Output the line.

Like descructor for splitLine except don't free memory. Instead, put the linked list of objects back on the free list.

These determine alignment type. Things may get more complicated than this once we have alternate contigs such as in build 38 of human genome.

Output the @PG line information into a SAM file header

Read a line from the file and split it.

Split the line into fields.

Unsplit the fields back into a single string. This will mung the strings, so only call this when all processing on the line is done.

A convenience function for outputing time is seconds in a more useful metric.

This calculates the position of the read in the sequence array, and in the reference genome.

Output the runtine stats. Used both for normal and premature exit.

Resize the buffer of a splitLine. Since the new buffer may not be in the same place, we need to first unsplit, resize, then resplit.

Free big blocks of memory. Not the size is needed.

Allocate big blocks of memory.

Change a field into a value. This will be tough given how we output lines. So, we might have to try a few things. Start with simply expanding/contract

Check the first line of a file (e.g. input) for bam signature.

Descructor for a list of splitLines

C style delete.

Destructor for split line.

Like constuctor, except take struct off free list if there is one.

Creator for splitLine

This is the main workhorse that determines if lines are dups or not.

This just test for end of string.

This will parse a base 10 int, and change ptr to one char beyond the end of the number.

This will the current char, and move the ptr ahead by one.

Need to change this if pos is unsigned.

Special version of write line that appends an id number to the output. Used to output splitters.

Sort ascending in SQO.

I don't think this is currently being called, as we always put the entire string of nodes on the freelist.

This was originally written to test for mismatched MC tags between BWA MEM and samblaster. I keep it around, as some version of this would be useful i

This is apparently no longer called.