[med-svn] [Git][med-team/lastz][master] 6 commits: New upstream version 1.04.22
Andreas Tille (@tille)
gitlab at salsa.debian.org
Wed Aug 24 07:05:04 BST 2022
Andreas Tille pushed to branch master at Debian Med / lastz
Commits:
878629d3 by Andreas Tille at 2022-08-24T07:52:24+02:00
New upstream version 1.04.22
- - - - -
4913d242 by Andreas Tille at 2022-08-24T07:52:24+02:00
routine-update: New upstream version
- - - - -
91e4eb4e by Andreas Tille at 2022-08-24T07:52:34+02:00
Update upstream source from tag 'upstream/1.04.22'
Update to upstream version '1.04.22'
with Debian dir 98a8703c85c792f2d33e92c83b22b32b4b62329f
- - - - -
b5bb9b88 by Andreas Tille at 2022-08-24T07:52:34+02:00
routine-update: Standards-Version: 4.6.1
- - - - -
2427c642 by Andreas Tille at 2022-08-24T07:58:13+02:00
Refresh patches
- - - - -
cc2377c5 by Andreas Tille at 2022-08-24T07:59:18+02:00
Upload to unstable
- - - - -
15 changed files:
- README.lastz.html
- README.md
- debian/changelog
- debian/control
- debian/patches/fix_signed_char.patch
- − debian/patches/gcc11.patch
- debian/patches/series
- debian/patches/spelling.patch
- src/gapped_extend.c
- src/gapped_extend.h
- src/genpaf.h
- src/lastz.c
- src/sequences.c
- src/sequences.h
- src/version.mak
Changes:
=====================================
README.lastz.html
=====================================
@@ -79,8 +79,8 @@
<body>
<p class=vvlarge>
-<h1>LASTZ Release 1.04.15,
- built August 27, 2021</h1>
+<h1>LASTZ Release 1.04.22,
+ built August 7, 2022</h1>
TABLE OF CONTENTS
@@ -4530,13 +4530,17 @@ be described by this field:
<h3>BLASTN (alignment output)</h3>
+<p>
+<em>Note: Prior to release 1.04.22, this format reported query positions
+incorrectly when alignments were on opposite strands.</em>
+
<p>
The BLASTN format reports pairwise alignments in a format similar to
NCBI’s BLASTN program. Output is modeled upon version 2.2.24+ of the
standalone version of BLASTN available from
<a href="ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/">
-NCBI’s BLAST ftp site</a>. Output should be similar that produced by the
-command
+NCBI’s BLAST ftp site</a>. (Note: that version of BLASTN is no longer
+available.) Output should be similar that produced by the command
<pre>
blastn -task blastn -db <target> -query <query> -outfmt 7
</pre>
@@ -7763,7 +7767,7 @@ These changes have no affect on the executable.
<tr class=newsect>
<td>
-<a name="history_recent"></a>1.04.15</td><td>Aug/27/2021</td><td>
+1.04.15</td><td>Aug/27/2021</td><td>
Fixed a bug in which the setting for
<code><a href="#option_queryhspbest">‑‑queryhspbest</a></code>
was ignored. For more details see
@@ -7801,6 +7805,25 @@ Some changes were made to the source code to placate compiler warnings. These
changes have no affect on the executable.
</td></tr>
+<!-- 1.04.22 -->
+
+<tr class=newsect>
+<td>
+<a name="history_recent"></a>1.04.22</td><td>Aug/7/2022</td><td>
+Fixed a serious bug in the <a href="#fmt_blastn">blastn format</a>.
+<p class=small>
+In previous versions query positions were misreported for alignments on
+opposite strands. Blastn (the program) always reports the position of the
+query along the forward strand. Previous versions of lastz reported it
+along the aligning strand.
+<p class=small>
+This has been corrected.
+<p class=small>
+For more details see
+<a href="https://github.com/lastz/lastz/issues/51">issue 51</a> at the lastz
+github repository.
+</td></tr>
+
</tbody></table>
<!---->
=====================================
README.md
=====================================
@@ -7,9 +7,9 @@ https://github.com/lastz/lastz/releases.
Users are encouraged to use a tagged release, as this working branch may not
be stable.
-As of this writing, the latest official release is version 1.04.03.
-Additional LASTZ releases, including all releases prior to March 2017, can be
-found at http://www.bx.psu.edu/~rsharris/lastz (in the form of tarballs)..
+As of this writing, the latest official release is version 1.04.22.
+Additional LASTZ releases, including all releases prior to September 2021, can
+be found at http://www.bx.psu.edu/~rsharris/lastz (in the form of tarballs).
