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Added a synthetic example
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‎README.md‎

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@@ -45,3 +45,7 @@ gcnvplot plot \
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--sample-name SAMPLE_01 \
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--output plot.svg
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```
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## Example data
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A tiny synthetic BRCA1 transcript example is available in [`examples/brca1_synthetic`](examples/brca1_synthetic). It demonstrates a highlighted multi-exon deletion, open dots for intervals outside exons, and an uncovered-exon marker.

‎examples/brca1_synthetic/README.md‎

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# BRCA1 synthetic plotting example
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This example is a tiny, synthetic dataset for exercising the transcript plotting features in `gcnvplot`.
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It contains:
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- `brca1_mane_minimal.gtf`: the BRCA1 `NM_007294.4` transcript line plus exon lines from an hg38 NCBI RefSeq GTF.
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- `background.tsv`: synthetic interval-wise background statistics with 20 mock background samples and interval-to-interval depth variation.
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- `sample_deletion.tsv`: a synthetic sample with realistic count jitter and a heterozygous deletion across BRCA1 exons 13-15.
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The intervals are roughly 1 kb and have different expected depths, mimicking variable probe efficiency. Two intervals are intentionally intronic so the plot shows open sample dots; one of those intronic intervals falls inside the deletion and is depressed with the deleted exons. Exon 12 has no overlapping interval so the transcript track shows the uncovered-exon triangle.
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Run from the repository root:
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```bash
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gcnvplot plot \
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--read-counts examples/brca1_synthetic/sample_deletion.tsv \
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--background examples/brca1_synthetic/background.tsv \
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--transcript NM_007294.4 \
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--gtf examples/brca1_synthetic/brca1_mane_minimal.gtf \
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--sample-name "Synthetic BRCA1 exon 13-15 deletion" \
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--highlight chr17:43070928-43076614 \
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--output examples/brca1_synthetic/brca1_synthetic.svg
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```
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The output should show:
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- a depressed log2 signal across the highlighted exon 13-15 deletion, including the intronic interval inside the deletion,
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- filled dots for intervals overlapping exons,
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- open dots for intervals outside exons,
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- a red triangle under exon 12, which has no overlapping synthetic interval.

‎examples/brca1_synthetic/background.tsv‎

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# normalization=median-of-ratios
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# baseline=synthetic-variable-counts
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# samples=20
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# lower_percentile=5
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# upper_percentile=95
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CONTIG START END BASELINE_MEDIAN N BG_NORM_MEAN BG_NORM_MEDIAN BG_NORM_SD BG_NORM_P5 BG_NORM_P95
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chr17 43044295 43045294 1180 20 1187 1180 93 1036 1333
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chr17 43045295 43046294 1125 20 1116 1125 82 998 1260
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chr17 43047174 43048173 980 20 998 980 82 853 1115
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chr17 43048658 43049657 1265 20 1249 1265 111 1093 1448
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chr17 43050600 43051599 910 20 929 910 70 802 1026
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chr17 43056600 43057599 1005 20 1013 1005 81 879 1139
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chr17 43062853 43063852 1088 20 1084 1088 81 962 1222
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chr17 43063853 43064852 960 20 973 960 83 831 1097
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chr17 43067152 43068151 1195 20 1184 1195 94 1049 1350
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chr17 43070583 43071582 1040 20 1058 1040 86 907 1182
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chr17 43073000 43073999 990 20 999 990 74 875 1112
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chr17 43073926 43074925 1135 20 1127 1135 101 978 1302
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chr17 43076052 43077051 970 20 985 970 76 852 1095
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chr17 43079000 43079999 1030 20 1019 1030 84 900 1169
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chr17 43090488 43091487 890 20 908 890 76 772 1015
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chr17 43091435 43092434 1325 20 1318 1325 101 1168 1492
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chr17 43092435 43093434 1420 20 1436 1420 124 1228 1625
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chr17 43093435 43094434 1490 20 1469 1490 121 1302 1690
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chr17 43094435 43095434 1385 20 1410 1385 102 1227 1553
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chr17 43095384 43096383 1060 20 1064 1060 93 916 1213
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chr17 43096767 43097766 1140 20 1131 1140 90 1000 1288
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chr17 43099328 43100327 1015 20 1031 1015 84 885 1154
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chr17 43103692 43104691 1210 20 1206 1210 93 1066 1363
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chr17 43104692 43105691 940 20 951 940 81 814 1074
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chr17 43105994 43106993 975 20 963 975 78 854 1104
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chr17 43115253 43116252 860 20 876 860 72 748 979
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chr17 43123566 43124565 720 20 724 720 56 633 812
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chr17 43124818 43125817 760 20 755 760 62 664 862

