73c8bb869d9706d2ed2d39c2df7deb351c43c07c hiram Wed Jul 13 11:57:30 2011 -0700 modernize to newer style of kent code diff --git src/hg/pslPairs/pslPairs.c src/hg/pslPairs/pslPairs.c index 56d9d74..0caf0fe 100644 --- src/hg/pslPairs/pslPairs.c +++ src/hg/pslPairs/pslPairs.c @@ -1,72 +1,106 @@ +/* pslPairs - join paired ends in psl alignments */ /* File: pslPairs.c Author: Terry Furey Date: 10/1/2003 Description: Create end sequence pairs from psl files */ #include "common.h" #include "linefile.h" #include "memalloc.h" #include "hash.h" #include "jksql.h" #include "hdb.h" #include "fuzzyFind.h" #include "portable.h" #include "psl.h" #include "options.h" #include "binRange.h" +static boolean VERBOSE = FALSE; +static boolean SLOP = FALSE; +static boolean SHORT = FALSE; +static boolean LONG = FALSE; +static boolean MISMATCH = FALSE; +static boolean ORPHAN = FALSE; +static boolean NORANDOM = FALSE; +static boolean NOBIN = FALSE; +static int MIN = 32000; +static int MAX = 47000; +static int SLOPVAL = 5000; +static float NEARTOP = 0.001; +static int TINSERT = 500; +static int HARDMAX = 75000; +static float MIN_ID = 0.96; +static float MIN_ORPHAN_ID = 0.96; + +static void usage() +/* Explain usage and exit */ +{ +errAbort( +"pslPairs - join paired ends in psl alignments\n" +"usage: pslPairs <pslFile> <pairFile> <pslTableName> <outFilePrefix>\n" +" creates: <outFilePrefix>.pairs file\n" +" pslFile\t- filtered psl alignments of ends from kluster run\n" +" pairFile\t- three column tab separated: forward reverse cloneId\n" +"\t\t- forward and reverse columns can be comma separated end ids\n" +" pslTableName\t- table name the psl alignments have been loaded into\n" +" outFilePrefix\t- prefix used for each output file name\n" +"Options:\n" +" -max=N\t- maximum length of clone sequence (default=%d)\n" +" -min=N\t- minimum length of clone sequence (default=%d)\n" +" -slopval=N\t- deviation from max/min clone lengths allowed for slop report\n\t\t- (default=%d)\n" +" -nearTop=N\t- maximium deviation from best match allowed (default=%0.3f)\n" +" -minId=N\t- minimum pct ID of at least one end (default=%0.2f)\n" +" -minOrphanId=N - minimum pct ID for orphan alignment (default=%0.2f)\n" +" -tInsert=N\t- maximum insert bases allowed in sequence alignment\n\t\t- (default=%d)\n" +" -hardMax=N\t- absolute maximum clone length for long report (default=%d)\n" +" -verbose\t- display all informational messages\n" +" -noBin\t- do not include bin column in output file\n" +" -noRandom\t- do not include placements on random portions\n\t\t- {length(chr name) < 7}\n" +" -slop\t\t- create <outFilePrefix>.slop file of pairs that fall within\n\t\t- slop length\n" +" -short\t- create <outFilePrefix>.short file of pairs shorter than\n\t\t- min size\n" +" -long\t\t- create <outFilePrefix>.long file of pairs longer than\n\t\t- max size, but less than hardMax size\n" +" -mismatch\t- create <outFilePrefix>.mismatch file of pairs with\n\t\t- bad orientation of ends\n" +" -orphan\t- create <outFilePrefix>.orphan file of unmatched end sequences", +MAX, MIN, SLOPVAL, NEARTOP, MIN_ID, MIN_ORPHAN_ID, TINSERT, HARDMAX +); +} + /* command line option specifications */ static struct optionSpec optionSpecs[] = { {"verbose", OPTION_BOOLEAN}, {"slop", OPTION_BOOLEAN}, {"short", OPTION_BOOLEAN}, {"long", OPTION_BOOLEAN}, {"mismatch", OPTION_BOOLEAN}, {"orphan", OPTION_BOOLEAN}, {"noRandom", OPTION_BOOLEAN}, {"noBin", OPTION_BOOLEAN}, {"min", OPTION_INT}, {"max", OPTION_INT}, {"slopval", OPTION_INT}, {"nearTop", OPTION_FLOAT}, {"minId", OPTION_FLOAT}, {"minOrphanId", OPTION_FLOAT}, {"tInsert", OPTION_INT}, {"hardMax", OPTION_INT}, {NULL, 