New Upstream Release - dazzdb
Ready changes
Summary
Merged new upstream version: 1.0+git20230515.8662b7d (was: 1.0+git20221215.aad3a46).
Resulting package
Built on 2023-05-21T05:59 (took 8m38s)
The resulting binary packages can be installed (if you have the apt repository enabled) by running one of:
apt install -t fresh-releases dazzdb-dbgsymapt install -t fresh-releases dazzdb
Lintian Result
Diff
diff --git a/DB2ONE.c b/DB2ONE.c
index 190bbe1..23314b0 100644
--- a/DB2ONE.c
+++ b/DB2ONE.c
@@ -43,10 +43,12 @@ static char *One_Schema =
"D H 1 6 STRING Original fasta/q header\n"
- "D W 3 3 INT 3 INT 3 INT well, pulse start, pulse end\n"
+ "D W 3 3 INT 3 INT 3 INT well, pulse start, pulse end (for db's)\n"
"D N 4 3 INT 3 INT 3 INT 3 INT SNR of ACGT channels (if Arrow-DB)\n"
"D Q 1 3 INT read quality (if Quiva-DB)\n"
+ "D G 3 3 INT 3 INT 3 INT contig, firstbp, lastbp (for dam's)\n"
+
"D X 2 3 INT 6 STRING Prolog: name of track idx\n"
"D T 2 3 INT 8 INT_LIST Track idx, interval pairs list\n";
@@ -204,9 +206,10 @@ int main(int argc, char *argv[])
fprintf(stderr," -a: Output truncated arrow pulse-width string (A line)\n");
fprintf(stderr," -q: Quiver edit vectors (D, C, I, M, and S lines)\n");
fprintf(stderr," -h: Output fasta header prefix (H line)\n");
- fprintf(stderr," -w: Output well, pulse start and end (W line)\n");
+ fprintf(stderr," -w: Output well, pulse start and end (if .db, W line)\n");
fprintf(stderr," + SNR of ACGT channels (if Arrow DB, N line)\n");
fprintf(stderr," + quality value of read (if Quiver DB, Q line)\n");
+ fprintf(stderr," -w: Contig, firstbp, and lastbp (if .dam, G line)\n");
fprintf(stderr,"\n");
fprintf(stderr," -f: group by origin file (f line)\n");
fprintf(stderr,"\n");
@@ -616,7 +619,10 @@ int main(int argc, char *argv[])
{ oneInt(file1,0) = r->origin;
oneInt(file1,1) = r->fpulse;
oneInt(file1,2) = r->fpulse+len;
- oneWriteLine(file1,'W',0,NULL);
+ if (DAM)
+ oneWriteLine(file1,'G',0,NULL);
+ else
+ oneWriteLine(file1,'W',0,NULL);
if (Quiva_DB && qv > 0)
{ oneInt(file1,0) = qv;
oneWriteLine(file1,'Q',0,NULL);
diff --git a/README.md b/README.md
index 768065b..c6e181e 100644
--- a/README.md
+++ b/README.md
@@ -142,6 +142,7 @@ a command such as DBshow.
All programs add suffixes (e.g. .db) as needed. The commands of the database library
are currently as follows:
+<a name="fasta2DB"></a>
```
1. fasta2DB [-v] <path:db> ( -f<file> | -i[<name>] | <input:fasta> ... )
```
@@ -166,6 +167,7 @@ partitioning of the database is updated to include the new data. A file may con
the data from multiple SMRT cells provided the reads for each SMRT cell are consecutive
in the file.
+<a name="DB2fasta"></a>
```
2. DB2fasta [-vU] [-w<int(80)>] <path:db>
```
@@ -180,6 +182,7 @@ By default the output sequences are in lower case and 80 chars per line. The -U
specifies upper case should be used, and the characters per line, or line width, can be
set to any positive value with the -w option.
+<a name="quiva2DB"></a>
```
3. quiva2DB [-vl] <path:db> ( -f<file> | -i | <input:quiva> ... )
```
@@ -194,6 +197,7 @@ FOO.quiva. This is enforced by the program. With the -l option
set the compression scheme is a bit lossy to get more compression (see the description
of dexqv in the DEXTRACTOR module here).
