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Address various comments
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- checks for memory allocation failures
- sanitize numeric types and clean up old comments
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@pd3
pd3 committed Jun 28, 2023
1 parent 6eb791d commit 2fd54e3
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Showing 2 changed files with 37 additions and 24 deletions.
46 changes: 32 additions & 14 deletions annot-tsv.c
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Original file line number Diff line number Diff line change
Expand Up @@ -77,7 +77,7 @@ typedef struct
dat_t;

// This is for the special -a annotations, keeps a list of
// soure regions that hit the destination region. The start
// source regions that hit the destination region. The start
// coordinates are converted to beg<<1 and end coordinates
// to (end<<1)+1.
#define NBP_SET_BEG(x) ((x)<<1)
Expand All @@ -87,8 +87,8 @@ dat_t;
#define NBP_IS_END(x) (((x)&1)==1)
typedef struct
{
int n,m; // n is a multiple of two: breakpoints are stored in regs, not regions
hts_pos_t *regs; // change to uint64_t for very large genomes
size_t n,m; // n is a multiple of two: breakpoints are stored in regs, not regions
hts_pos_t *regs;
hts_pos_t beg,end; // the current destination interval
}
nbp_t;
Expand All @@ -103,7 +103,7 @@ typedef struct
char *temp_dir, *out_fname;
BGZF *out_fp;
int allow_dups, reciprocal, ignore_headers, max_annots, mode;
float overlap;
double overlap;
regidx_t *idx;
regitr_t *itr;
kstring_t tmp_kstr;
Expand All @@ -123,7 +123,9 @@ void error(const char *format, ...)

static nbp_t *nbp_init(void)
{
return calloc(1,sizeof(nbp_t));
nbp_t *nbp = calloc(1,sizeof(nbp_t));
if ( !nbp ) error("Out of memory, failed to allocatae %zu bytes\n",sizeof(nbp_t));
return nbp;
}
static void nbp_destroy(nbp_t *nbp)
{
Expand All @@ -138,12 +140,12 @@ static inline void nbp_reset(nbp_t *nbp, hts_pos_t beg, hts_pos_t end)
}
static inline void nbp_add(nbp_t *nbp, hts_pos_t beg, hts_pos_t end)
{
if ( end >= REGIDX_MAX>>1 ) error("Error: the coordinate is too big (%u). Possible todo: switch to uint64_t\n",end);
nbp->n += 2;
if ( nbp->n >= nbp->m )
{
nbp->m += 2;
nbp->regs = realloc(nbp->regs, nbp->m*sizeof(*nbp->regs));
if ( !nbp->regs ) error("Out of memory, failed to allocate %zu bytes\n",nbp->m*sizeof(*nbp->regs));
}
nbp->regs[nbp->n - 2] = NBP_SET_BEG(beg);
nbp->regs[nbp->n - 1] = NBP_SET_END(end);
Expand All @@ -156,11 +158,11 @@ static int compare_hts_pos(const void *aptr, const void *bptr)
if (a > b) return 1;
return 0;
}
static int nbp_length(nbp_t *nbp)
static hts_pos_t nbp_length(nbp_t *nbp)
{
qsort(nbp->regs, nbp->n, sizeof(*nbp->regs), compare_hts_pos);
int i, nopen = 0, length = 0;
hts_pos_t beg = 0;
int i, nopen = 0;
hts_pos_t beg = 0, length = 0;
for (i=0; i<nbp->n; i++)
{
if ( NBP_IS_BEG(nbp->regs[i]) )
Expand All @@ -178,9 +180,11 @@ static int nbp_length(nbp_t *nbp)
cols_t *cols_split(const char *line, cols_t *cols, char delim)
{
if ( !cols ) cols = (cols_t*) calloc(1,sizeof(cols_t));
if ( !cols ) error("Out of memory, failed to allocate %zu bytes\n",sizeof(cols_t));
if ( cols->rmme ) free(cols->rmme);
cols->n = 0;
cols->rmme = strdup(line);
if ( !cols->rmme ) error("Out of memory\n");
char *ss = cols->rmme;
while (1)
{
Expand All @@ -193,6 +197,7 @@ cols_t *cols_split(const char *line, cols_t *cols, char delim)
{
cols->m += 10;
cols->off = realloc(cols->off, sizeof(*cols->off)*cols->m);
if ( !cols->off ) error("Out of memory, failed to allocate %zu bytes\n",sizeof(*cols->off)*cols->m);
}
cols->off[ cols->n - 1 ] = ss;
if ( !tmp ) break;
Expand All @@ -211,8 +216,10 @@ void cols_append(cols_t *cols, char *str)
size_t tot_len = 2 + str_len + lst_len + (cols->off[ cols->n - 1 ] - cols->rmme);

cols_t *tmp_cols = (cols_t*)calloc(1,sizeof(cols_t));
if ( !tmp_cols ) error("Out of memory, failed to allocate %zu bytes\n",sizeof(cols_t));
tmp_cols->rmme = calloc(tot_len,1);
tmp_cols->off = calloc(cols->n+1,sizeof(*tmp_cols->off));
if ( !tmp_cols->rmme || !tmp_cols->off ) error("Out of memory\n");

