Commits for angie

4942ea5baf9a2b0f232b08e69fa9969fe640b925 Mon Mar 14 16:57:17 2022 -0700

Thanks Lou for a test case (mm39 rs3399875136, NM_146282.2) in which a frameshifting deletion causes a stop loss but the transcript has no 3'UTR sequence so we cannot find a new stop codon. Instead, truncated predicted sequence led to incorrect coords from trimRefAlt and then an end < start error from indelShift. Now, just set vpPep->cantPredict and skip the rest of the steps since we just don't have enough info.
- src/hg/lib/variantProjector.c - lines changed 8, context: html, text, full: html, text

498826cbc4a360849640a2f9ee0f6987169c5c15 Mon Mar 14 16:58:05 2022 -0700

Add a couple more IDs from pango-designation.
- src/hg/utils/otto/sarscov2phylo/includeRecombinants.tsv - lines changed 2, context: html, text, full: html, text

8ca78d3a7a71282970c6cefd998a19504271d520 Tue Mar 15 18:23:41 2022 -0700

In hashTwoColumnFile, first check if the input is tab-separated so we can tolerate spaces in the second column. If no tabs, then fall back to space-separated.
- src/lib/obscure.c - lines changed 7, context: html, text, full: html, text

838794ab7f4eed40bd79e058846b83ac1fe7bce3 Wed Mar 16 17:48:55 2022 -0700

Added recombinants XD, XE, XF -- pango-designation v1.2.133. Also a little correction to BA.1.3.
- src/hg/utils/otto/sarscov2phylo/pango.clade-mutations.tsv - lines changed 4, context: html, text, full: html, text

f2c38b414669a86d1dd00a73ff17cfd62b8f1a10 Thu Mar 17 15:39:25 2022 -0700

Getting a bit ahead of pango-designation: adding back BC.1 even though it has been temporarily withdrawn while pipelines are tested, and some of the proposed recombinant lineages for ease of spotting/tracking in the tree.
- src/hg/utils/otto/sarscov2phylo/pango.clade-mutations.tsv - lines changed 10, context: html, text, full: html, text

81f98040bb5b097503e8096db9a664ecdbeedb51 Sun Mar 20 10:15:58 2022 -0700

Oops, forgot to mask 241 in a couple of the propsed lineages - necessary for annotating a pango-masked protobuf. Also missed the last few mutations for proposed448, thx Cornelius Roemer for spotting.
- src/hg/utils/otto/sarscov2phylo/pango.clade-mutations.tsv - lines changed 3, context: html, text, full: html, text

f30a323bbecc0ff1d3c9fd0bbe20be9ceabafbbb Sun Mar 20 10:18:00 2022 -0700

Added a designated lineage column. Removed witdrawn issue 470 (duplicate) and some duplicate lines. Added a few updates.
- src/hg/utils/otto/sarscov2phylo/includeRecombinants.tsv - lines changed 839, context: html, text, full: html, text

e0ceb707ee674eed7c05ace93e71d4e958a15537 Sun Mar 20 10:19:28 2022 -0700

Filter out sequences with missing EPI_ISL_ID from new GISAID download format.
- src/hg/utils/otto/sarscov2phylo/makeNewMaskedVcf.sh - lines changed 1, context: html, text, full: html, text

feb0c6c24faed625f7e15874ade55a3f8968886c Sun Mar 20 10:20:35 2022 -0700

Adding some BA.1 Spike/amplicon dropout positions that are problematic but so far don't affect proposed Delta/BA.1 recombinants.
- src/hg/utils/otto/sarscov2phylo/maskDelta.sh - lines changed 7, context: html, text, full: html, text

1318c99c7958fcfacf703bf6047b7ae25bd6efc9 Sun Mar 20 10:25:12 2022 -0700

Make hgwdev URL to share daily directories with processed COG-UK files.
- src/hg/utils/otto/sarscov2phylo/getCogUk.sh - lines changed 3, context: html, text, full: html, text

9aa849960d756c2cc2c2a1f5bfe5916051f6f95c Sun Mar 20 10:25:56 2022 -0700

De-duplicate NCBI fasta. Make hgwdev URL to share daily directories with processed INSDC/GenBank files.
- src/hg/utils/otto/sarscov2phylo/getNcbi.sh - lines changed 7, context: html, text, full: html, text