Add average quality score to stats

[apcamargo]

Right now seqkit stats displays the % of bases with quality score over 20 and 30. It would also be useful to have the average quality score information, since this can be used for quality control.

[shenwei356]

seqkit seq has one flag:

-Q, --min-qual float            only print sequences with average quality greater or equal than this
                                limit (-1 for no limit) (default -1)

seqkit fx2tab also has one flag to filter records before piping to seqkit tab2fx.

  -q, --avg-qual               print average quality of a read

[apcamargo]

I don't think those replace a computation of the average quality within a FASTQ. I could achieve that by using fx2tab, taking a average quality across all reads and weighing by the read length.

[shenwei356]

Oh, people often use Q20 and Q30, I don't know how many people use the average quality score of the whole FASTQ file. Technically, it's very easy to add the metric.

[shenwei356]

added.

$  seqkit stats *.f{a,q}.gz -a
processed files:  6 / 6 [======================================] ETA: 0s. done
file               format  type  num_seqs    sum_len  min_len  avg_len  max_len   Q1   Q2   Q3  sum_gap  N50  Q20(%)  Q30(%)  AvgQual  GC(%)
hairpin.fa.gz      FASTA   RNA     28,645  2,949,871       39      103    2,354   76   91  111        0  101       0       0        0  45.77
mature.fa.gz       FASTA   RNA     35,828    781,222       15     21.8       34   21   22   22        0   22       0       0        0   47.6
Illimina1.8.fq.gz  FASTQ   DNA     10,000  1,500,000      150      150      150  150  150  150        0  150   96.16   89.71    24.82  49.91
nanopore.fq.gz     FASTQ   DNA      4,000  1,798,723      153    449.7    6,006  271  318  391        0  395   40.79   12.63     9.48  46.66
reads_1.fq.gz      FASTQ   DNA      2,500    567,516      226      227      229  227  227  227        0  227   91.24   86.62    15.45  53.63
reads_2.fq.gz      FASTQ   DNA      2,500    560,002      223      224      225  224  224  224        0  224   91.06   87.66    14.62  54.77

• seqkit_darwin_arm64.tar.gz
• seqkit_darwin_amd64.tar.gz
• seqkit_linux_amd64.tar.gz

[apcamargo]

Thank you!!