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Merged
dpryan79 merged 1 commit into from
Apr 20, 2026
Merged

Support version 1 files #12

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11 changes: 7 additions & 4 deletions 2bit.c
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Original file line number Diff line number Diff line change
Expand Up @@ -452,6 +452,7 @@ void twobitIndexRead(TwoBit *tb, int storeMasked) {
if(!idx->nBlockStart) goto error;
if(!idx->nBlockSizes) goto error;
idx->maskBlockCount = calloc(tb->hdr->nChroms, sizeof(uint32_t));

if(!idx->maskBlockCount) goto error;
if(storeMasked) {
idx->maskBlockStart = calloc(tb->hdr->nChroms, sizeof(uint32_t*));
Expand Down Expand Up @@ -584,11 +585,13 @@ void twobitChromListRead(TwoBit *tb) {
uint8_t byte;
char *str = NULL;
TwoBitCL *cl = calloc(1, sizeof(TwoBitCL));
uint8_t useLong = tb->hdr->version == 1;
size_t offsetSz = (useLong) ? sizeof(uint64_t) : sizeof(uint32_t);

//Allocate cl and do error checking
if(!cl) goto error;
cl->chrom = calloc(tb->hdr->nChroms, sizeof(char*));
cl->offset = malloc(sizeof(uint32_t) * tb->hdr->nChroms);
cl->offset = calloc(tb->hdr->nChroms, offsetSz);
if(!cl->chrom) goto error;
if(!cl->offset) goto error;

Expand All @@ -604,7 +607,7 @@ void twobitChromListRead(TwoBit *tb) {
str = NULL;

//Read in the size
if(twobitRead(cl->offset + i, sizeof(uint32_t), 1, tb) != 1) goto error;
if(twobitRead(cl->offset + i, offsetSz, 1, tb) != 1) goto error;
}

tb->cl = cl;
Expand Down Expand Up @@ -657,8 +660,8 @@ void twobitHdrRead(TwoBit *tb) {

//Version
hdr->version = data[1];
if(hdr->version != 0) {
fprintf(stderr, "[twobitHdrRead] The file version is %"PRIu32" while only version 0 is defined!\n", hdr->version);
if(hdr->version != 0 && hdr->version != 1) {
fprintf(stderr, "[twobitHdrRead] The file version is %"PRIu32" while only versions 0 and 1 are defined!\n", hdr->version);
goto error;
}

Expand Down
2 changes: 1 addition & 1 deletion 2bit.h
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Original file line number Diff line number Diff line change
Expand Up @@ -45,7 +45,7 @@ typedef struct {
*/
typedef struct {
char **chrom; /**<A list of null terminated chromosomes */
uint32_t *offset; /**<The file offset for the beginning of each chromosome */
uint64_t *offset; /**<The file offset for the beginning of each chromosome */
} TwoBitCL;

/*!
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