htslib//wiki č.cc

Zero initialize `bam1_t` memory!

htslib expects bam1_t to be initially zeroed, e.g.

// on the stack
bam1_t badbamrecord; // any attempts to use this will likely crash!
bam1_t goodbamrecord = {0}; // this works.

// on the heap
bam1_t* badbamrecord_ptr = malloc(sizeof(bam1_t)); // will likely fail
bam1_t* goodbamrecord_ptr = calloc(1, sizeof(bam1_t)); // good.

Iterator weirdness

When iterating over a file sans index, i.e. by invoking sam_itr_queryi with idx == NULL and tid == HTS_IDX_REST, you need to access the header via sam_hdr_read (even if nothing is being done with it) in order to advance the file pointer up to the first read:
```
htsFile* bam = hts_open(<path/to/bam>, "r");
hts_itr_t* bamiter = sam_itr_queryi(NULL, HTS_IDX_REST, 0, 0);

bam1_t bamrecord = {0};

//sam_hdr_read(bam); // uncomment for iterator to work

while(sam_itr_next(bam, bamiter, &bamrecord) >= 0) {
   // process read
}
```
If the header is not read, then the first call to sam_itr_next will try unpacking a read from the start of the file, which will fail.
Iterators do not work on raw SAM files (due to lack of SAM indexing), even if they are not constrained to a region (as above). Easiest fix is to just add a samtools view -u before the tool to convert to uncompressed BAM.

Output weirdness

To output an uncompressed BAM, you cannot use

htsFile* bam_out = hts_open("-", "wbu");

as you might expect; this will segfault. You must instead use

htsFile* bam_out = hts_open("-", "wb0");

This is because a BAM must still be in block GZIP format, even if no compression is applied.

Note that specifying output "wu" will output a plaintext SAM file.

Zero initialize bam1_t memory!

Iterator weirdness

Output weirdness

Zero initialize `bam1_t` memory!