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/makeDb/hgCalStat/hgCalStat.c src/hg/makeDb/hgCalStat/hgCalStat.c index 9c376a8..9361af1 100644 --- src/hg/makeDb/hgCalStat/hgCalStat.c +++ src/hg/makeDb/hgCalStat/hgCalStat.c @@ -1,322 +1,322 @@ /* hgCalStat - calculate genome assembly statistics */ /* Copyright (C) 2013 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. */ #include "common.h" #include "hCommon.h" #include "hdb.h" void usage() /* Explain usage and exit. */ { errAbort( "hgCalStat - calculate genome assembly statistics\n" "usage:\n" " hgCalStat statFile db outFile\n" " statFile the output file generated by stats.pl\n" " db is the genome db\n" " outFile is the output file\n" "example:\n" " hgCalStat stats.pl.out hg18 hg18.out\n"); } int main(int argc, char *argv[]) { struct sqlConnection *conn2, *conn3; struct sqlResult *sr2; char **row2; char query2[256]; char cond_str[500]; char *statFileName; boolean chromDone = FALSE; boolean chromRandomDone = FALSE; boolean hasRandom; char *chromRandom; int chromRandomSize; int orderedCnt = 0; int randomCnt = 0; int n50Total = 0; int n50RandomTotal = 0; int halfTotalSize; int halfTotalRandomSize; char *outfileName; FILE *inf, *outf; char line[1000]; char line2[1000]; char overallLine[1000]; char *chrom; int chromSize; char *ctgSize; char *chp, *chp1; char *genomeDBname; char *contig; unsigned long sumL; int sum, sumRandom; char *ctgCnt, *ctgRandomCnt; if (argc != 4) usage(); statFileName = argv[1]; genomeDBname = argv[2]; outfileName = argv[3]; hSetDb(genomeDBname); outf = mustOpen(outfileName, "w"); conn2= hAllocConn(); conn3= hAllocConn(); inf = mustOpen(statFileName, "r"); /* skip the labels line */ fgets(line, 1000, inf); while (fgets(line, 1000, inf) != NULL) { *(line+strlen(line)-1) = '\0'; strcpy(line2, line); chp = strstr(line2, "\t"); *chp = '\0'; /* special processing needed for overall line */ if (sameWord(line2, "overallChrom")) { strcpy(overallLine, line); break; } chp1 = chp + 1; chrom = strdup(line2); sprintf(line, "%s_random", chrom); chromRandom = strdup(line); sqlSafefFrag(cond_str, sizeof cond_str, "chrom='%s'", chrom); /* reformat and output the first 9 columns */ chp = strstr(chrom, "chr")+strlen("chr"); fprintf(outf,"%5s ", chp); chp = strstr(chp1, "\t"); while (chp != NULL) { *chp = '\0'; fprintf(outf,"%11s", chp1); chp1 = chp+1; chp = strstr(chp1, "\t"); } fprintf(outf,"%19s", chp1); chromSize = atoi(sqlGetField(genomeDBname, "chromInfo", "size", cond_str)); sqlSafefFrag(cond_str, sizeof cond_str, "chrom='%s'", chromRandom); if (sqlGetField(genomeDBname, "chromInfo", "size", cond_str) != NULL) { hasRandom = TRUE; chromRandomSize = atoi(sqlGetField(genomeDBname, "chromInfo", "size", cond_str)); } else { hasRandom = FALSE; chromRandomSize = 0; } sqlSafefFrag(cond_str, sizeof cond_str, "chrom='%s'", chrom); ctgCnt = sqlGetField(genomeDBname, "ctgPos", "count(*)", cond_str); fprintf(outf,"%12s", ctgCnt); orderedCnt = orderedCnt + atoi(ctgCnt); /* calculate N50 for ordered contigs */ sqlSafef(query2, sizeof query2, "select contig, size from %s.ctgPos where chrom='%s' order by size desc", genomeDBname, chrom); sr2 = sqlMustGetResult(conn2, query2); row2 = sqlNextRow(sr2); sum = 0; chromDone = FALSE; while ((row2 != NULL) && !chromDone) { contig = row2[0]; ctgSize = row2[1]; sum = sum + atoi(ctgSize); if (sum >= (chromSize/2)) { fprintf(outf,"%10s", ctgSize); chromDone = TRUE; } row2 = sqlNextRow(sr2); } if (!chromDone) fprintf(outf,"%10s", "?"); sqlFreeResult(&sr2); /* calculate N50 for random contigs */ if (hasRandom) { sqlSafefFrag(cond_str, sizeof cond_str, "chrom='%s'", chromRandom); ctgRandomCnt = sqlGetField(genomeDBname, "ctgPos", "count(*)", cond_str); sqlSafef(query2, sizeof query2, "select contig, size from %s.ctgPos where chrom='%s' order by size desc", genomeDBname, chromRandom); sr2 = sqlMustGetResult(conn2, query2); row2 = sqlNextRow(sr2); sumRandom = 0; chromRandomDone = FALSE; while ((row2 != NULL) && !chromRandomDone) { contig = row2[0]; ctgSize = row2[1]; sumRandom = sumRandom + atoi(ctgSize); if (sumRandom >= (chromRandomSize/2)) { fprintf(outf,"%12s%9s", ctgRandomCnt, ctgSize); randomCnt = randomCnt + atoi(ctgRandomCnt); chromRandomDone = TRUE; } row2 = sqlNextRow(sr2); } sqlFreeResult(&sr2); } else { fprintf(outf,"%12s%9s", "-", "-"); } fprintf(outf,"\n"); } /* first calculate total chromosome size */ sqlSafef(query2, sizeof query2, "select chrom, size from %s.ctgPos where chrom not like '%crandom%c' and chrom not like '%chap%c' order by size desc", genomeDBname, '%', '%', '%', '%'); sr2 = sqlMustGetResult(conn2, query2); row2 = sqlNextRow(sr2); sumL = 0; while ((row2 != NULL) && !chromDone) { chrom = row2[0]; ctgSize = row2[1]; sumL = sumL + atoi(ctgSize); row2 = sqlNextRow(sr2); } sqlFreeResult(&sr2); halfTotalSize = (int)(sumL/2L); /* calculate N50 totoal */ sqlSafef(query2, sizeof query2, "select chrom, size from %s.ctgPos where chrom not like '%crandom%c' and chrom not like '%chap%c' order by size desc", genomeDBname, '%', '%', '%', '%'); sr2 = sqlMustGetResult(conn2, query2); row2 = sqlNextRow(sr2); sumL = 0L; while ((row2 != NULL) && !chromDone) { chrom = row2[0]; ctgSize = row2[1]; sumL = sumL + atoi(ctgSize); if ((int)sumL >= halfTotalSize) { n50Total = atoi(ctgSize); break; } row2 = sqlNextRow(sr2); } sqlFreeResult(&sr2); /* calculate total random chromosome size */ sqlSafef(query2, sizeof query2, "select chrom, size from %s.ctgPos where chrom like '%crandom%c' order by size desc", genomeDBname, '%', '%'); sr2 = sqlMustGetResult(conn2, query2); row2 = sqlNextRow(sr2); sumL = 0; while ((row2 != NULL) && !chromDone) { chrom = row2[0]; ctgSize = row2[1]; sumL = sumL + atoi(ctgSize); row2 = sqlNextRow(sr2); } sqlFreeResult(&sr2); halfTotalRandomSize = (int)(sumL/2L); /* calculate N50 of randome total */ sqlSafef(query2, sizeof query2, "select chrom, size from %s.ctgPos where chrom like '%crandom%c' order by size desc", genomeDBname, '%', '%'); sr2 = sqlMustGetResult(conn2, query2); row2 = sqlNextRow(sr2); sumL = 0L; while ((row2 != NULL) && !chromDone) { chrom = row2[0]; ctgSize = row2[1]; sumL = sumL + atoi(ctgSize); if ((int)sumL >= halfTotalRandomSize) { n50RandomTotal = atoi(ctgSize); break; } row2 = sqlNextRow(sr2); } sqlFreeResult(&sr2); fprintf(outf,"%s\n", " ----------------------------------------------------------------------------------------------------------------------------------------------------"); /* process overall line */ fprintf(outf," Overall\n"); fprintf(outf," Chrom "); chp1 = strstr(overallLine, "\t"); chp1++; chp = strstr(chp1, "\t"); while (chp != NULL) { *chp = '\0'; fprintf(outf,"%11s", chp1); chp1 = chp+1; chp = strstr(chp1, "\t"); } fprintf(outf,"%19s", chp1); /* print out overall N50s */ fprintf(outf,"%12d%10d%12d%9d\n", orderedCnt, n50Total, randomCnt, n50RandomTotal); fprintf(outf,"\n"); hFreeConn(&conn2); fclose(outf); return(0); }