excpect tabs in read headers

mikolmogorov · Apr 5, 2019 · a5ba370 · a5ba370
1 parent f54bd0f
commit a5ba370
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Showing 2 changed files with 6 additions and 10 deletions.
diff --git a/flye/utils/fasta_parser.py b/flye/utils/fasta_parser.py
@@ -120,7 +120,7 @@ def _read_fasta(file_handle):
             if header:
                 yield header, "".join(seq)
                 seq = []
-            header = line[1:].split(" ")[0]
+            header = line[1:].split()[0]
         else:
             seq.append(line)
 
@@ -143,7 +143,7 @@ def _read_fastq(file_handle):
             if line[0] != "@":
                 raise FastaError("Fastq format error: {0} at line {1}"
                                     .format(file_handle.name, no))
-            header = line[1:].split(" ")[0]
+            header = line[1:].split()[0]
 
         if state_counter == 1:
             seq = line

diff --git a/src/sequence/sequence_container.cpp b/src/sequence/sequence_container.cpp
@@ -305,17 +305,13 @@ size_t SequenceContainer::readFastq(std::vector<FastaRecord>& record,
 
 void SequenceContainer::validateHeader(std::string& header)
 {
-	size_t delim = header.find(' ');
-	if (delim == std::string::npos)
+	size_t delim = 0;
+	for (delim = 0; delim < header.length(); ++delim)
 	{
-		delim = header.length() - 1;
-	}
-	else
-	{
-		--delim;
+		if (std::isspace(header[delim])) break;
 	}
 
-	header = header.substr(1, delim);
+	header = header.substr(1, delim - 1);
 	if (header.empty()) throw ParseException("empty header");
 }