5359edc160de518d8e43fdd3448365c15b912c3c galt Mon Jul 22 11:48:10 2019 -0700 Added ipv6 support. Listening processes us hybrid dual stack feature of OS to simplify implementation and use a single listening socket. Works with both TCP and UDP. Parasol working. geoIp also updated and ready for IPv6. Should be invisible to most users, while providing connections via ipv6 where available. Supports both ipv4 and ipv6. diff --git src/gfClient/gfClient.c src/gfClient/gfClient.c index 95185d3..95d9458 100644 --- src/gfClient/gfClient.c +++ src/gfClient/gfClient.c @@ -1,174 +1,174 @@ /* gfClient - A client for the genomic finding program that produces a .psl file. */ /* Copyright 2001-2003 Jim Kent. All rights reserved. */ #include "common.h" #include "linefile.h" #include "aliType.h" #include "fa.h" #include "genoFind.h" #include "psl.h" #include "options.h" #include "fuzzyFind.h" static struct optionSpec optionSpecs[] = { {"prot", OPTION_BOOLEAN}, {"q", OPTION_STRING}, {"t", OPTION_STRING}, {"minIdentity", OPTION_FLOAT}, {"minScore", OPTION_INT}, {"dots", OPTION_INT}, {"out", OPTION_STRING}, {"maxIntron", OPTION_INT}, {"nohead", OPTION_BOOLEAN}, {NULL, 0} }; /* Variables that can be overridden by command line. */ int dots = 0; int minScore = 30; double minIdentity = 90; char *outputFormat = "psl"; char *qType = "dna"; char *tType = "dna"; void usage() /* Explain usage and exit. */ { printf( "gfClient v. %s - A client for the genomic finding program that produces a .psl file\n" "usage:\n" " gfClient host port seqDir in.fa out.psl\n" "where\n" " host is the name of the machine running the gfServer\n" " port is the same port that you started the gfServer with\n" - " seqDir is the path of the .nib or .2bit files relative to the current dir\n" + " seqDir is the path of the .2bit or .nib files relative to the current dir\n" " (note these are needed by the client as well as the server)\n" " in.fa is a fasta format file. May contain multiple records\n" " out.psl is where to put the output\n" "options:\n" " -t=type Database type. Type is one of:\n" " dna - DNA sequence\n" " prot - protein sequence\n" " dnax - DNA sequence translated in six frames to protein\n" " The default is dna.\n" " -q=type Query type. Type is one of:\n" " dna - DNA sequence\n" " rna - RNA sequence\n" " prot - protein sequence\n" " dnax - DNA sequence translated in six frames to protein\n" " rnax - DNA sequence translated in three frames to protein\n" " -prot Synonymous with -t=prot -q=prot.\n" " -dots=N Output a dot every N query sequences.\n" " -nohead Suppresses 5-line psl header.\n" " -minScore=N Sets minimum score. This is twice the matches minus the \n" " mismatches minus some sort of gap penalty. Default is 30.\n" " -minIdentity=N Sets minimum sequence identity (in percent). Default is\n" " 90 for nucleotide searches, 25 for protein or translated\n" " protein searches.\n" " -out=type Controls output file format. Type is one of:\n" " psl - Default. Tab-separated format without actual sequence\n" " pslx - Tab-separated format with sequence\n" " axt - blastz-associated axt format\n" " maf - multiz-associated maf format\n" " sim4 - similar to sim4 format\n" " wublast - similar to wublast format\n" " blast - similar to NCBI blast format\n" " blast8- NCBI blast tabular format\n" " blast9 - NCBI blast tabular format with comments\n" " -maxIntron=N Sets maximum intron size. Default is %d.\n", gfVersion, ffIntronMaxDefault); exit(-1); } struct gfOutput *gvo; void gfClient(char *hostName, char *portName, char *tSeqDir, char *inName, char *outName, char *tTypeName, char *qTypeName) /* gfClient - A client for the genomic finding program that produces a .psl file. */ { struct lineFile *lf = lineFileOpen(inName, TRUE); static bioSeq seq; FILE *out = mustOpen(outName, "w"); enum gfType qType = gfTypeFromName(qTypeName); enum gfType tType = gfTypeFromName(tTypeName); int dotMod = 0; char databaseName[256]; struct hash *tFileCache = gfFileCacheNew(); snprintf(databaseName, sizeof(databaseName), "%s:%s", hostName, portName); gvo = gfOutputAny(outputFormat, round(minIdentity*10), qType == gftProt, tType == gftProt, optionExists("nohead"), databaseName, 23, 3.0e9, minIdentity, out); gfOutputHead(gvo, out); while (faSomeSpeedReadNext(lf, &seq.dna, &seq.size, &seq.name, qType != gftProt)) { int conn = gfConnect(hostName, portName); if (dots != 0) { if (++dotMod >= dots) { dotMod = 0; fputc('.', stdout); fflush(stdout); } } if (qType == gftProt && (tType == gftDnaX || tType == gftRnaX)) { gvo->reportTargetStrand = TRUE; gfAlignTrans(&conn, tSeqDir, &seq, minScore, tFileCache, gvo); } else if ((qType == gftRnaX || qType == gftDnaX) && (tType == gftDnaX || tType == gftRnaX)) { gvo->reportTargetStrand = TRUE; gfAlignTransTrans(&conn, tSeqDir, &seq, FALSE, minScore, tFileCache, gvo, qType == gftRnaX); if (qType == gftDnaX) { reverseComplement(seq.dna, seq.size); close(conn); conn = gfConnect(hostName, portName); gfAlignTransTrans(&conn, tSeqDir, &seq, TRUE, minScore, tFileCache, gvo, FALSE); } } else if ((tType == gftDna || tType == gftRna) && (qType == gftDna || qType == gftRna)) { gfAlignStrand(&conn, tSeqDir, &seq, FALSE, minScore, tFileCache, gvo); conn = gfConnect(hostName, portName); reverseComplement(seq.dna, seq.size); gfAlignStrand(&conn, tSeqDir, &seq, TRUE, minScore, tFileCache, gvo); } else { errAbort("Comparisons between %s queries and %s databases not yet supported", qTypeName, tTypeName); } gfOutputQuery(gvo, out); } if (out != stdout) printf("Output is in %s\n", outName); gfFileCacheFree(&tFileCache); } int main(int argc, char *argv[]) /* Process command line. */ { optionInit(&argc, argv, optionSpecs); if (argc != 6) usage(); if (optionExists("prot")) qType = tType = "prot"; qType = optionVal("q", qType); tType = optionVal("t", tType); if (sameWord(tType, "prot") || sameWord(tType, "dnax") || sameWord(tType, "rnax")) minIdentity = 25; minIdentity = optionFloat("minIdentity", minIdentity); minScore = optionInt("minScore", minScore); dots = optionInt("dots", 0); outputFormat = optionVal("out", outputFormat); /* set global for fuzzy find functions */ setFfIntronMax(optionInt("maxIntron", ffIntronMaxDefault)); gfClient(argv[1], argv[2], argv[3], argv[4], argv[5], tType, qType); return 0; }