Tomioka said Suhr has also written a letter to the American Society of Crime Lab Directors Laboratory Accreditation Board asking them to redo an audit of the crime lab that took place in the summer of 2010. Officials at the lab accreditation board and the DOJ have both said Harmon's memo was not shared with them before SF Weekly reported on its existence.

SFPD brass and forensic scientists were not the only ones implicated in Harmon's testimony to Haines. Braden Woods, chief of the criminal division of the DA's office, was also singled out by Harmon for his opposition to sharing the memo with DOJ auditors. "I hate to bring Braden into this, but he's right in the middle of this," Harmon said, according to the transcript.

"The day that Braden told me the [DOJ] inspection was imminent, I said: 'We can't do that,'" Harmon recalled in his testimony. "And he said to me: 'Well, Rock, what happens if the lab ends up getting closed because of this?' And I said: 'Hey, if that is what is supposed to happen, that is what is supposed to happen.'" Harmon said he also called Pfeifer to alert him to his concerns.

Haines was clearly impressed by the importance of the information Harmon laid out in their interview. "I have to make a note, it's always the cover-up that makes the things worse than the problem to begin with," Haines said to Harmon. "It makes things look worse than perhaps what they are in reality."

The DA's office, when first questioned about Harmon's memo in December 2010, denied the document existed. It later released an appendix to the memo, but not the report itself. In January 2011, Woo sent a letter to defense attorneys falsely suggesting that this appendix was the memo in its entirety.

Prosecutors only acknowledged the memo when defense lawyers requested it following an August cover story on its suppression by SF Weekly. The public defender's office has sought the memo as evidence that could help prove the innocence of James Mayfield, a Bayview church deacon charged with the 1976 murder of Jenny Read, a young sculptor. The case against Mayfield is based largely on DNA evidence analyzed by Boland, and defense attorneys could use the memo to discredit her testimony at trial.

In September, after his closed-door session with Harmon, Haines ruled that the memo, as well as a transcript of Harmon's testimony to him, were exculpatory evidence that should be shared with defense lawyers. The DA's office appealed the ruling, but a panel of state appeals court judges unanimously affirmed Haines' decision.

Nevertheless, the documents remained under a court protective order preventing attorneys from sharing them with the public, except for a single page of Harmon's memo dealing with Boland. The rest of the memo, Haines has ruled, is not immediately relevant to the Mayfield case and falls under an exemption from disclosure for attorneys' private thoughts and opinions.

The public defender's office inadvertently e-mailed the sealed transcript and correspondence from Giuntini to SF Weekly last week, along with the unsealed portion of Harmon's memo. The DA's office threatened to move for Deputy Public Defender Mark Jacobs to be held in contempt of court as a result.

On Monday, however — after Jacobs apologized in court for the mishap, and recounted how he and Public Defender Jeff Adachi had urged a reporter in "strong terms" not to publish the sealed documents — prosecutors relented. Haines said he would not have punished Jacobs for the accident. "You don't want to hold him in contempt? Well, I wasn't going to, anyway," Haines told Woo, who spoke on behalf of the DA's office at the Monday hearing on the documents' release.

Woo and Woods declined to comment on the allegations in the transcript.

Massullo is expected to convene a hearing in the coming weeks on how the revelations in the transcript will affect four separate rape cases that rely on DNA evidence. Last week, when she ordered the DA's office and SFPD to preserve communications among the officials mentioned in the document, she signaled that Harmon's memo, and his testimony, would likely be significant for those cases.

"I think if you read the transcript, and match it up with the memo, it's pretty clear why Judge Haines found it exculpatory,"she said.

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