selgt_main.c

/*
The MIT License (MIT)

Copyright (c) 2020 Pierre Lindenbaum

Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
copies of the Software, and to permit persons to whom the Software is
furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all
copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
SOFTWARE.

*/
#include <getopt.h>
#include <unistd.h>
#include <ctype.h>
#include "selgt.h"
#include "selgt.tab.h"
#include "lex.yy.h"

extern int yyparse();

NodePtr g_node = NULL;
bcf_hdr_t *g_header;

static int int_compare(int a, int op,int b) {
	switch(op) {
		case LEX_EQ : return a==b;
		case LEX_NE : return a!=b;
		case LEX_LT : return a < b;
		case LEX_LE : return a <= b;
		case LEX_GE : return a>=b;
		case LEX_GT : return a>b;
		default: ERROR("Illegal state %d",op);
		}
	}

static int eval_variant(IntArrayPtr gts,NodePtr node) {
	int i;
	int matching=0;
	assert(gts!=NULL);
	assert(node!=NULL);
	
	switch(node->type) {
		case NODE_TYPE_COMPARE:
				{
				for(i=0; i< IntArraySize(node->check->samples);i++) {
					int sample_index=  IntArrayAt(node->check->samples,i);
					int sample_gt= IntArrayAt(gts,sample_index);
					int found = IntArrayContains(node->check->gtypes,sample_gt);
					
					if(node->check->negate && !found) {
						matching++;	
						}
					else if(!node->check->negate && found) {
						matching++;	
						}
					}
				return int_compare(matching, node->check->cmp_operator,node->check->expect_n_samples);
				}
		case NODE_TYPE_AND:
			return eval_variant(gts,node->left) && eval_variant(gts,node->right);
		case NODE_TYPE_OR:
			return eval_variant(gts,node->left) || eval_variant(gts,node->right);
		case NODE_TYPE_NOT:
			return !eval_variant(gts,node->left);
		default: ERROR("bad state"); abort(); break;
		}
	return 0;
	}

void NodeFree(NodePtr node) {
	if(node==NULL) return;
	switch(node->type) {
		case NODE_TYPE_COMPARE:
			CheckGtFree(node->check);
			break;
		case NODE_TYPE_AND: case NODE_TYPE_OR:
			NodeFree(node->left);
			NodeFree(node->right);
			break;
		case NODE_TYPE_NOT:
			NodeFree(node->left);
			break;
		}
	free((void*)node);
	}

CheckGtPtr CheckGtNew() {
	CheckGtPtr ptr = (CheckGtPtr)malloc(sizeof(CheckGt));
	if(ptr==NULL) ERROR("out of memory");
	memset((void*)ptr,0,sizeof(CheckGt));
	return ptr;
	}

void CheckGtFree(CheckGtPtr ptr) {
	if(ptr==NULL) return;
	IntArrayFree(ptr->samples);
	IntArrayFree(ptr->gtypes);
	free((void*)ptr);
	}

NodePtr NodeNew() {
	NodePtr ptr = (NodePtr)malloc(sizeof(Node));
	if(ptr==NULL) ERROR("out of memory");
	memset((void*)ptr,0,sizeof(Node));
	return ptr;
	}

IntArrayPtr IntArrayNew() {
	IntArrayPtr ptr = (IntArrayPtr)malloc(sizeof(IntArray));
	if(ptr==NULL) ERROR("out of memory");
	ptr->data= 0;
	ptr->size=0;
	return ptr;
	}

IntArrayPtr IntArrayAdd(IntArrayPtr ptr,int sample_idx) {
	ptr->data = (int*)realloc((void*)ptr->data,sizeof(int)*(ptr->size+1));
	if( (ptr->data) == NULL) ERROR("out of memory");
	ptr->data[ptr->size] = sample_idx;
	ptr->size++;
	return ptr;
	}

int IntArrayContains(IntArrayPtr ptr,int sample_idx) {
	int i;
	for(i=0;i< ptr->size ; i++) {
		if(ptr->data[i] == sample_idx) return 1;
		}
	return 0;
	}