+<a name="DB2quiva"></a>
```
4. DB2quiva [-vU] <path:db>
```
@@ -208,6 +212,7 @@ By .fastq convention each QV vector is output as a line without new-lines, and b
default the Deletion Tag entry is in lower case letters. The -U option specifies
upper case letters should be used instead.
+<a name="arrow2DB"></a>
```
5. arrow2DB [-v] <path:db> ( -f<file> | -i | <input:arrow> ... )
```
@@ -220,6 +225,7 @@ incrementally but must be added in the
same order as the .fasta files were and have the same root names, e.g. FOO.fasta and
FOO.quiva. This is enforced by the program.
+<a name="DB2arrow"></a>
```
6. DB2arrow [-v] [-w<int(80)>] <path:db>
```
@@ -234,6 +240,7 @@ By default the output sequences are formatted 80 chars per line,
but the characters per line, or line width, can be
set to any positive value with the -w option.
+<a name="fasta2DAM"></a>
```
7. fasta2DAM [-v] <path:dam> ( -f<file> | -i[<name>] | <input:fasta> ... )
```
@@ -248,6 +255,7 @@ entry that has a run of N's in it will be split into separate "contig" entries a
interval of the contig in the original entry recorded. The header for each .fasta entry
is saved with the contigs created from it.
+<a name="DAM2fasta"></a>
```
8. DAM2fasta [-vU] [-w<int(80)>] <path:dam>
```
@@ -262,6 +270,7 @@ sequences are in lower case and 80 chars per line. The -U option specifies upper
should be used, and the characters per line, or line width, can be set to any positive
value with the -w option.
+<a name="DBsplit"></a>
```
9. DBsplit [-aflm] [-x<int>] [-s<double(200.)>] <path:db|dam>
```
@@ -288,6 +297,7 @@ primary read instead. One can at any later time change this back to the default
by splitting again with the -l parameter set. The setting of the primary reads occurs
regardless of whether the -a parameter is set or not.
+<a name="DBtrim"></a>
```
10. DBtrim [-af] [-x<int>] <path:db|dam>
```
@@ -295,6 +305,7 @@ regardless of whether the -a parameter is set or not.
Exactly like DBsplit except that it only resets the trimming parameters (and not the split
partition itself).
+<a name="DBdust"></a>
```
11. DBdust [-b] [-w<int(64)>] [-t<double(2.)>] [-m<int(10)>] <path:db|dam>
```
@@ -316,6 +327,7 @@ and .FOO.3.dust.data, given FOO.3 on the command line. We call this a *block tr
This permits job parallelism in block-sized chunks, and the resulting sequence of
block tracks can then be merged into a track for the entire untrimmed DB with Catrack.
+<a name="Catrack"></a>
```
12. Catrack [-vfd] <path:db|dam> <track:name> ...
```
@@ -329,6 +341,7 @@ concatenation takes place regardless of whether or not the single, combined trac
already exists or not. If the -d option is set then every block track is removed after
the successful construction of the combined track.
+<a name="DBshow"></a>
```
13. DBshow [-unqaUQA] [-w<int(80)>] [-m<mask>]+
<path:db|dam> [ <reads:FILE> | <reads:range> ... ]
@@ -368,6 +381,7 @@ The .fasta, .quiva, and .arrow files that are output can be used to build a new
fasta2DB, quiva2D, and arrow2DB, giving one a simple way to make a DB of a subset of
the reads for testing purposes.
+<a name="DB2ONE"></a>
```
14. DB2ONE [-u] [-aqhwf] [-m<mask>]+
<path:db|dam> [ <reads:FILE> | <reads:range> ... ]
@@ -416,9 +430,9 @@ outputs five 1-code lines containing the Quiver odds vectors as indicated in the
```
If the -h flag is set, then DB2ONE outputs an H line giving
the fasta header line that was associated with each read on input.
-If the -w flag is set, then DB2ONE outputs a W line giving the well number and pulse start and end. Furthermore, if the database is an A-DB then an N line containing the SNR for each channel for
-that well is output, and if the database is a Q-DB then a Q line is output giving an estimate of the
-error rate of the read based on the Quiver vectors.