char *ptr = tmp_cols->rmme;
int i;
Expand Down Expand Up @@ -240,6 +247,7 @@ void cols_append(cols_t *cols, char *str)
{
cols->m++;
cols->off = realloc(cols->off,sizeof(*cols->off)*cols->m);
if ( !cols->off ) error("Out of memory, failed to allocate %zu bytes\n",sizeof(*cols->off)*cols->m);
}
cols->off[cols->n-1] = str;
}
Expand Down Expand Up @@ -399,13 +407,16 @@ void destroy_header(dat_t *dat)
static int read_next_line(dat_t *dat)
{
if ( dat->line.l ) return dat->line.l;
if ( hts_getline(dat->fp, KS_SEP_LINE, &dat->line) > 0 ) return dat->line.l;
int ret = hts_getline(dat->fp, KS_SEP_LINE, &dat->line);
if ( ret > 0 ) return dat->line.l;
if ( ret < -1 ) error("Error encountered while reading %s\n",dat->fname);
return 0;
}

void sanity_check_columns(char *fname, hdr_t *hdr, cols_t *cols, int **col2idx, int force)
{
*col2idx = (int*)malloc(sizeof(int)*cols->n);
if ( !*col2idx ) error("Out of memory, failed to allocate %zu bytes\n",sizeof(int)*cols->n);
int i, idx;
for (i=0; i<cols->n; i++)
{
Expand Down Expand Up @@ -474,13 +485,18 @@ void init_data(args_t *args)
}
args->tmp_cols = (cols_t*)calloc(args->src.transfer->n,sizeof(cols_t));
args->tmp_hash = (khash_t(str2int)**)calloc(args->src.transfer->n,sizeof(khash_t(str2int)*));
if ( !args->tmp_cols || !args->tmp_hash ) error("Out of memory\n");
for (i=0; i<args->src.transfer->n; i++)
args->tmp_hash[i] = khash_str2int_init();
cols_destroy(tmp);
}
else
{
args->src.transfer = calloc(1,sizeof(*args->src.transfer));
if ( !args->src.transfer ) error("Out of memory\n");
}
args->src.nannots_added = calloc(args->src.transfer->n,sizeof(*args->src.nannots_added));
if ( !args->src.nannots_added ) error("Out of memory\n");

// -a, annotation columns
if ( args->annots_str )
Expand All @@ -490,6 +506,7 @@ void init_data(args_t *args)
args->dst.annots = cols_split(tmp->n==2 ? tmp->off[1] : tmp->off[0],NULL,',');
if ( args->src.annots->n!=args->dst.annots->n ) error("Different number of src and dst columns in %s\n",args->annots_str);
args->dst.annots_idx = (int*) malloc(sizeof(int)*args->dst.annots->n);
if ( !args->dst.annots_idx ) error("Out of memory\n");
for (i=0; i<args->src.annots->n; i++)
{
if ( !strcasecmp(args->src.annots->off[i],"nbp") )
Expand Down Expand Up @@ -581,7 +598,8 @@ static void write_annots(args_t *args)
if ( !args->dst.annots ) return;

args->tmp_kstr.l = 0;
int i, len = nbp_length(args->nbp);
int i;
hts_pos_t len = nbp_length(args->nbp);
for (i=0; i<args->dst.annots->n; i++)
{
if ( args->dst.annots_idx[i]==ANN_NBP )
Expand Down Expand Up @@ -642,9 +660,9 @@ void process_line(args_t *args, char *line, size_t size)
{
if ( args->overlap )
{
float len1 = end - beg + 1;
float len2 = args->itr->end - args->itr->beg + 1;
float isec = (args->itr->end < end ? args->itr->end : end) - (args->itr->beg > beg ? args->itr->beg : beg) + 1;
double len1 = end - beg + 1;
double len2 = args->itr->end - args->itr->beg + 1;
double isec = (args->itr->end < end ? args->itr->end : end) - (args->itr->beg > beg ? args->itr->beg : beg) + 1;
if ( args->reciprocal )
{
if ( isec/len1 < args->overlap || isec/len2 < args->overlap ) continue;
Expand Down
15 changes: 5 additions & 10 deletions annot-tsv.txt
View file
Original file line number Diff line number Diff line change
@@ -1,14 +1,9 @@
// annot-tsv.txt -- asciidoc template for the bcftools man page and html.
// annot-tsv.txt -- asciidoctor template for the bcftools man page and html.
//
// Please do not modify annot-tsv.1 or annot-tsv.html directly,
// edit this file and convert using the following commands:
// Please do not modify annot-tsv.1 directly,
// edit this file and convert using the following command:
//
// make docs
//
// or
//
// a2x --doctype manpage --format manpage annot-tsv.txt
// a2x --doctype manpage --format xhtml annot-tsv.txt
// asciidoctor -b manpage annot-tsv.txt
//
// Contributions are welcome, simply edit this file and send
// a pull request or email the modified file directly.
Expand Down Expand Up @@ -162,6 +157,6 @@ The program was written by Petr Danecek and was originally published on github a

COPYING
-------
The MIT/Expat License or GPL License, see the LICENSE document for details.
The MIT/Expat License, see the LICENSE document for details.
Copyright (c) Genome Research Ltd.

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