[WIP]

src/bowtie2/align/config.vsh.yaml

@@ -82,6 +82,10 @@ functionality:
           description: trim <int> bases from 3'/right end of reads (0)
           type: integer
           default: 0
+        - name: --trim-to
+          description: "[3:|5:]<int> trim reads exceeding <int> bases from either 3' or 5' end. If the read end is not specified then it defaults to 3 (0)"
+          type: string
+        - name: phred
 
 
   resources:

src/bowtie2/align/help.txt

@@ -20,7 +20,7 @@ Usage:
 
 Options (defaults in parentheses):
 
- Input:
+ ###Input:
   -q                 query input files are FASTQ .fq/.fastq (default)
   --tab5             query input files are TAB5 .tab5
   --tab6             query input files are TAB6 .tab6
@@ -41,7 +41,7 @@ Options (defaults in parentheses):
   --phred64          qualities are Phred+64
   --int-quals        qualities encoded as space-delimited integers
 
- Presets:                 Same as:
+ ###Presets:                 Same as:
   For --end-to-end:
    --very-fast            -D 5 -R 1 -N 0 -L 22 -i S,0,2.50
    --fast                 -D 10 -R 2 -N 0 -L 22 -i S,0,2.50
@@ -54,7 +54,7 @@ Options (defaults in parentheses):
    --sensitive-local      -D 15 -R 2 -N 0 -L 20 -i S,1,0.75 (default)
    --very-sensitive-local -D 20 -R 3 -N 0 -L 20 -i S,1,0.50
 
- Alignment:
+ ###Alignment:
   -N <int>           max # mismatches in seed alignment; can be 0 or 1 (0)
   -L <int>           length of seed substrings; must be >3, <32 (22)
   -i <func>          interval between seed substrings w/r/t read len (S,1,1.15)
@@ -70,7 +70,7 @@ Options (defaults in parentheses):
    OR
   --local            local alignment; ends might be soft clipped (off)
 
- Scoring:
+ ###Scoring:
   --ma <int>         match bonus (0 for --end-to-end, 2 for --local) 
   --mp <int>         max penalty for mismatch; lower qual = lower penalty (6)
   --np <int>         penalty for non-A/C/G/Ts in read/ref (1)
@@ -79,18 +79,18 @@ Options (defaults in parentheses):
   --score-min <func> min acceptable alignment score w/r/t read length
                      (G,20,8 for local, L,-0.6,-0.6 for end-to-end)
 
- Reporting:
+ ###Reporting:
   (default)          look for multiple alignments, report best, with MAPQ
    OR
   -k <int>           report up to <int> alns per read; MAPQ not meaningful
    OR
   -a/--all           report all alignments; very slow, MAPQ not meaningful
 
- Effort:
+ ###Effort:
   -D <int>           give up extending after <int> failed extends in a row (15)
   -R <int>           for reads w/ repetitive seeds, try <int> sets of seeds (2)
 
- Paired-end:
+ ###Paired-end:
   -I/--minins <int>  minimum fragment length (0)
   -X/--maxins <int>  maximum fragment length (500)
   --fr/--rf/--ff     -1, -2 mates align fw/rev, rev/fw, fw/fw (--fr)
@@ -100,14 +100,14 @@ Options (defaults in parentheses):
   --no-contain       not concordant when one mate alignment contains other
   --no-overlap       not concordant when mates overlap at all
 
- BAM:
+ ###BAM:
   --align-paired-reads
                      Bowtie2 will, by default, attempt to align unpaired BAM reads.
                      Use this option to align paired-end reads instead.
   --preserve-tags    Preserve tags from the original BAM record by
                      appending them to the end of the corresponding SAM output.
 
- Output:
+ ###Output:
   -t/--time          print wall-clock time taken by search phases
   --un <path>        write unpaired reads that didn't align to <path>
   --al <path>        write unpaired reads that aligned at least once to <path>
@@ -135,12 +135,12 @@ Options (defaults in parentheses):
   --sam-append-comment
                      Append FASTA/FASTQ comment to SAM record
 
- Performance:
+ ###Performance:
   -p/--threads <int> number of alignment threads to launch (1)
   --reorder          force SAM output order to match order of input reads
   --mm               use memory-mapped I/O for index; many 'bowtie's can share
 
- Other:
+ ###Other:
   --qc-filter        filter out reads that are bad according to QSEQ filter
   --seed <int>       seed for random number generator (0)
   --non-deterministic