For information about installation and use, see https://lastz.github.io/lastz
(equivalent to README.lastz.html in this repository).
@@ -21,5 +21,8 @@ binaries (the version there might lag behind the latest version here):
http://hgdownload.soe.ucsc.edu/admin/exe/macOSX.x86_64/
```
-Updated Apr/6/2018 by Bob Harris (the LASTZ guy)
+A GPU accelerated version, SegAlign, can be found at
+https://github.com/gsneha26/SegAlign.
+
+Updated Aug/7/2022 by Bob Harris (the LASTZ guy)
=====================================
debian/changelog
=====================================
@@ -1,3 +1,10 @@
+lastz (1.04.22-1) unstable; urgency=medium
+
+ * New upstream version
+ * Standards-Version: 4.6.1 (routine-update)
+
+ -- Andreas Tille <tille at debian.org> Wed, 24 Aug 2022 07:58:31 +0200
+
lastz (1.04.15-2) unstable; urgency=medium
* Team upload.
=====================================
debian/control
=====================================
@@ -6,7 +6,7 @@ Uploaders: Andreas Tille <tille at debian.org>
Build-Depends: debhelper-compat (= 13),
dh-python,
python3
-Standards-Version: 4.6.0
+Standards-Version: 4.6.1
Vcs-Browser: https://salsa.debian.org/med-team/lastz
Vcs-Git: https://salsa.debian.org/med-team/lastz.git
Homepage: https://github.com/lastz/lastz
=====================================
debian/patches/fix_signed_char.patch
=====================================
@@ -5,7 +5,7 @@ Last-Update: Thu, 15 Oct 2020 11:02:55 +0200
--- a/src/sequences.c
+++ b/src/sequences.c
-@@ -5093,14 +5093,14 @@ static int find_next_general_fasta_coi
+@@ -5101,14 +5101,14 @@ static int find_next_general_fasta_coi
// find the next header
ch = seq_getc (_seq);
@@ -22,7 +22,7 @@ Last-Update: Thu, 15 Oct 2020 11:02:55 +0200
}
continue;
}
-@@ -5124,12 +5124,12 @@ static int find_next_general_fasta_coi
+@@ -5132,12 +5132,12 @@ static int find_next_general_fasta_coi
leadingWhite = 0;
ch = seq_getc (_seq);
@@ -37,7 +37,7 @@ Last-Update: Thu, 15 Oct 2020 11:02:55 +0200
}
if (ch == '\n')
-@@ -5144,7 +5144,7 @@ static int find_next_general_fasta_coi
+@@ -5152,7 +5152,7 @@ static int find_next_general_fasta_coi
break; // .. truncate the header)
*(s++) = ch;
ch = seq_getc (_seq);
@@ -46,7 +46,7 @@ Last-Update: Thu, 15 Oct 2020 11:02:55 +0200
}
*s = 0;
-@@ -5239,7 +5239,7 @@ static int find_next_fastq_coi
+@@ -5247,7 +5247,7 @@ static int find_next_fastq_coi
debugNamesFile_14;
ch = seq_getc (_seq);
@@ -55,7 +55,7 @@ Last-Update: Thu, 15 Oct 2020 11:02:55 +0200
if (ch != '@')
suicidef ("internal error in find_next_fastq_coi\n"
-@@ -5249,7 +5249,7 @@ static int find_next_fastq_coi
+@@ -5257,7 +5257,7 @@ static int find_next_fastq_coi
// read the header
ch = seq_getc (_seq);
@@ -64,7 +64,7 @@ Last-Update: Thu, 15 Oct 2020 11:02:55 +0200
s = buffer;
while ((ch != '\n') && (ch != '\r'))
-@@ -5258,7 +5258,7 @@ static int find_next_fastq_coi
+@@ -5266,7 +5266,7 @@ static int find_next_fastq_coi
break; // .. truncate the header)
*(s++) = ch;
ch = seq_getc (_seq);
=====================================
debian/patches/gcc11.patch deleted
=====================================
@@ -1,31 +0,0 @@
-Description: fix ftbfs with gcc 11
- Inspired from upstream commit d00249da148a011a8c2d819f702356908859c51c.
