v2.22.4 - more bug fixes

ChangeLog.md

@@ -1,3 +1,14 @@
+2.22.4 [2024-07-31]
+
+Fix bugs in `grep`, `consensus`, `head`, and `tail`
+
+ * grep failed when no explicit pattern was given (only patterns from -f)
+ * consensus failed on `--table` option due to incomplete implementation
+ * head and tail both failed when reading STDIN when using default
+   ("-1") cutting pattern
+
+More residual bugs from the modularization effort of the early 20s.
+
 2.22.3 [2023-03-03]
 
  * Fix bug in `subseq`

sample-data/test.sh

@@ -3,30 +3,16 @@
 set -e
 set -u
 
-diff <(smof grep -P '(S16|S12|S13)' aa.faa) aa-sub.faa
-diff <(smof grep -f pattern-list.txt aa.faa) aa-sub.faa
+diff <(smof grep -P '(YP_008964013.1|YP_008964017.1|YP_008964016.1)' aa.faa) aa-sub.faa
+diff <(smof grep -f ids.txt aa.faa) aa-sub.faa
 diff <(smof grep --fastain aa-sub.faa aa.faa) aa-sub.faa
 
 diff <(smof head -3 aa.faa) <(head -17 aa.faa)
 diff <(smof tail -3 aa.faa) <(tail -13 aa.faa)
 
-diff <(smof subseq -b 1 3 aa.faa) <(smof subseq --gff <(smof grep --gff -qP '^...' aa.faa) aa.faa)
-
 diff <(smof head -2 trna.fna | smof tail)    <(smof cut -f2 trna.fna)
 diff <(smof tail trna.fna | smof head)       <(smof cut -f10 trna.fna)
 diff <(smof tail -5 trna.fna | smof head -2) <(smof cut -f6-7 trna.fna)
 
 smof consensus trna.aln > /dev/null
 smof consensus -t trna.aln > /dev/null
-
-    # clean               cleans fasta files
-    # filter              extracts sequences meeting the given conditions
-    # md5sum              calculate an md5 checksum for the input sequences
-    # permute             randomly order sequence
-    # reverse             reverse each sequence (or reverse complement)
-    # sample              randomly select entries from fasta file
-    # sniff               extract info about the sequence
-    # sort                sort sequences
-    # split               split a fasta file into smaller files
-    # stat                calculate sequence statistics
-    # translate           translate a DNA sequence into a protein sequence