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2012-06-19	peterjc	Update @SQ lines during 'samtools depad'	commit \| commitdiff \| tree
2012-06-19	peterjc	Calculate unpadded reference length, update BAM header...	commit \| commitdiff \| tree
2012-06-19	peterjc	SAM/BAM input to 'samtools depad' not linked to FASTA...	commit \| commitdiff \| tree
2012-06-19	peterjc	Wording of error messages	commit \| commitdiff \| tree
2012-06-19	peterjc	Catch missing reference error in faidx (avoids floating...	commit \| commitdiff \| tree
2012-06-19	peterjc	Check embedded reference against FASTA if given in...	commit \| commitdiff \| tree
2012-06-19	peterjc	Use FASTA file when no embedded reference in 'samtools...	commit \| commitdiff \| tree
2012-06-19	peterjc	Load FAI in 'samtools depad' (not used yet)	commit \| commitdiff \| tree
2012-06-19	peterjc	Add reference FASTA file to 'samtools depad' command...	commit \| commitdiff \| tree
2012-06-19	peterjc	Support SAM or BAM input/output in 'samtools depad...	commit \| commitdiff \| tree
2012-06-19	peterjc	Minimal 'samtools depad' command line parsing (-? only...	commit \| commitdiff \| tree
2012-06-19	peterjc	Adding a usage function to 'samtools depad' following...	commit \| commitdiff \| tree
2012-06-19	peterjc	Add a tiny bit of help text to 'samtools depad' command.	commit \| commitdiff \| tree
2012-06-19	peterjc	Revert one of my earlier changes - Heng was right,...	commit \| commitdiff \| tree
2012-06-19	peterjc	Fix buffer overflow in 'samtools depad' with CIGAR...	commit \| commitdiff \| tree
2012-06-19	peterjc	Fixed the next silly error on that line.	commit \| commitdiff \| tree
2012-06-19	peterjc	Fix silly typo	commit \| commitdiff \| tree
2012-06-19	peterjc	More elegant solution to avoid superfluous leading...	commit \| commitdiff \| tree
2012-06-19	peterjc	Refine logic for removing superfluous P ops (still...	commit \| commitdiff \| tree
2012-06-12	peterjc	Fix missing declaration for getopt on Mac OS X	commit \| commitdiff \| tree
2012-03-26	peterjc	Check reference length in BAM header against embedded...	commit \| commitdiff \| tree
2012-03-26	peterjc	Cope with trailing CIGAR H (or S and H) in 'samtools...	commit \| commitdiff \| tree
2012-03-26	peterjc	Cope with leading CIGAR H (or H and S) in 'samtools...	commit \| commitdiff \| tree
2012-03-26	peterjc	Tolerate CIGAR H operators in 'samtools depad'	commit \| commitdiff \| tree
2012-03-26	peterjc	Include leading CIGAR P operators in 'samtools depad'	commit \| commitdiff \| tree
2012-03-26	peterjc	Record actual sequence in unpad_seq (fixes apparently...	commit \| commitdiff \| tree
2012-03-23	peterjc	Correct my error message; assed some comments	commit \| commitdiff \| tree
2012-03-23	peterjc	Add TODO note about reference lengths	commit \| commitdiff \| tree
2012-03-23	peterjc	Cope with CIGAR D or P to mark gaps in an embedded...	commit \| commitdiff \| tree
2012-03-22	peterjc	Check current reference sequence matches RNAME in samtools...	commit \| commitdiff \| tree
2012-03-22	peterjc	Support CIGAR X/= in depad	commit \| commitdiff \| tree
2012-03-22	peterjc	Helpful error message on bad CIGAR in unpad_seq	commit \| commitdiff \| tree

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