9c4b7225d91f5180fcddbecd843b71c4e6503688 angie Tue Mar 30 10:39:22 2021 -0700 Add subtree JSON URLs to single-subtree JSON, using Auspice's new url attribute. Allow up to 1000 VCF samples and extend timeout to 15 minutes. diff --git src/hg/hgPhyloPlace/phyloPlace.h src/hg/hgPhyloPlace/phyloPlace.h index 6d43265..8777e91 100644 --- src/hg/hgPhyloPlace/phyloPlace.h +++ src/hg/hgPhyloPlace/phyloPlace.h @@ -153,32 +153,32 @@ struct usherResults *runUsher(char *usherPath, char *usherAssignmentsPath, char *vcfFile, int subtreeSize, struct slName *userSampleIds, struct hash *condensedNodes, int *pStartTime); /* Open a pipe from Yatish Turakhia's usher program, save resulting big trees and * subtrees to trash files, return list of slRef to struct tempName for the trash files * and parse other results out of stderr output. */ struct slPair *getAaMutations(struct singleNucChange *sncList, struct geneInfo *geneInfoList, struct seqWindow *gSeqWin); /* Given lists of SNVs and genes, return a list of pairs of { gene name, AA change list }. */ struct geneInfo *getGeneInfoList(char *bigGenePredFile, struct dnaSeq *refGenome); /* If config.ra has a source of gene annotations, then return the gene list. */ void treeToAuspiceJson(struct subtreeInfo *sti, char *db, struct geneInfo *geneInfoList, - struct seqWindow *gSeqWin, struct hash *sampleMetadata, char *jsonFile, - char *source); + struct seqWindow *gSeqWin, struct hash *sampleMetadata, + struct hash *sampleUrls, char *jsonFile, char *source); /* Write JSON for tree in Nextstrain's Augur/Auspice V2 JSON format * (https://github.com/nextstrain/augur/blob/master/augur/data/schema-export-v2.json). */ struct tempName *writeCustomTracks(struct tempName *vcfTn, struct usherResults *ur, struct slName *sampleIds, struct phyloTree *bigTree, char *source, int fontHeight, struct phyloTree **retSampleTree, int *pStartTime); /* Write one custom track per subtree, and one custom track with just the user's uploaded samples. */ struct sampleMetadata *metadataForSample(struct hash *sampleMetadata, char *sampleId); /* Look up sampleId in sampleMetadata, by accession if sampleId seems to include an accession. */ struct phyloTree *phyloPruneToIds(struct phyloTree *node, struct slName *sampleIds); /* Prune all descendants of node that have no leaf descendants in sampleIds. */