/* doOmimLocation - This is a one shot program used in the OMIM related subtracks build pipeline */

/* Copyright (C) 2013 The Regents of the University of California 
 * See kent/LICENSE or http://genome.ucsc.edu/license/ for licensing information. */
#include "common.h"
#include "hCommon.h"
#include "dnautil.h"
#include "hdb.h"

void usage()
/* Explain usage and exit. */
{
errAbort(
  "doOmimLocation - This program is part of the OMIM related subtracks build pipeline.\n"
  "usage:\n"
  "   doOmimLocation db outFileName\n"
  "      db is the database name\n"
  "      outFileName is the filename of the output file\n"
  "example: doOmimLocation hg19 omimLocation.tab\n");
}

char *avId, *omimId;
char *location;
FILE   *outf;

int main(int argc, char *argv[])
{
char *database;
char *outFn;
char pqc;
boolean has2Bands;

char gapTableName[255];

struct sqlConnection *conn,*conn2;
char query[1024];
char query2[1024];
struct sqlResult *sr;
struct sqlResult *sr2;
char **row;
char **row2;

int startPos;
int endPos;
int startPosBand1 = 0;
int endPosBand1 = 0;
int startPosBand2;
int endPosBand2;

char locSav[255];

char *chp;
char *chpTer;
char *chpCen;
char chrom[255];

char band1[255];
char band2[255];

if (argc != 3) usage();

database = argv[1];
conn= hAllocConn(database);
conn2= hAllocConn(database);

outFn   = argv[2];
outf    = mustOpen(outFn, "w");

/* process omimGeneMap records with *p* or *q* locations */
sqlSafef(query2, sizeof query2, 
        "select omimId, location from omimGeneMap2New where location like '%cp%c' or location like '%cq%c'", 
        '%','%', '%','%');
sr2 = sqlMustGetResult(conn2, query2);
row2 = sqlNextRow(sr2);
while (row2 != NULL)
    {
    boolean band1Success;
    
    boolean band1HasTer;
    
    band1Success      = FALSE;
    band1HasTer       = FALSE;

    omimId   = row2[0];
    location = row2[1];

    /* save original location string */
    strcpy(locSav, location);
    
    /* break band1 and band2 if there is one */
    chp = strstr(location, "-");
    if (chp != NULL)
        {
        has2Bands = TRUE;
        *chp = '\0';
        chp++;
        strncpy(band2, chp, (size_t)(sizeof(band2)));
        }
    else
        has2Bands = FALSE;

    /* construct chrom first */    
    safef(chrom, sizeof(chrom), "chr%s", location);
    chp = chrom;
    
    /* skip "chr" */
    chp++; 
    chp++; 
    chp++; 
   
    /* get the end position of "chrX" */
    while (! ( (*chp == 'p') || (*chp == 'q') || \
               (*chp == 'c') || (*chp == '\0') ) ) chp++;
    
    if (*chp == '\0')
        {
        /* something is wrong, skip this record */
        fprintf(stderr, "in chrom processing, did not get p, q, or c got %s, locSav=%s, omimId=%s\n", location, locSav, omimId);
        goto skip1;
        }

    /* now we have p or q or c (first char of "cen") */
    pqc = *chp;

    /* construct band1 */
    strncpy(band1, chp, sizeof(band1));
    
    /* terminate the chrom str*/
    *chp = '\0';
    
    // process band1 first 
    
    strcpy(gapTableName, "gap");

    if (sameWord(database, "hg18")) 
        safef(gapTableName, sizeof(gapTableName), "%s_gap", chrom);

    band1Success  = FALSE;
    chpTer = strstr(band1, "ter");
    if (chpTer != NULL)
        {
        band1HasTer = TRUE;
        *chpTer = '\0';
        }
    
    if (band1HasTer == TRUE)
        {
        sqlSafef(query, sizeof query,
            "select chromStart, chromEnd from %s where chrom = '%s' and type ='telomere' and chromStart = 0", gapTableName, chrom);
        }
    else
        {
        /* process "cen" */
        if (pqc == 'c') 
            {
            if (sameWord(database, "hg38"))
                sqlSafef(query, sizeof query,
                    "select min(chromStart), max(chromEnd) from centromeres where chrom = '%s'", chrom);
            else
                sqlSafef(query, sizeof query,
                    "select chromStart, chromEnd from %s where chrom = '%s' and type ='centromere'", gapTableName, chrom);
            }
        else
            {
            /* process p or q */
            if ((pqc == 'p') || (pqc == 'q'))
                {
                sqlSafef(query, sizeof query,
                        "select chromStart, chromEnd from cytoBand where chrom = '%s' and name = '%s'", chrom, band1);
                }
            else
                {
                fprintf(stderr, "can not deal with omimId=%s locaSav=%s band1=%s\n", omimId, locSav, band1);
                goto skip1;
                }
            }
        }

