Your message dated Fri, 27 Jul 2012 14:48:09 +0000 with message-id <[email protected]> and subject line Bug#671524: fixed in samtools 0.1.18-2 has caused the Debian Bug report #671524, regarding samtools depth caps coverage at 8000 to be marked as done.
This means that you claim that the problem has been dealt with. If this is not the case it is now your responsibility to reopen the Bug report if necessary, and/or fix the problem forthwith. (NB: If you are a system administrator and have no idea what this message is talking about, this may indicate a serious mail system misconfiguration somewhere. Please contact [email protected] immediately.) -- 671524: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=671524 Debian Bug Tracking System Contact [email protected] with problems
--- Begin Message ---Package: samtools Version: 0.1.18-1 samtools depth sets a cap of 8000 for coverage. It becomes an issue when used to calculate depth for targeted sequencing applications. Attached patch increases the threshold to 1 million. Is this safe to apply? Thanks -Dominique Index: bam2depth.c =================================================================== --- bam2depth.c (revision 995) +++ bam2depth.c (working copy) @@ -80,6 +80,7 @@ // the core multi-pileup loop mplp = bam_mplp_init(n, read_bam, (void**)data); // initialization + bam_mplp_set_maxcnt(mplp,1000000); // set maxdepth to 1M n_plp = calloc(n, sizeof(int)); // n_plp[i] is the number of covering reads from the i-th BAM plp = calloc(n, sizeof(void*)); // plp[i] points to the array of covering reads (internal in mplp) while (bam_mplp_auto(mplp, &tid, &pos, n_plp, plp) > 0) { // come to the next covered position Patch taken from here: http://sourceforge.net/mailarchive/message.php?msg_id=28166483
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--- Begin Message ---Source: samtools Source-Version: 0.1.18-2 We believe that the bug you reported is fixed in the latest version of samtools, which is due to be installed in the Debian FTP archive. A summary of the changes between this version and the previous one is attached. Thank you for reporting the bug, which will now be closed. If you have further comments please address them to [email protected], and the maintainer will reopen the bug report if appropriate. Debian distribution maintenance software pp. Dominique Belhachemi <[email protected]> (supplier of updated samtools package) (This message was generated automatically at their request; if you believe that there is a problem with it please contact the archive administrators by mailing [email protected]) -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Format: 1.8 Date: Thu, 26 Jul 2012 18:30:48 -0400 Source: samtools Binary: samtools libbam-dev Architecture: source amd64 Version: 0.1.18-2 Distribution: unstable Urgency: low Maintainer: Debian Med Packaging Team <[email protected]> Changed-By: Dominique Belhachemi <[email protected]> Description: libbam-dev - manipulates nucleotide sequence alignments in BAM or SAM format samtools - processing sequence alignments in SAM and BAM formats Closes: 544976 671524 Changes: samtools (0.1.18-2) unstable; urgency=low . * added patch to fix segfault in mpileup (Closes: #544976) * added patch to fix coverage cap (Closes: #671524) Checksums-Sha1: 84c61887d42fb7ddc0f040283860d47ac777c1da 1429 samtools_0.1.18-2.dsc 2047645cf492115f000fc49c9ab7b8afb6af7d81 8901 samtools_0.1.18-2.debian.tar.gz 69aa0366c748881b25a51dfaa53d48bd5f464587 532436 samtools_0.1.18-2_amd64.deb 32b2d326c6fd8260163f4dcf84c8c8b407d9c26e 156420 libbam-dev_0.1.18-2_amd64.deb Checksums-Sha256: b6bf6be3bc7f2e2bec92711baa39a87544f746ce410fc34b03c70f77393ea688 1429 samtools_0.1.18-2.dsc 1eb31cf4073334bf20322f3c2d81f8abc7a9d8ec2d685b6ae8ad0baeba6eb574 8901 samtools_0.1.18-2.debian.tar.gz 240923389e65ce779970bce5febc17a5efcba43d2ca12cddacbc384a6757a1b0 532436 samtools_0.1.18-2_amd64.deb 2dfdeec0c06993476b7b8c9a5e519edd8d1cb94fa4182e2d6f7cd1f490a98c96 156420 libbam-dev_0.1.18-2_amd64.deb Files: 3c38a9da7f38ded68adb6c13d48d6dfb 1429 science optional samtools_0.1.18-2.dsc bdfe4d096674cf540f9a5d9727bba3e6 8901 science optional samtools_0.1.18-2.debian.tar.gz 1771be5b6406176f04832e3c0ddf1f89 532436 science optional samtools_0.1.18-2_amd64.deb 9a2da27fa8681b3a02b321dd5e7bb7d2 156420 libdevel optional libbam-dev_0.1.18-2_amd64.deb -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.11 (GNU/Linux) iEYEARECAAYFAlASkvkACgkQGACh+LNRqQC9EwCfXwvqkvmhLAX4HrfDYPz6QQfi hUcAmgOfhZArIDLxbBG/Bw1/1AsJnV8R =hVaY -----END PGP SIGNATURE-----
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