Store cigar offsets in lightweight index

[bkille]

Similar to an .fai index, create an .impg index which stores the byte offset and byte size of the cigar string (the cg:Z tag value), as opposed to storing the entire cigar itself. Then, whenever a record is queried, impg looks up the corresponding byte offset/size values, opens the PAF file, seeks the offset, and reads the bytes into a cigar buffer.

TODO:

• Compute byte position/offset from .gz files
• Get tests working

Benchmark

Ran on 23Gb bgzipped PAF file (80 threads for Main and 16 threads for this PR)

impg --paf-file test-data/primates16.20231205_wfmash-v0.12.5.paf.bgz --query chm13#1#chr6:28385000-33300000 -x

Main

Index:

User time (seconds): 113885.48
System time (seconds): 15729.87
Elapsed (wall clock) time (h:mm:ss or m:ss): 30:59.03
Maximum resident set size (kbytes): 147000032

Query:

User time (seconds): 53.11
System time (seconds): 14.96
Elapsed (wall clock) time (h:mm:ss or m:ss): 1:08.11
Maximum resident set size (kbytes): 19346680

This PR

Index:

User time (seconds): 600.19
System time (seconds): 23.18
Elapsed (wall clock) time (h:mm:ss or m:ss): 0:45.43
Maximum resident set size (kbytes): 272596

Query:

User time (seconds): 0.65
System time (seconds): 0.08
Elapsed (wall clock) time (h:mm:ss or m:ss): 0:00.74
Maximum resident set size (kbytes): 67592