    sr = sqlMustGetResult(conn, query);
    row = sqlNextRow(sr);
    if (row != NULL) 
        {
        startPosBand1 = atoi(row[0]);
        endPosBand1   = atoi(row[1]);
        band1Success  = TRUE;
        }
    else
        {
        sqlFreeResult(&sr);
        sqlSafef(query, sizeof query,
                "select min(chromStart), max(chromEnd) from cytoBand where chrom = '%s' and name like '%s%c'", chrom, band1, '%');
        sr = sqlMustGetResult(conn, query);
        row = sqlNextRow(sr);
        if ((row != NULL) && (row[0] != NULL) && (row[1] != NULL))
            {
            startPosBand1 = atoi(row[0]);
            endPosBand1   = atoi(row[1]);
        
            // special treatment for "...ter" band1 location
            if ((band1HasTer) && (pqc == 'p') && (has2Bands))
                endPosBand1   = 0;
        
            band1Success  = TRUE;
            }
        else
            {
            band1Success  = FALSE;
            fprintf(stderr, "band1 processing failed and skipped: band1=%s, locSav=%s, omimId=%s\n", band1, locSav, omimId);
            }
        }
    sqlFreeResult(&sr);
  
    /* now process band2 */
    if (band1Success && has2Bands)
        {
        boolean band2Success;
        band2Success = FALSE;

        // do a special processing here for cases like "2q32-34" 
        if (isdigit(band2[0]) && pqc == 'q')
            {
            char temp[300];
            safef(temp, sizeof(temp), "q%s", band2);
            safef(band2, sizeof(band2), "%s", temp);
            }

        chpTer = strstr(band2, "ter");
        if (chpTer != NULL) 
            {
            *chpTer = '\0';
            sqlSafef(query, sizeof query,
                    "select max(chromEnd), max(chromEnd) from cytoBand where chrom = '%s' and name like '%s%c'", chrom, band2, '%');
            }
        else
            {
            chpCen = strstr(band2, "cen");
            if (chpCen != NULL) 
                {
                if (sameWord(database, "hg38"))
                    sqlSafef(query, sizeof query,
                            "select min(chromStart), max(chromEnd) from centromeres where chrom = '%s'", chrom);
                else
                    sqlSafef(query, sizeof query,
                            "select chromStart, chromEnd from %s where chrom = '%s' and type = 'centromere'", gapTableName, chrom);
                }
            else
                {
                sqlSafef(query, sizeof query,
                        "select chromStart, chromEnd from cytoBand where chrom = '%s' and name = '%s'", chrom, band2);
                }
            }

        sr = sqlMustGetResult(conn, query);
        row = sqlNextRow(sr);
        if (row != NULL) 
            {
            startPosBand2 = atoi(row[0]);
            endPosBand2   = atoi(row[1]);
            band2Success  = TRUE;
            } 
        else
            {
            sqlFreeResult(&sr);
            sqlSafef(query, sizeof query, 
                    "select min(chromStart), max(chromEnd) from cytoBand where chrom = '%s' and name like '%s%c'", chrom, band2, '%');

            sr = sqlMustGetResult(conn, query);
            row = sqlNextRow(sr);
            if ((row != NULL) && (row[0] != NULL) && (row[1] != NULL))
                {
                startPosBand2 = atoi(row[0]);
                endPosBand2   = atoi(row[1]);
                endPos   = atoi(row[1]);
                band2Success = TRUE;
                }
            else
                {
                band2Success  = FALSE;
                fprintf(stderr, "band2 processing failed and skipped: band2=%s, locSav=%s, omimId=%s\n", band2, locSav, omimId);
                }
            }
    
    if (band2Success) 
        {
        startPos = min(startPosBand1, startPosBand2);
        endPos   = max(endPosBand1,   endPosBand2);

        fprintf(outf, "%s\t%d\t%d\t%s\n", chrom, startPos, endPos, omimId);
        }

        }
    else
        {
        if (band1Success) 
            {
            fprintf(outf, "%s\t%d\t%d\t%s\n", chrom, startPosBand1, endPosBand1, omimId);
            }
        }
    sqlFreeResult(&sr);
skip1:    
    row2 = sqlNextRow(sr2);
    }
sqlFreeResult(&sr2);

fclose(outf);
hFreeConn(&conn2);
return(0);
}