Your message dated Fri, 27 Jul 2012 15:33:11 +0000 with message-id <[email protected]> and subject line Bug#671524: fixed in samtools 0.1.18-3 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
--- End Message ---
--- Begin Message ---Source: samtools Source-Version: 0.1.18-3 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: Fri, 27 Jul 2012 11:11:41 -0400 Source: samtools Binary: samtools libbam-dev Architecture: source amd64 Version: 0.1.18-3 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: 653042 671524 Changes: samtools (0.1.18-3) unstable; urgency=low . * upload 0.1.18-2 closed the wrong bug, correction: * added patch to fix segfault in mpileup (Closes: #653042) * added patch to fix coverage cap (Closes: #671524) Checksums-Sha1: 98e1d8edc80169ef5b2f26724d38c3662b72a1ee 1429 samtools_0.1.18-3.dsc c43f7b1a333f7c0a58b68f9eeec5199de94b10d1 8884 samtools_0.1.18-3.debian.tar.gz 824955461e99e6c8ae2a93c83e216b53426de3fb 532546 samtools_0.1.18-3_amd64.deb e9d444c0636085ea5b8095846b7110f1604e5b32 156424 libbam-dev_0.1.18-3_amd64.deb Checksums-Sha256: f99ba2ef9e8bac618815628d6edf6472b13b337ca409af597ddba3813cee8a0e 1429 samtools_0.1.18-3.dsc 5fbe6ec93be478820a0dacf370efe19d0bda57e5fb24d9e68ef64f02177c6436 8884 samtools_0.1.18-3.debian.tar.gz c4450f28757598f9c8f1281207e126ab0c8286b312489545b4ce1ca6d4fa079f 532546 samtools_0.1.18-3_amd64.deb 627ac170799d272f8345ba3ba04d5cce11c2d5766aaf0e1016c90206abaa99ac 156424 libbam-dev_0.1.18-3_amd64.deb Files: d8e2907c097041227b9ad32d7f9494ab 1429 science optional samtools_0.1.18-3.dsc 514bc41eebb0f3fb9508cfb108710df5 8884 science optional samtools_0.1.18-3.debian.tar.gz d191d23990dba49bd53b5dbbaeed9146 532546 science optional samtools_0.1.18-3_amd64.deb 8a4822d6eb8ae813f6c0b9381b88bf19 156424 libdevel optional libbam-dev_0.1.18-3_amd64.deb -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.11 (GNU/Linux) iEYEARECAAYFAlASseUACgkQGACh+LNRqQB8IwCeLW8jYZOATmTKsGhMa4ZkMC63 MGsAnRXGC2dxzPAJtYO0SqSUCwmxjiAk =7nwL -----END PGP SIGNATURE-----
--- End Message ---
