* Frees an hts_opt list. */

64-bit itf8 variant */

! Deallocates all storage used by a SAM_hdr struct. * * This also decrements the header reference count. If after decrementing * it is still non-z

Current RSEM only accept matches

Copies all fields except IDX.

\cond show_private returns x(i-r+index), where index is in 0..r-1

* Returns a portion of a reference sequence from start to end inclusive. * The returned pointer is owned by either the cram_file fd or by the * inte

len : length threshold, any length <= len should be calculated refL : reference sequence length

* Accepts a string file format (sam, bam, cram, vcf, bam) optionally * followed by a comma separated list of key=value options and splits * these up

* For creating existing mFILE pointers directly from memory buffers. */

HELPER FUNCTIONS FOR OPERATORS >> ( ... ) ********************************/

calculates alignment end position, based on starting position and CIGAR operations

calculates alignment end position, based on starting position and CIGAR operations

seek to position in BGZF file

seek to position in BGZF file

Add a new region into a list sorted by start,end. On input the coordinates are 1-based, stored 0-based, inclusive.