-Author: Étienne Mollier <emollier at debian.org>
-Bug: https://github.com/lastz/lastz/issues/42
-Bug-Debian: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=984081
-Applied-Upstream: d00249da148a011a8c2d819f702356908859c51c
-Last-Update: 2021-11-02
----
-This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
---- lastz.orig/src/sequences.c
-+++ lastz/src/sequences.c
-@@ -3621,7 +3621,7 @@
- //----------
-
- static int find_2bit_sequence (seq* _seq, char* name);
--static u32 read_2bit_index_entry (seq* _seq, char seqName[256], u32 seqNum);
-+static u32 read_2bit_index_entry (seq* _seq, char seqName[maxSequenceName+1], u32 seqNum);
-
- //--- read_2bit_header ---
-
---- lastz.orig/src/sequences.h
-+++ lastz/src/sequences.h
-@@ -192,7 +192,7 @@
- //
- //----------
-
--#define maxSequenceName 100
-+#define maxSequenceName 255
- #define maxSequenceHeader 992
- #define seqBufferSize (maxSequenceHeader+32)
- #define maxFastqSequenceLen 10000
=====================================
debian/patches/series
=====================================
@@ -1,4 +1,3 @@
propagate_cflags.patch
fix_signed_char.patch
spelling.patch
-gcc11.patch
=====================================
debian/patches/spelling.patch
=====================================
@@ -15,7 +15,7 @@ Last-Update: Thu, 15 Oct 2020 11:02:55 +0200
suicidef (scoreFmt " is not a valid gap extension penalty (in %s)\n",
--- a/src/lastz.c
+++ b/src/lastz.c
-@@ -4882,7 +4882,7 @@ static void format_options (void)
+@@ -4883,7 +4883,7 @@ static void format_options (void)
fprintf (helpout, "there may be a question as to whether or not lastz completed successfully. The\n");
fprintf (helpout, "line \"# lastz end-of-file\" is written to output as the last line. Note that\n");
fprintf (helpout, "in some formats this is *not* a legal line; the user must remove it before any\n");
@@ -24,7 +24,7 @@ Last-Update: Thu, 15 Oct 2020 11:02:55 +0200
exit (EXIT_FAILURE);
}
-@@ -8758,7 +8758,7 @@ static void parse_options
+@@ -8771,7 +8771,7 @@ static void parse_options
if ((haveGapOpen) && (gapOpen + gapExtend <= 0))
chastise ("%s is not a valid gap open penalty with extension penalty %s\n"
=====================================
src/gapped_extend.c
=====================================
@@ -1288,6 +1288,31 @@ alignel* gapped_extend
{
mp = msp[i];
+ if ((gapped_extend_dbgAnchorsProgress != 0) && (i % gapped_extend_dbgAnchorsProgress == 0))
+ {
+ int reportStrand = true;
+ fprintf (stderr, "processing");
+ if ((seq2->shortHeader != NULL) && (!seq2->useFullNames))
+ fprintf (stderr, " %s", seq2->shortHeader);
+ else if (seq2->header != NULL)
+ fprintf (stderr, " %s", seq2->header);
+ else
+ reportStrand = false;
+ if (reportStrand)
+ {
+ if (seq2->revCompFlags == rcf_comp)
+ fprintf (stderr, "(complement)");
+ else if (seq2->revCompFlags == rcf_rev)
+ fprintf (stderr, "(reverse)");
+ else if (seq2->revCompFlags == rcf_revcomp)
+ fprintf (stderr, "-");
+ else
+ fprintf (stderr, "+");
+ }
+ fprintf (stderr, " anchor #%u (%.2f%% of %u) hspId=" u64Fmt "\n",
+ i+1, 100.0*i/anchors->len, anchors->len, mp->hspId);
+ }
+
debugGappedExtendVerbosity_1;
debugSnoopAnchorToGapped_1;
debugsnoopSpecialHsp_1;
=====================================
src/gapped_extend.h
=====================================
@@ -31,6 +31,7 @@ int gapped_extend_dbgShowIdentity = false;
int gapped_extend_dbgShowHsps = false;
int gapped_extend_dbgShowAnchors = false;
int gapped_extend_dbgShowAnchorsHowOften = 0;
+int gapped_extend_dbgAnchorsProgress = 0;
int gapped_extend_dbgAllowBatches = false;
#ifdef tryout
int gapped_extend_dbgTriviality = false;
@@ -42,6 +43,7 @@ global int gapped_extend_dbgShowIdentity;
global int gapped_extend_dbgShowHsps;
global int gapped_extend_dbgShowAnchors;
global int gapped_extend_dbgShowAnchorsHowOften;
+global int gapped_extend_dbgAnchorsProgress;
