Update README.md

README.md

@@ -56,11 +56,17 @@ Fastlin output consists of a tab-delimited file with the following fields:
 + log_barcodes: kmer barcodes passing the minimum occurence threshold, indicated by their kmer occurence and grouped by lineages
 
 Here is a simple example:
-> #sample    nb_files    k_cov    mixture    lineages    log_barcodes  
+> #sample    nb_files    k_cov    mixture    lineages    log_barcodes    log_errors  
 ERRxxxxx    paired    118    no    2 (45)    2 (42, 48, 39, 43, 54, 47, 45), 4.1 (4)
 
 The sample ERRxxxxx contains a single strain belonging to lineage 2. This typing is supported by 7 kmer barcodes, with a median number of occurences of 45. Since the abundance of the strain is far below the theoretical kmer coverage (equal here to 118), we can conclude that the sample is likely to contain high level of contaminations or sequencing errors.
 
+### Error handling
+<p>When fastlin cannot read a fastq file (e.g. faulty record within the fastq file, corrupt gzip file), it stops scanning it, re-initialise all values to 0 and report the error message in the last field of the output file. Here is an example of output with 3 different errors:</p>
+> #sample&nbsp;&nbsp;&nbsp;&nbsp;nb_files&nbsp;&nbsp;&nbsp;&nbsp;k_cov&nbsp;&nbsp;&nbsp;&nbsp;mixture&nbsp;&nbsp;&nbsp;&nbsp;lineages&nbsp;&nbsp;&nbsp;&nbsp;log_barcodes&nbsp;&nbsp;&nbsp;&nbsp;log_errors 
+dummy1&nbsp;&nbsp;&nbsp;single&nbsp;&nbsp;&nbsp;0&nbsp;&nbsp;&nbsp;no&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Error in file "reads/dummy1.fastq.gz": FASTQ parse error: sequence length is 150, but quality length is 50 (record 'ERR551806.5' at line 17).
+dummy2&nbsp;&nbsp;&nbsp;single&nbsp;&nbsp;&nbsp;0&nbsp;&nbsp;&nbsp;no&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Error in file "reads/dummy2.fastq.gz": invalid gzip header
+dummy3&nbsp;&nbsp;&nbsp;single&nbsp;&nbsp;&nbsp;0&nbsp;&nbsp;&nbsp;no&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Error in file "reads/dummy3.fastq.gz": corrupt deflate stream
 
 ### TO DO LIST
 + multi-threading