Can we get the offset of the first alignment within a range?
The answer seems to be “no”. Building the iterator (sam_itr_queryi)
does not seek, and the first time you use advance the iterator
(bam_itr_next), you are already past the first read.
Here are the offsets of the first reads in the file, along with their
[tStart, tEnd) spans:
./htslib_read_tell bam_mapping.bam | head -10#+RESULTS[42d729a36eb2cca2afa3f0e29c4368acb3d4b55b]:
0x2390000 0 471 0x2391d38 302 1019 0x2393275 675 1026 0x2393c78 2168 2326 0x23941d3 2170 2397 0x23949a8 3572 5015 # This is the first read in our query window 0x2397209 4506 6125 0x239a0e2 4507 5860 0x239c73e 4592 5203 0x239d92b 4658 5011
Now here’s what happens when we try to query the range [5000, 6000)
./htslib_itr_tell bam_mapping.bam#+RESULTS[dbc566df424a2a721ebc5917e95e8486b37271b3]:
0x2390000 3572 5015 # Note incorrect offset here, from pre-seek 0x2397209 4506 6125 0x239a0e2 4507 5860 0x239c73e 4592 5203 0x239d92b 4658 5011 0x239e3ba 4842 5215 0x239ef0c 4903 5380 0x537e0000 5135 5388 0x537e07da 5426 7039 0x537e353a 5942 6134