0} }; -boolean VERBOSE = FALSE; -boolean SLOP = FALSE; -boolean SHORT = FALSE; -boolean LONG = FALSE; -boolean MISMATCH = FALSE; -boolean ORPHAN = FALSE; -boolean NORANDOM = FALSE; -boolean NOBIN = FALSE; -int MIN; -int MAX; -int SLOPVAL; -float NEARTOP; -int TINSERT; -int HARDMAX; -float MIN_ID; -float MIN_ORPHAN_ID; - FILE *of, *orf, *sf, *mf, *esf, *elf; struct cloneName { char name[32]; }; struct pslAli { struct pslAli *next; int score; float id; float cov; struct psl *psl; }; @@ -464,54 +498,52 @@ else if ((clone->orphan) && (ORPHAN)) { printOrphan(orf, clone->end1, clone, pslTable); printOrphan(orf, clone->end2, clone, pslTable); } } } int main(int argc, char *argv[]) { struct lineFile *pf, *prf; char filename[64], *pslTable; optionInit(&argc, argv, optionSpecs); if (argc < 4) - { - fprintf(stderr, "USAGE: pslPairs <psl file> <pair file> <psl table name> <out file prefix>\n Options:\n\t-max=N\t\tmaximum length of clone sequence (default=50000)\n\t-min=N\t\tminimum length of clone sequence (default=30000)\n\t-slopval=N\tdeviation from max/min clone lengths allowed for slop report (default=5000)\n\t-nearTop=N\tmaximium deviation from best match allowed (default=0.001)\n\t-minId=N\tminimum pct ID of at least one end (default=0.96)\n\t-minOrphanId=N\tminimum pct ID for orphan alignment (default=0.96)\n\t-tInsert=N\tmaximum insert bases allowed in sequence alignment (default=500)\n\t-hardMax=N\tabsolute maximum clone length for long report (default=75000)\n\t-verbose\tdisplay all informational messages\n\t-noBin\t\tdo not include bin column in output file\n\t-noRandom\tdo not include placements on random portions\n\t-slop\t\tcreate file of pairs that fall within slop length\n\t-short\t\tcreate file of pairs shorter than min size\n\t-long\t\tcreate file of pairs longer than max size, but less than hardMax size\n\t-mismatch\tcreate file of pairs with bad orientation of ends\n\t-orphan\t\tcreate file of unmatched end sequences\n"); - return 1; - } + usage(); + VERBOSE = optionExists("verbose"); SLOP = optionExists("slop"); SHORT = optionExists("short"); LONG = optionExists("long"); MISMATCH = optionExists("mismatch"); ORPHAN = optionExists("orphan"); NORANDOM = optionExists("noRandom"); NOBIN = optionExists("noBin"); - MIN = optionInt("min",32000); - MAX = optionInt("max",47000); - TINSERT = optionInt("tInsert",500); - HARDMAX = optionInt("hardMax",75000); + MIN = optionInt("min",MIN); + MAX = optionInt("max",MAX); + TINSERT = optionInt("tInsert",TINSERT); + HARDMAX = optionInt("hardMax",HARDMAX); if (SLOP) - SLOPVAL = optionInt("slopval",5000); + SLOPVAL = optionInt("slopval",SLOPVAL); else SLOPVAL = 0; - NEARTOP = optionFloat("nearTop",0.001); + NEARTOP = optionFloat("nearTop",NEARTOP); NEARTOP = 1 - NEARTOP; - MIN_ID = optionFloat("minId",0.96); - MIN_ORPHAN_ID = optionFloat("minOrphanId",0.96); + MIN_ID = optionFloat("minId",MIN_ID); + MIN_ORPHAN_ID = optionFloat("minOrphanId",MIN_ORPHAN_ID); pf = pslFileOpen(argv[1]); prf = lineFileOpen(argv[2],TRUE); pslTable = cloneString(argv[3]); sprintf(filename, "%s.pairs", argv[4]); of = mustOpen(filename, "w"); if (SLOP) { sprintf(filename, "%s.slop", argv[4]); sf = mustOpen(filename, "w"); } if (ORPHAN) { sprintf(filename, "%s.orphan", argv[4]);