c2-d8bd8da14025"
 authors = ["Jiacheng Chuan <jiacheng_chuan@outlook.com>"]
-version = "4.1.1"
+version = "4.1.2"
 
 [deps]
 ArgParse = "c7e460c6-2fb9-53a9-8c5b-16f535851c63"

src/FqRecords/thread_input.jl

@@ -92,7 +92,10 @@ function load_fqs_threads!(
     n_r2 = append_loop!(r2s, vr2s, tasks2; remove_first_n=n_remove_r2)
     # @info "load_fqs_threads! StringChunk2FqRecord! - stop - R2"
 
-    (n_r1 == 0 || n_r2 == 0) && throw(error("Numbers of reads in R1 and R2 not the same!"))
+    if n_r1 == n_r2 == 0  # input r1.fastq and r2.fastq are empty (no reads)
+    elseif n_r1 == 0 || n_r2 == 0
+        throw(error("Numbers of reads in R1 and R2 not the same!"))
+    end
 
     return n_r1, n_r2, r1s, r2s, ncopyed
 end
@@ -280,7 +283,10 @@ function load_fqs_threads!(
 
     n_r2 = FqRecords.append_loop!(r2s, vr2s, tasks2; remove_first_n=n_remove_r2)
 
-    (n_r1 == 0 || n_r2 == 0) && throw(error("Numbers of reads in R1 and R2 not the same!"))
+    if n_r1 == n_r2 == 0  # input r1.fastq and r2.fastq are empty (no reads)
+    elseif n_r1 == 0 || n_r2 == 0
+        throw(error("Numbers of reads in R1 and R2 not the same!"))
+    end
 
     return n_r1, n_r2, r1s, r2s, in1bytes_nremain, in2bytes_nremain, ncopyed
 end
@@ -446,6 +452,10 @@ Return (chunk_size1, chunk_size2):Tuple{Int,Int}
     n_r1_read = n_r1 - n_r1_before
     n_r2_read = n_r2 - n_r2_before
 
+    if n_r1_read == n_r2_read == 0  # input r1.fastq and r2.fastq are empty (no reads)
+        return length(in1bytes), length(in2bytes)
+    end
+
     avg_length_r1 = length(in1bytes) / n_r1_read
     avg_length_r2 = length(in2bytes) / n_r2_read