IntArrayPtr IntArrayInsert(IntArrayPtr ptr,int sample_idx) {
	if(IntArrayContains(ptr,sample_idx)==1) return ptr;
	return IntArrayAdd(ptr,sample_idx);
	}


void IntArrayFree(IntArrayPtr ptr) {
	if(ptr==NULL) return;
	free(ptr->data);
	free(ptr);
	}

static void usage(const char* name,FILE* out) {
    fprintf(out,"%s: Compiled %s %s. Pierre Lindenbaum\n",name,__DATE__,__TIME__);
    fprintf(out,"version: %s\n", BCF_SELECT_GT_VERSION);
    fprintf(out,"htslib: %s\n",hts_version());
    fprintf(out,"Usage: %s [ -O (o|v|z) ] [ -F <FILTER> ] [-o fileout] (-e <expression> | -f <file> ) (stdin|bcf|vcf)\n",name);
    fprintf(out,"Options:\n");
    fprintf(out,"  -h print help\n");
    fprintf(out,"  -F (string) soft FILTER name. (default: filter out variants)\n");
    fprintf(out,"  -e (string) expression. See manual. Required or use -f.\n");
    fprintf(out,"  -f (file) script file. See manual. Required or use -e.\n");
    fprintf(out,"  -o (file) output file (default stdout)\n");
    fprintf(out,"  -O (char) output format z:bgzip v:vcf b:bcf (default v)\n");
    fprintf(out,"\n");
    }
    
int main(int argc,char** argv) {
 int c;
 int ret=0;
 int i;
 int filter_id=-1;
 char* script_file = NULL;
 char* filter=NULL;
 char* fileout=NULL;
 char format[3]={'v','w',0};
 char* user_expr_str = NULL;
 while ((c = getopt (argc, argv, "o:O:e:F:f:h")) != -1)
    switch (c)
      {
      case 'f':
      	script_file = optarg;
      	break;
      case 'F': filter=optarg; 
      	if(strlen(filter)==0) ERROR("empty filter name");
      	break;
      case 'O':
            if(strlen(optarg)!=1) {
                usage(argv[0],stderr);
                ERROR("Bad format '%s'.",optarg);
                return EXIT_FAILURE;                
                }
            format[0]=optarg[0];
            break;
      case 'o': fileout=strdup(optarg);break;
      case 'h':
            usage(argv[0],stdout);
            return EXIT_SUCCESS;
      case 'e':
            user_expr_str = strdup(optarg);
            break;
      default:
          usage(argv[0],stderr);
          ERROR("Argument error.");
          return EXIT_FAILURE;
      }

if( user_expr_str !=NULL &&  script_file !=NULL) {
    ERROR("both option -e and -f were used");
    return EXIT_FAILURE;    
	}
else if( user_expr_str ==NULL &&  script_file ==NULL ) {
    ERROR("expression (or script file) is missing");
    return EXIT_FAILURE;    
	}
else if(script_file!=NULL)
	{
	FILE * fp = fopen (script_file, "rb");
	if(fp==NULL) ERROR("Cannot open script file %s (%s)",script_file,strerror(errno));
	fseek (fp, 0, SEEK_END);
	long length = ftell (fp);
	fseek (fp, 0, SEEK_SET);
	user_expr_str  = (char*)malloc (length+1);
	if(user_expr_str==NULL) ERROR("Cannot read script file");
	if( (long)fread (user_expr_str, sizeof(char), length, fp) != length) {
		ERROR("Cannot read script file");
		}
	fclose (fp);
	user_expr_str[length]=0;
	}
	
