4898794edd81be5285ea6e544acbedeaeb31bf78 max Tue Nov 23 08:10:57 2021 -0800 Fixing pointers to README file for license in all source code files. refs #27614 diff --git src/hg/inc/pseudoGeneLink.h src/hg/inc/pseudoGeneLink.h index 0862412..fef3504 100644 --- src/hg/inc/pseudoGeneLink.h +++ src/hg/inc/pseudoGeneLink.h @@ -1,115 +1,115 @@ /* pseudoGeneLink.h was originally generated by the autoSql program, which also * generated pseudoGeneLink.c and pseudoGeneLink.sql. This header links the database and * the RAM representation of objects. */ /* Copyright (C) 2007 The Regents of the University of California - * See README in this or parent directory for licensing information. */ + * See kent/LICENSE or http://genome.ucsc.edu/license/ for licensing information. */ #ifndef PSEUDOGENELINK_H #define PSEUDOGENELINK_H #define PSEUDOGENELINK_NUM_COLS 56 struct pseudoGeneLink /* links a gene/pseudogene prediction to an ortholog or paralog. */ { struct pseudoGeneLink *next; /* Next in singly linked list. */ char *chrom; /* Reference sequence chromosome or scaffold */ unsigned chromStart; /* pseudogene alignment start position */ unsigned chromEnd; /* pseudogene alignment end position */ char *name; /* Name of pseudogene */ unsigned score; /* score of pseudogene with gene */ char strand[3]; /* + or - */ unsigned thickStart; /* Start of where display should be thick (start codon) */ unsigned thickEnd; /* End of where display should be thick (stop codon) */ unsigned reserved; /* Always zero for now */ int blockCount; /* Number of blocks */ int *blockSizes; /* Comma separated list of block sizes */ int *chromStarts; /* Start positions relative to chromStart */ float trfRatio; /* ratio of tandem repeats */ char *type; /* type of evidence */ int axtScore; /* blastz score, gene mrna aligned to pseudogene */ char *gChrom; /* Chromosome name */ int gStart; /* gene alignment start position */ int gEnd; /* gene alignment end position */ char gStrand[3]; /* strand of gene */ unsigned exonCount; /* # of exons in gene */ unsigned geneOverlap; /* bases overlapping */ unsigned polyA; /* count of As in polyA */ int polyAstart; /* start of polyA, relative to end of pseudogene */ int exonCover; /* number of exons in Gene covered */ unsigned intronCount; /* number of introns in pseudogene */ unsigned bestAliCount; /* number of good mrnas aligning */ unsigned matches; /* matches + repMatches */ unsigned qSize; /* aligning bases in pseudogene */ unsigned qEnd; /* end of cdna alignment */ unsigned tReps; /* repeats in gene */ int overlapRhesus; /* percent of retro that breaks net relative to Rhesus */ int overlapMouse; /* percent of retro that breaks net relative to Mouse */ unsigned coverage; /* % of bases that align to gene */ int label; /* 1=pseudogene,-1 not pseudogene -2 expressed retroGene */ unsigned milliBad; /* milliBad score, pseudogene aligned to genome */ unsigned oldScore; /* another heuristic */ int oldIntronCount; /* old simple intron count */ int processedIntrons; /* intron prcessed out of retrogene */ int conservedSpliceSites; /* conserved splice site count */ int maxOverlap; /* largest overlap with another mrna */ char *refSeq; /* Name of closest regSeq to gene */ int rStart; /* refSeq alignment start position */ int rEnd; /* refSeq alignment end position */ char *mgc; /* Name of closest mgc to gene */ int mStart; /* mgc alignment start position */ int mEnd; /* mgc alignment end position */ char *kgName; /* Name of closest knownGene to gene */ int kStart; /* kg alignment start position */ int kEnd; /* kg alignment end position */ char *overName; /* name of overlapping mrna */ int overStart; /* overlapping mrna start position */ int overEnd; /* overlapping mrna end position */ char overStrand[3]; /* strand of overlapping mrna */ int overlapDog; /* percent of retro that breaks net relative to dog */ float posConf; /* pvalue for positive */ unsigned polyAlen; /* length of polyA */ }; struct pseudoGeneLink *pseudoGeneLinkLoad(char **row); /* Load a pseudoGeneLink from row fetched with select * from pseudoGeneLink * from database. Dispose of this with pseudoGeneLinkFree(). */ struct pseudoGeneLink *pseudoGeneLinkLoadAll(char *fileName); /* Load all pseudoGeneLink from whitespace-separated file. * Dispose of this with pseudoGeneLinkFreeList(). */ struct pseudoGeneLink *pseudoGeneLinkLoadAllByChar(char *fileName, char chopper); /* Load all pseudoGeneLink from chopper separated file. * Dispose of this with pseudoGeneLinkFreeList(). */ #define pseudoGeneLinkLoadAllByTab(a) pseudoGeneLinkLoadAllByChar(a, '\t'); /* Load all pseudoGeneLink from tab separated file. * Dispose of this with pseudoGeneLinkFreeList(). */ struct pseudoGeneLink *pseudoGeneLinkCommaIn(char **pS, struct pseudoGeneLink *ret); /* Create a pseudoGeneLink out of a comma separated string. * This will fill in ret if non-null, otherwise will * return a new pseudoGeneLink */ void pseudoGeneLinkFree(struct pseudoGeneLink **pEl); /* Free a single dynamically allocated pseudoGeneLink such as created * with pseudoGeneLinkLoad(). */ void pseudoGeneLinkFreeList(struct pseudoGeneLink **pList); /* Free a list of dynamically allocated pseudoGeneLink's */ void pseudoGeneLinkOutput(struct pseudoGeneLink *el, FILE *f, char sep, char lastSep); /* Print out pseudoGeneLink. Separate fields with sep. Follow last field with lastSep. */ #define pseudoGeneLinkTabOut(el,f) pseudoGeneLinkOutput(el,f,'\t','\n'); /* Print out pseudoGeneLink as a line in a tab-separated file. */ #define pseudoGeneLinkCommaOut(el,f) pseudoGeneLinkOutput(el,f,',',','); /* Print out pseudoGeneLink as a comma separated list including final comma. */ /* -------------------------------- End autoSql Generated Code -------------------------------- */ #endif /* PSEUDOGENELINK_H */