From feba306a22c9c2944c286d5cbd2a336ce8852a8d Mon Sep 17 00:00:00 2001
From: Mark Chernyshev <mark26111@gmail.com>
Date: Thu, 24 Oct 2024 16:14:04 +0200
Subject: [PATCH] fixed IgBLAST startup error handling. No longer hangs.

---
 README.md  |  2 +-
 src/run.jl | 21 +++++++++++----------
 2 files changed, 12 insertions(+), 11 deletions(-)

diff --git a/README.md b/README.md
index 2039f80..134b282 100644
--- a/README.md
+++ b/README.md
@@ -38,7 +38,7 @@ run_igblast(
     "data/Macaca_mulatta_J.fasta",
     "data/rhesus_monkey_gl.aux",
     "ERR4238106.tsv",
-    additional_params = Dict("organism" => "rhesus_monkey", "ig_seqtype" => "ig")
+    additional_params = Dict("organism" => "rhesus_monkey", "ig_seqtype" => "Ig")
 )
 ```
 
diff --git a/src/run.jl b/src/run.jl
index 2506259..b63cfa0 100644
--- a/src/run.jl
+++ b/src/run.jl
@@ -1,9 +1,9 @@
 """
     run_igblast(
         igblast_type::Type{T},
-        query_file::String, 
-        v_database::String, 
-        d_database::String, 
+        query_file::String,
+        v_database::String,
+        d_database::String,
         j_database::String,
         aux_file::String,
         output_file::String,
@@ -39,9 +39,9 @@ run_igblast(IgBLASTn, "query.fasta", "V.fasta", "D.fasta", "J.fasta", "aux.txt",
 """
 function run_igblast(
     igblast_type::Type{T},
-    query_file::String, 
-    v_database::String, 
-    d_database::String, 
+    query_file::String,
+    v_database::String,
+    d_database::String,
     j_database::String,
     aux_file::String,
     output_file::String,
@@ -138,7 +138,9 @@ function run_igblast(
             end
         end
 
-        process = run(cmd, wait=false)
+        out = IOBuffer()
+        err = IOBuffer()
+        process = run(pipeline(cmd, stdout=out, stderr=err), wait=false)
 
         while process_running(process)
             if isready(done_channel)
@@ -154,9 +156,8 @@ function run_igblast(
         end
 
         if !success(process)
-            error_output = read(stderr, String)
-            @error "IgBLAST failed to run successfully" error_output
-            error("IgBLAST execution failed. Check the error message above.")
+            error_output = String(take!(err))
+            error("$(error_output)\nIgBLAST execution failed. Check the error message above.")
         end
 
         @info "IgBLAST analysis completed. Output saved to $output_file"