//cleanup script
i=0;
while(user_expr_str[i]!=0) {
	if(isspace(user_expr_str[i])) user_expr_str[i]=' ';
	i++;
	}
	
if(!(optind==argc || optind+1==argc)) {
    ERROR("Illegal number of arguments");
    return EXIT_FAILURE;    
    }
htsFile *in = hts_open(optind==argc ?"-":argv[optind],"r");
if(in==NULL) {
    ERROR("Cannot open input vcf %s. (%s)",(optind==argc ?"<stdin>":argv[optind]),strerror(errno));
    return EXIT_FAILURE;    
    }
bcf_hdr_t *header = bcf_hdr_read(in);
if(header==NULL) {
    ERROR("Cannot read header for input vcf %s.",(optind==argc ?"<stdin>":argv[optind]));
    return EXIT_FAILURE;    
    }

int nsmpl = bcf_hdr_nsamples(header);
if( nsmpl ==0) {
	ERROR("No Genotypes in input.");
	return EXIT_FAILURE;
	}

g_header = header; 
YY_BUFFER_STATE buffer_state = yy_scan_string(user_expr_str);
yyparse();
yy_delete_buffer(buffer_state);
if( g_node == NULL) {
 	ERROR("Illegal state.");
    return EXIT_FAILURE;   
	}


htsFile *out = hts_open((fileout==NULL?"-":fileout),format);
if(out==NULL) {
    ERROR("Cannot open output vcf %s. (%s)",(fileout==NULL?"<STDOUT>":fileout),strerror(errno));
    return EXIT_FAILURE;    
    }
kstring_t xheader = {0,0,0};
ksprintf(&xheader, "##gtselect.command=%s (version:%s)\n",user_expr_str,BCF_SELECT_GT_VERSION);
bcf_hdr_append(header, xheader.s);
free(xheader.s);

if(filter!=NULL) {
	if( bcf_hdr_id2int(header, BCF_DT_ID, filter) >=0 ) {
		ERROR("##FILTER=%s already defined in header.",filter);
		}
	bcf_hdr_printf(header, "##FILTER=<ID=%s,Description=\"filtered with %s>", filter,argv[0]);
    filter_id = bcf_hdr_id2int(header, BCF_DT_ID, filter);
    assert( filter_id >=0);
	}
if ( bcf_hdr_write(out, header)!=0 ) {
    ERROR("Cannot write header.");
    return EXIT_FAILURE;      
    }

bcf1_t* bcf = bcf_init();
if(bcf==NULL) {
    ERROR("Out of memory.");
    return EXIT_FAILURE;    
    }



IntArrayPtr genotype_types  = IntArrayNew();
for(i=0;i< nsmpl ;i++) {
	IntArrayAdd(genotype_types,-1);
	}
assert(genotype_types->size == nsmpl);
	    
while((ret=bcf_read(in, header, bcf))==0) {
	bcf_fmt_t *gt_fmt;
	if(bcf->errcode!=0) {
		WARNING("Skipping Error in VCF record at tid %d:%"PRIhts_pos,bcf->rid, bcf->pos+1);
		continue;
		}
        
   	bcf_unpack(bcf,BCF_UN_IND);
	
    if ( (gt_fmt=bcf_get_fmt(header,bcf,"GT")) ==NULL ) continue;
    

    for(i=0;i< nsmpl ;i++) {
		int type = bcf_gt_type(gt_fmt,i,NULL,NULL);
		genotype_types->data[i]=type;
		}
	int keep =  eval_variant(genotype_types,g_node);
	
	
	
	if(keep==0) {
		if(filter==NULL) continue;
		 bcf_add_filter(header,bcf,filter_id);
		}
	
    if(bcf_write1(out, header, bcf)!=0) {
        ERROR("IO error. Cannot write record.");
        return EXIT_FAILURE;
        }
  	}

IntArrayFree(genotype_types);
if(fileout) free(fileout);
bcf_destroy(bcf);
bcf_hdr_destroy(header);
hts_close(in);
hts_close(out);
NodeFree(g_node);
free(user_expr_str);
  return EXIT_SUCCESS;
}