From cc8f99d50236b7d0c365990398785ecc319323ea Mon Sep 17 00:00:00 2001
From: AndreaGuarracino
Date: Fri, 28 Aug 2020 10:47:48 +0200
Subject: qc_fasta returns also the seq_type; verified that only one FASTA is
 sent at a time; code cleaning

---
 bh20sequploader/qc_fasta.py | 7 +++----
 1 file changed, 3 insertions(+), 4 deletions(-)

(limited to 'bh20sequploader/qc_fasta.py')

diff --git a/bh20sequploader/qc_fasta.py b/bh20sequploader/qc_fasta.py
index e5c039e..215d6fd 100644
--- a/bh20sequploader/qc_fasta.py
+++ b/bh20sequploader/qc_fasta.py
@@ -63,8 +63,7 @@ def qc_fasta(arg_sequence, check_with_mimimap2=True):
                     tmp2.write(submitlabel.encode("utf8"))
                     tmp2.write(("".join(submitseq)).encode("utf8"))
                     tmp2.flush()
-                    subbp = 0
-                    refbp = 0
+
                     similarity = 0
                     try:
                         cmd = ["minimap2", "-c", tmp1.name, tmp2.name]
@@ -85,10 +84,10 @@ def qc_fasta(arg_sequence, check_with_mimimap2=True):
                     if similarity < 70.0:
                         raise ValueError("QC fail: alignment to reference was less than 70%% (was %2.2f%%)" % (similarity))
 
-        return ("sequence.fasta"+gz, seqlabel)
+        return ("sequence.fasta"+gz, seqlabel, seq_type)
     elif seq_type == "text/fastq":
         sequence.seek(0)
         sequence.detach()
-        return ("reads.fastq"+gz, seqlabel)
+        return ("reads.fastq"+gz, seqlabel, seq_type)
     else:
         raise ValueError("Sequence file does not look like a DNA FASTA or FASTQ")
-- 
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