<commit_before>APER is designed to be ran on SAM files, that have the MD field included, to show errors and quality scores for each base pair position.

Standard behavior of the program includes: reading from stdin, outputting to stdout, looking at local base pair position (not reference base pair position), and enforcing that the 0x2 bit is set on the FLAG field (proper alignment is seen). If deletions occur, it is counted on the base pair previous to that deletion, and has the same quality score as the position.

-Ignores lines starting with '@' character
-MD field must be in the SAM file
-Currently it does not support hard-clippings (H in the cigar string)
-If the -r (--to_reference) argument is used, base pair position (Pos) incrementing starts at the integer specified in the SAM file in the POS field. Otherwise, it starts at 1.


Arguments.
	<commit_msg>Update help.txt<commit_after>APER is designed to be ran on SAM files, that have the MD field included, to show errors and quality scores for each base pair position.

Standard behavior of the program includes: reading from stdin, outputting to stdout, looking at local base pair position (not reference base pair position), and enforcing that the 0x2 bit is set on the FLAG field (proper alignment is seen). If deletions occur, it is counted on the base pair previous to that deletion, and has the same quality score as the position.

-Ignores lines starting with '@' character
-MD field must be in the SAM file
-Currently it does not support hard-clippings (H in the cigar string )
-If the -r (--to_reference) argument is used, base pair position (Pos) incrementing starts at the integer specified in the SAM file in the POS field. Otherwise, it starts at 1.


Arguments.
	
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{'dir': 'git-commits-cleaned', 'id': '1144649', 'n_tokens_mistral': 454, 'n_tokens_neox': 418, 'n_words': 287}