‎examples/brca1_synthetic/brca1_mane_minimal.gtf‎

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chr17 ncbiRefSeq.2022-10-28 transcript 43044295 43125364 . - . gene_id "BRCA1"; transcript_id "NM_007294.4"; gene_name "BRCA1";
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chr17 ncbiRefSeq.2022-10-28 exon 43044295 43045802 . - . gene_id "BRCA1"; transcript_id "NM_007294.4"; exon_number "23"; exon_id "NM_007294.4.23"; gene_name "BRCA1";
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chr17 ncbiRefSeq.2022-10-28 exon 43047643 43047703 . - . gene_id "BRCA1"; transcript_id "NM_007294.4"; exon_number "22"; exon_id "NM_007294.4.22"; gene_name "BRCA1";
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chr17 ncbiRefSeq.2022-10-28 exon 43049121 43049194 . - . gene_id "BRCA1"; transcript_id "NM_007294.4"; exon_number "21"; exon_id "NM_007294.4.21"; gene_name "BRCA1";
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chr17 ncbiRefSeq.2022-10-28 exon 43051063 43051117 . - . gene_id "BRCA1"; transcript_id "NM_007294.4"; exon_number "20"; exon_id "NM_007294.4.20"; gene_name "BRCA1";
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chr17 ncbiRefSeq.2022-10-28 exon 43057052 43057135 . - . gene_id "BRCA1"; transcript_id "NM_007294.4"; exon_number "19"; exon_id "NM_007294.4.19"; gene_name "BRCA1";
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chr17 ncbiRefSeq.2022-10-28 exon 43063333 43063373 . - . gene_id "BRCA1"; transcript_id "NM_007294.4"; exon_number "18"; exon_id "NM_007294.4.18"; gene_name "BRCA1";
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chr17 ncbiRefSeq.2022-10-28 exon 43063874 43063951 . - . gene_id "BRCA1"; transcript_id "NM_007294.4"; exon_number "17"; exon_id "NM_007294.4.17"; gene_name "BRCA1";
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chr17 ncbiRefSeq.2022-10-28 exon 43067608 43067695 . - . gene_id "BRCA1"; transcript_id "NM_007294.4"; exon_number "16"; exon_id "NM_007294.4.16"; gene_name "BRCA1";
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chr17 ncbiRefSeq.2022-10-28 exon 43070928 43071238 . - . gene_id "BRCA1"; transcript_id "NM_007294.4"; exon_number "15"; exon_id "NM_007294.4.15"; gene_name "BRCA1";
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chr17 ncbiRefSeq.2022-10-28 exon 43074331 43074521 . - . gene_id "BRCA1"; transcript_id "NM_007294.4"; exon_number "14"; exon_id "NM_007294.4.14"; gene_name "BRCA1";
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chr17 ncbiRefSeq.2022-10-28 exon 43076488 43076614 . - . gene_id "BRCA1"; transcript_id "NM_007294.4"; exon_number "13"; exon_id "NM_007294.4.13"; gene_name "BRCA1";
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chr17 ncbiRefSeq.2022-10-28 exon 43082404 43082575 . - . gene_id "BRCA1"; transcript_id "NM_007294.4"; exon_number "12"; exon_id "NM_007294.4.12"; gene_name "BRCA1";
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chr17 ncbiRefSeq.2022-10-28 exon 43090944 43091032 . - . gene_id "BRCA1"; transcript_id "NM_007294.4"; exon_number "11"; exon_id "NM_007294.4.11"; gene_name "BRCA1";
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chr17 ncbiRefSeq.2022-10-28 exon 43091435 43094860 . - . gene_id "BRCA1"; transcript_id "NM_007294.4"; exon_number "10"; exon_id "NM_007294.4.10"; gene_name "BRCA1";
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chr17 ncbiRefSeq.2022-10-28 exon 43095846 43095922 . - . gene_id "BRCA1"; transcript_id "NM_007294.4"; exon_number "9"; exon_id "NM_007294.4.9"; gene_name "BRCA1";
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chr17 ncbiRefSeq.2022-10-28 exon 43097244 43097289 . - . gene_id "BRCA1"; transcript_id "NM_007294.4"; exon_number "8"; exon_id "NM_007294.4.8"; gene_name "BRCA1";
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chr17 ncbiRefSeq.2022-10-28 exon 43099775 43099880 . - . gene_id "BRCA1"; transcript_id "NM_007294.4"; exon_number "7"; exon_id "NM_007294.4.7"; gene_name "BRCA1";
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chr17 ncbiRefSeq.2022-10-28 exon 43104122 43104261 . - . gene_id "BRCA1"; transcript_id "NM_007294.4"; exon_number "6"; exon_id "NM_007294.4.6"; gene_name "BRCA1";
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chr17 ncbiRefSeq.2022-10-28 exon 43104868 43104956 . - . gene_id "BRCA1"; transcript_id "NM_007294.4"; exon_number "5"; exon_id "NM_007294.4.5"; gene_name "BRCA1";
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chr17 ncbiRefSeq.2022-10-28 exon 43106456 43106533 . - . gene_id "BRCA1"; transcript_id "NM_007294.4"; exon_number "4"; exon_id "NM_007294.4.4"; gene_name "BRCA1";
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chr17 ncbiRefSeq.2022-10-28 exon 43115726 43115779 . - . gene_id "BRCA1"; transcript_id "NM_007294.4"; exon_number "3"; exon_id "NM_007294.4.3"; gene_name "BRCA1";
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chr17 ncbiRefSeq.2022-10-28 exon 43124017 43124115 . - . gene_id "BRCA1"; transcript_id "NM_007294.4"; exon_number "2"; exon_id "NM_007294.4.2"; gene_name "BRCA1";
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chr17 ncbiRefSeq.2022-10-28 exon 43125271 43125364 . - . gene_id "BRCA1"; transcript_id "NM_007294.4"; exon_number "1"; exon_id "NM_007294.4.1"; gene_name "BRCA1";

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