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Computes the percentage of properly paired reads. Includes '=' and 'X' CIGAR operators when counting mapped bases. Implements overlap remove logic for paired-end reads in coverage calculation and mapped base counting. Overlap removal can be turned on using the stats `-p` or `--remove-overlaps` option. When a target file is in use calculates and prints the number of bases inside the target, and the percentage of target bases with coverage over a given threshold. The coverage threshold can be set using the `-g` or `--cov-threshold` option. Adds more unit tests and augments some of the old ones.
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,166 @@ | ||
| # CHK, Checksum [2]Read Names [3]Sequences [4]Qualities | ||
| # CHK, CRC32 of reads which passed filtering followed by addition (32bit overflow) | ||
| CHK cb2d2d82 bcd83869 62ec814e | ||
| # Summary Numbers. Use `grep ^SN | cut -f 2-` to extract this part. | ||
| SN raw total sequences: 26 | ||
| SN filtered sequences: 0 | ||
| SN sequences: 26 | ||
| SN is sorted: 1 | ||
| SN 1st fragments: 14 | ||
| SN last fragments: 12 | ||
| SN reads mapped: 26 | ||
| SN reads mapped and paired: 26 # paired-end technology bit set + both mates mapped | ||
| SN reads unmapped: 0 | ||
| SN reads properly paired: 24 # proper-pair bit set | ||
| SN reads paired: 26 # paired-end technology bit set | ||
| SN reads duplicated: 0 # PCR or optical duplicate bit set | ||
| SN reads MQ0: 1 # mapped and MQ=0 | ||
| SN reads QC failed: 0 | ||
| SN non-primary alignments: 0 | ||
| SN total length: 260 # ignores clipping | ||
| SN total first fragment length: 140 # ignores clipping | ||
| SN total last fragment length: 120 # ignores clipping | ||
| SN bases mapped: 260 # ignores clipping | ||
| SN bases mapped (cigar): 206 # more accurate | ||
| SN bases trimmed: 0 | ||
| SN bases duplicated: 0 | ||
| SN mismatches: 0 # from NM fields | ||
| SN error rate: 0.000000e+00 # mismatches / bases mapped (cigar) | ||
| SN average length: 10 | ||
| SN average first fragment length: 10 | ||
| SN average last fragment length: 10 | ||
| SN maximum length: 10 | ||
| SN maximum first fragment length: 10 | ||
| SN maximum last fragment length: 10 | ||
| SN average quality: 13.1 | ||
| SN insert size average: 34.0 | ||
| SN insert size standard deviation: 0.0 | ||
| SN inward oriented pairs: 12 | ||
| SN outward oriented pairs: 0 | ||
| SN pairs with other orientation: 0 | ||
| SN pairs on different chromosomes: 1 | ||
| SN percentage of properly paired reads (%): 92.3 | ||
| SN bases inside the target: 42 | ||
| SN percentage of target genome with coverage > 4 (%): 85.71 | ||
| # First Fragment Qualities. Use `grep ^FFQ | cut -f 2-` to extract this part. | ||
| # Columns correspond to qualities and rows to cycles. First column is the cycle number. | ||
| FFQ 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 | ||
| FFQ 2 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 | ||
| FFQ 3 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 | ||
| FFQ 4 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 | ||
| FFQ 5 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 | ||
| FFQ 6 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 | ||
| FFQ 7 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 | ||
| FFQ 8 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 | ||
| FFQ 9 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 | ||
| FFQ 10 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 | ||
| # Last Fragment Qualities. Use `grep ^LFQ | cut -f 2-` to extract this part. | ||
| # Columns correspond to qualities and rows to cycles. First column is the cycle number. | ||
| LFQ 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 | ||
| LFQ 2 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 | ||
| LFQ 3 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 | ||
| LFQ 4 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 | ||
| LFQ 5 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 | ||
| LFQ 6 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 | ||
| LFQ 7 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 | ||
| LFQ 8 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 | ||
| LFQ 9 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 | ||
| LFQ 10 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 | ||
| # GC Content of first fragments. Use `grep ^GCF | cut -f 2-` to extract this part. | ||
| GCF 19.85 0 | ||
