snptab.c

#include <string.h>
#include <stdio.h>

#include <hdf5.h>
#include <hdf5_hl.h>


#include "memutil.h"
#include "snptab.h"
#include "err.h"
#include "util.h"
#include "snp.h"


/**
 * Allocates memory for and initializes data structure
 * that describes the HDF5 table used to store SNP data.
 * A single SNPTab data structure should be created for 
 * each chromosome, and be freed after use.
 *
 */
SNPTab *snp_tab_new(hid_t h5file, const char *chrom_name,
		    size_t max_record) {
  herr_t status;
  SNPTab *tab;
  SNP snp_desc;

  const char *field_names[] =
    {"name", "pos", "allele1", "allele2"};

  tab = my_malloc(sizeof(SNPTab));
  
  tab->h5file = h5file;  
  
  /* set datatypes for each field */
  tab->name_type = H5Tcopy(H5T_C_S1);
  H5Tset_size(tab->name_type, SNP_MAX_NAME);
  /* no longer store chromosome as each chromosome
   * gets its own table 
   */
  /* tab->chrom_type = H5Tcopy(H5T_C_S1);
   * H5Tset_size(tab->chrom_type, SNP_MAX_CHROM);
   */
  tab->allele_type = H5Tcopy(H5T_C_S1);
  H5Tset_size(tab->allele_type, SNP_MAX_ALLELE);
  tab->field_type[0] = tab->name_type; /* name */
  /* tab->field_type[1] = tab->chrom_type; */ /* chromosome */
  tab->field_type[1] = H5T_NATIVE_LONG; /* pos */
  tab->field_type[2] = tab->allele_type; /* allele1 */
  tab->field_type[3] = tab->allele_type; /* allele2 */

  /* sizes of record and each field */
  tab->record_size = sizeof(SNP);
  tab->field_size[0] = sizeof(snp_desc.name);
  /* tab->field_size[1] = sizeof(snp_desc.chrom); */
  tab->field_size[1] = sizeof(snp_desc.pos);
  tab->field_size[2] = sizeof(snp_desc.allele1);
  tab->field_size[3] = sizeof(snp_desc.allele2);
    
  /* offsets of each field */
  tab->field_offset[0] = HOFFSET(SNP, name);
  /* tab->field_offset[1] = HOFFSET(SNP, chrom); */
  tab->field_offset[1] = HOFFSET(SNP, pos);
  tab->field_offset[2] = HOFFSET(SNP, allele1);
  tab->field_offset[3] = HOFFSET(SNP, allele2);
    
  /* title and name of table */
  tab->title = util_str_concat(chrom_name, " SNPs", NULL);  
  tab->name = util_str_dup(chrom_name);

  /* set chunk size and compression */
  tab->chunk_size = SNPTAB_CHUNK_SIZE;
  tab->compress = 1;

  tab->n_record = 0;
  tab->max_record = max_record;
  
  status = H5TBmake_table(tab->title, tab->h5file, tab->name,
			  SNPTAB_N_FIELDS, tab->max_record,
			  tab->record_size, field_names,
			  tab->field_offset, tab->field_type,
			  tab->chunk_size, NULL, tab->compress, NULL);
  
  if(status < 0) {
    my_err("%s:%d: could not create SNP table\n", __FILE__, __LINE__);
  }

  
  return tab;
}


void snp_tab_free(SNPTab *tab) {
  H5Tclose(tab->allele_type);
  H5Tclose(tab->name_type);
  my_free(tab->title);
  my_free(tab->name);
  
  my_free(tab);
}


/**
 * Appends row to table described by provided SNPTab datastructure.
 */
void snp_tab_append_row(SNPTab *tab, SNP *data) {
  herr_t status;
  hsize_t n_to_write;

  n_to_write = 1;

  /* status = H5TBappend_records(tab->h5file, tab->name, */
  /* 			      n_records, tab->record_size, */
  /* 			      tab->field_offset, tab->field_size, */
  /* 			      data); */

  status = H5TBwrite_records(tab->h5file, tab->name,
			     tab->n_record, n_to_write,
			     tab->record_size, tab->field_offset,
			     tab->field_size, data);

  tab->n_record += 1;
  
  if(status < 0) {
    my_err("%s:%d: failed to write record %ld for SNP '%s' to SNP table\n",
	   __FILE__, __LINE__, tab->n_record, data->name);
  }
  
  /* if((tab->n_record % 10000) == 0) { */
  /*   /\* there is a problem where HDF5 library can run out of  */
  /*    * identifiers. Try to flush periodically as workaround. */
  /*    * (see https://github.com/JuliaIO/HDF5.jl/issues/172 */
  /*    *  and  http://hdf-forum.184993.n3.nabble.com/H5SL-insert-common-can-t-insert-duplicate-key-with-HDF5-1-8-13-td4027464.html) */
  /*    *\/ */
  /*   if(H5Fflush(tab->h5file, H5F_SCOPE_GLOBAL) < 0) { */
  /*     my_err("%s:%d: failed to flush SNP table buffers\n", */
  /* 	     __FILE__, __LINE__); */
  /*   } */
  /* } */
  

}