global int gapped_extend_dbgAllowBatches;
#ifdef tryout
global int gapped_extend_dbgTriviality;
=====================================
src/genpaf.h
=====================================
@@ -115,7 +115,7 @@ enum
#define genpafStandardKeys "#NDSZEndszeIC"
#define genpafMappingKeys "NZEnd>,IC^"
#define genpafSegmentKeys "NBEnbed#"
-#define genpafBlastKeys "nNmWvybeQR%$"
+#define genpafBlastKeys "nNmWvy<,QR%$" // was, erroneously, "nNmWvybeQR%$"
#define genpafRDotplotKeys "02!13!XX"
#define genpafRDotplotScoreKeys "02#!13#!XXX"
#define genpafPafWfMashKeys "ns>,dNSZEuW{|}"
=====================================
src/lastz.c
=====================================
@@ -459,6 +459,7 @@ static int dbgAnchorParsing = false;
static int dbgAnchorContent = false;
static int dbgShowAnchors = false;
static int dbgShowAnchorsHowOften = 0;
+static int dbgAnchorsProgress = 0;
static int dbgSortAnchorsByDiag = false;
static int dbgInhibitSegmentReduction = false;
static int dbgMasking = false;
@@ -7781,6 +7782,18 @@ static void parse_options_loop
goto next_arg;
}
+ if ((strcmp_prefix (arg, "--debug=segmentprogress:") == 0)
+ || (strcmp_prefix (arg, "--debug=segmentsprogress:") == 0)
+ || (strcmp_prefix (arg, "--debug=anchorprogress:") == 0)
+ || (strcmp_prefix (arg, "--debug=anchorsprogress:") == 0))
+ {
+ scan = strchr(argStr,':') + 1;
+ dbgAnchorsProgress = string_to_unitized_int (scan, true /*units of 1,000*/);
+ if (dbgAnchorsProgress <= 0)
+ dbgAnchorsProgress = 0;
+ goto next_arg;
+ }
+
if (strcmp (arg, "--debug=sort:diag") == 0)
{ dbgSortAnchorsByDiag = true; goto next_arg; }
@@ -9190,6 +9203,7 @@ threshold_check_done:
gapped_extend_dbgShowHsps = dbgShowHsps;
gapped_extend_dbgShowAnchors = dbgShowAnchors;
gapped_extend_dbgShowAnchorsHowOften = dbgShowAnchorsHowOften;
+ gapped_extend_dbgAnchorsProgress = dbgAnchorsProgress;
sequences_keepFastaArrow = lzParams->lajCompatible;
=====================================
src/sequences.c
=====================================
@@ -3621,7 +3621,7 @@ static void load_nib_sequence
//----------
static int find_2bit_sequence (seq* _seq, char* name);
-static u32 read_2bit_index_entry (seq* _seq, char seqName[256], u32 seqNum);
+static u32 read_2bit_index_entry (seq* _seq, char seqName[maxSequenceName+1], u32 seqNum);
//--- read_2bit_header ---
@@ -4025,6 +4025,12 @@ static int find_2bit_sequence
//--- read_2bit_index_entry ---
+// complain if someone has tried to set maxSequenceName too small
+
+#if maxSequenceName < 255
+#error ***** maxSequenceName is too small (names in 2bit files can be up to 255 characters) *****
+#endif
+
static u32 read_2bit_index_entry
(seq* _seq,
char seqName[maxSequenceName+1],
@@ -4034,6 +4040,8 @@ static u32 read_2bit_index_entry
size_t bytesRead;
// read the name
+ //
+ // nota bene: 0<=nameSize<=255
nameSize = getc_or_die (_seq->f, _seq->filename);
if (nameSize > 0)
=====================================
src/sequences.h
=====================================
@@ -192,7 +192,7 @@ typedef struct interval { unspos s; unspos e; } interval;
//
//----------
-#define maxSequenceName 100
+#define maxSequenceName 255 // has to be at least this big to accomodate 2bit files
#define maxSequenceHeader 992
#define seqBufferSize (maxSequenceHeader+32)
#define maxFastqSequenceLen 10000
=====================================
src/version.mak
=====================================
@@ -1,4 +1,4 @@
VERSION_MAJOR=1
VERSION_MINOR=04
-VERSION_SUBMINOR=15
-REVISION_DATE=20210827
+VERSION_SUBMINOR=22
+REVISION_DATE=20220807
View it on GitLab: https://salsa.debian.org/med-team/lastz/-/compare/6fa527dd3b0dedb41579461eb41ec832a79e26d9...cc2377c54bea976f614ae16e309931bd96a838cb
--
View it on GitLab: https://salsa.debian.org/med-team/lastz/-/compare/6fa527dd3b0dedb41579461eb41ec832a79e26d9...cc2377c54bea976f614ae16e309931bd96a838cb
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