| GCF 44.72 1 | ||
| GCF 54.77 4 | ||
| GCF 64.82 2 | ||
| GCF 74.87 4 | ||
| GCF 84.92 3 | ||
| # GC Content of last fragments. Use `grep ^GCL | cut -f 2-` to extract this part. | ||
| GCL 19.85 0 | ||
| GCL 44.72 2 | ||
| GCL 59.80 3 | ||
| GCL 74.87 4 | ||
| # ACGT content per cycle. Use `grep ^GCC | cut -f 2-` to extract this part. The columns are: cycle; A,C,G,T base counts as a percentage of all A/C/G/T bases [%]; and N and O counts as a percentage of all A/C/G/T bases [%] | ||
| GCC 1 19.23 42.31 15.38 23.08 0.00 0.00 | ||
| GCC 2 19.23 19.23 46.15 15.38 0.00 0.00 | ||
| GCC 3 23.08 38.46 19.23 19.23 0.00 0.00 | ||
| GCC 4 23.08 23.08 38.46 15.38 0.00 0.00 | ||
| GCC 5 11.54 38.46 26.92 23.08 0.00 0.00 | ||
| GCC 6 23.08 23.08 34.62 19.23 0.00 0.00 | ||
| GCC 7 15.38 34.62 26.92 23.08 0.00 0.00 | ||
| GCC 8 26.92 23.08 38.46 11.54 0.00 0.00 | ||
| GCC 9 23.08 26.92 26.92 23.08 0.00 0.00 | ||
| GCC 10 23.08 23.08 38.46 15.38 0.00 0.00 | ||
| # ACGT content per cycle for first fragments. Use `grep ^FBC | cut -f 2-` to extract this part. The columns are: cycle; A,C,G,T base counts as a percentage of all A/C/G/T bases [%]; and N and O counts as a percentage of all A/C/G/T bases [%] | ||
| FBC 1 21.43 42.86 21.43 14.29 0.00 0.00 | ||
| FBC 2 7.14 28.57 42.86 21.43 0.00 0.00 | ||
| FBC 3 28.57 35.71 21.43 14.29 0.00 0.00 | ||
| FBC 4 14.29 28.57 35.71 21.43 0.00 0.00 | ||
| FBC 5 14.29 35.71 35.71 14.29 0.00 0.00 | ||
| FBC 6 14.29 28.57 28.57 28.57 0.00 0.00 | ||
| FBC 7 14.29 28.57 35.71 21.43 0.00 0.00 | ||
| FBC 8 21.43 28.57 28.57 21.43 0.00 0.00 | ||
| FBC 9 21.43 21.43 35.71 21.43 0.00 0.00 | ||
| FBC 10 14.29 28.57 35.71 21.43 0.00 0.00 | ||
| # ACGT content per cycle for last fragments. Use `grep ^LBC | cut -f 2-` to extract this part. The columns are: cycle; A,C,G,T base counts as a percentage of all A/C/G/T bases [%]; and N and O counts as a percentage of all A/C/G/T bases [%] | ||
| LBC 1 16.67 41.67 8.33 33.33 0.00 0.00 | ||
| LBC 2 33.33 8.33 50.00 8.33 0.00 0.00 | ||
| LBC 3 16.67 41.67 16.67 25.00 0.00 0.00 | ||
| LBC 4 33.33 16.67 41.67 8.33 0.00 0.00 | ||
| LBC 5 8.33 41.67 16.67 33.33 0.00 0.00 | ||
| LBC 6 33.33 16.67 41.67 8.33 0.00 0.00 | ||
| LBC 7 16.67 41.67 16.67 25.00 0.00 0.00 | ||
| LBC 8 33.33 16.67 50.00 0.00 0.00 0.00 | ||
| LBC 9 25.00 33.33 16.67 25.00 0.00 0.00 | ||
| LBC 10 33.33 16.67 41.67 8.33 0.00 0.00 | ||
| # Insert sizes. Use `grep ^IS | cut -f 2-` to extract this part. The columns are: insert size, pairs total, inward oriented pairs, outward oriented pairs, other pairs | ||
| IS 0 0 0 0 0 | ||
| IS 1 0 0 0 0 | ||
| IS 2 0 0 0 0 | ||
| IS 3 0 0 0 0 | ||
| IS 4 0 0 0 0 | ||
| IS 5 0 0 0 0 | ||
| IS 6 0 0 0 0 | ||
| IS 7 0 0 0 0 | ||
| IS 8 0 0 0 0 | ||
| IS 9 0 0 0 0 | ||
| IS 10 0 0 0 0 | ||
| IS 11 0 0 0 0 | ||
| IS 12 0 0 0 0 | ||
| IS 13 0 0 0 0 | ||
| IS 14 0 0 0 0 | ||
| IS 15 0 0 0 0 | ||
| IS 16 0 0 0 0 | ||
| IS 17 0 0 0 0 | ||
| IS 18 0 0 0 0 | ||
| IS 19 0 0 0 0 | ||
| IS 20 0 0 0 0 | ||
| IS 21 0 0 0 0 | ||
| IS 22 0 0 0 0 | ||
| IS 23 0 0 0 0 | ||
| IS 24 0 0 0 0 | ||
| IS 25 0 0 0 0 | ||
| IS 26 0 0 0 0 | ||
| IS 27 0 0 0 0 | ||
| IS 28 0 0 0 0 | ||
| IS 29 0 0 0 0 | ||
| IS 30 0 0 0 0 | ||
| IS 31 0 0 0 0 | ||
| IS 32 0 0 0 0 | ||
| IS 33 0 0 0 0 | ||
| IS 34 12 12 0 0 | ||
| # Read lengths. Use `grep ^RL | cut -f 2-` to extract this part. The columns are: read length, count | ||
| RL 10 26 | ||
| # Read lengths - first fragments. Use `grep ^FRL | cut -f 2-` to extract this part. The columns are: read length, count | ||
| FRL 10 14 | ||
| # Read lengths - last fragments. Use `grep ^LRL | cut -f 2-` to extract this part. The columns are: read length, count | ||
| LRL 10 12 | ||
| # Indel distribution. Use `grep ^ID | cut -f 2-` to extract this part. The columns are: length, number of insertions, number of deletions | ||
| # Indels per cycle. Use `grep ^IC | cut -f 2-` to extract this part. The columns are: cycle, number of insertions (fwd), .. (rev) , number of deletions (fwd), .. (rev) | ||
| # Coverage distribution. Use `grep ^COV | cut -f 2-` to extract this part. | ||
| COV [1-1] 1 1 | ||
| COV [2-2] 2 1 | ||
| COV [3-3] 3 2 | ||
| COV [4-4] 4 2 | ||
| COV [5-5] 5 23 | ||
| COV [6-6] 6 13 | ||
| # GC-depth. Use `grep ^GCD | cut -f 2-` to extract this part. The columns are: GC%, unique sequence percentiles, 10th, 25th, 50th, 75th and 90th depth percentile | ||
| GCD 0.0 100.000 0.000 0.000 0.000 0.000 0.000 |
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