hack to print out qualities in cutadapt’s info file (will crash when trimming FASTA files)

info-file-with-qualities.patch

diff --git i/cutadapt/scripts/cutadapt.py w/cutadapt/scripts/cutadapt.py
index 855721d..2eaf435 100755
--- i/cutadapt/scripts/cutadapt.py
+++ w/cutadapt/scripts/cutadapt.py
@@ -155,6 +155,7 @@ class AdapterCutter(object):
                # TODO write only one line, even for multiple matches
                for match in matches:
                        seq = match.read.sequence
+                       qualities = match.read.qualities
                        if match is None:
                                print(match.read.name, -1, seq, sep='\t', file=self.info_file)
                        else:
@@ -167,6 +168,9 @@ class AdapterCutter(object):
                                        seq[match.rstart:match.rstop],
                                        seq[match.rstop:],
                                        match.adapter.name,
+                                       qualities[0:match.rstart],
+                                       qualities[match.rstart:match.rstop],
+                                       qualities[match.rstop:],
                                        sep='\t', file=self.info_file
                                )