+If the -w flag is set, then for a .db database DB2ONE outputs a W line giving the well number and pulse start and end. Furthermore, if the database is an A-DB then an N line containing the SNR for each channel for that well is output, and if the database is a Q-DB then a Q line is output giving an estimate of the error rate of the read based on the Quiver vectors.
+On the other hand if the database is a .dam, then DB2ONE outputs a G line in response to the
+-w flag, which gives the contig # within a .fasta scaffold and the first and last base positions in the fasta file entry from which the contig was extracted.
Finally, if the -f flag is output, then the output is grouped by original source files where
each group begins with an f line giving the name of the file and the number of reads from that
file.
@@ -429,7 +443,9 @@ file.
W <well: int> <pulse start: int> <pulse end: int>
N <SNR A-channel> <SNR C-channel> <SNR G-channel> <SNR T-channel>
Q <read quality value: int>
-
+
+ G <contig int> <first bp: int> <last bp: int>
+
f <count: int> <file name: string>
```
Lastly, for each -m option specifying a *mask* track name, a T-line is output that first indicates which mask it is for and then contains an integer list of interval begin-end pairs.
@@ -441,6 +457,7 @@ the mapping between the track index and its name as it appeared in the -m option
X <track idx: int> <name: string> // Once in prolog for each track
```
+<a name="DBstats"></a>
```
15. DBstats [-nu] [-b<int(1000)] [-m<mask>]+ <path:db|dam>
```
@@ -453,6 +470,7 @@ is not displayed. Any track such as a "dust" track that gives a series of
intervals along the read can be specified with the -m option in which case a summary
and a histogram of the interval lengths is displayed.
+<a name="DBrm"></a>
```
16. DBrm [-vnf] <path:db|dam> ...
```
@@ -463,6 +481,7 @@ files, and all of these are removed by DBrm.
If the -v option is set then every file deleted is listed.
The -n, and -f options are as for the UNIX "rm" command.
+<a name="DBmv"></a>
```
17. DBmv [-vinf] <old:db|dam> <new:db|dam|dir>
```
@@ -472,6 +491,7 @@ to the diretory, otherwise, all the files for \<old> are renamed to the given ta
If the -v option is set then every file move is displayed.
The -i, -n, and -f options are as for the UNIX "mv" command.
+<a name="DBcp"></a>
```
18. DBcp [-vinf] <old:db|dam> <new:db|dam|dir>
```
@@ -481,6 +501,7 @@ to the diretory, otherwise, a copy of all the files for \<old> are created with
If the -v option is set then every file move is displayed.
The -i, -n, and -f options are as for the UNIX "cp" command.
+<a name="DBwipe"></a>
```
19. DBwipe <path:db|dam>
```
@@ -489,6 +510,7 @@ Delete any Arrow or Quiver data from the given databases. This removes the .arw
.qvs file and resets information in the .idx file containing information for Arrow
or Quiver. Basically, converts an A-DB or Q-DB back to a simple S-DB.
+<a name="simulator"></a>
```
20. simulator <genome:dam> [-CU] [-m<int(10000)>] [-s<int(2000)>] [-e<double(.15)]
[-c<double(50.)>] [-f<double(.5)>] [-x<int(4000)>]
@@ -524,6 +546,7 @@ an assembly and is very useful for debugging and testing purposes. If the map li
a read is say 's b e' then if b \< e the read is a perturbed copy of s[b,e] in the
forward direction, and a perturbed copy s[e,b] in the reverse direction otherwise.
+<a name="rangen"></a>
```
21. rangen <genlen:double> [-U] [-b<double(.5)>] [-w<int(80)>] [-r<int>]
```
diff --git a/debian/changelog b/debian/changelog
index 04bd88f..b0790d2 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,9 @@
+dazzdb (1.0+git20230515.8662b7d-1) UNRELEASED; urgency=low
+
+ * New upstream snapshot.
+
+ -- Debian Janitor <janitor@jelmer.uk> Sun, 21 May 2023 05:51:53 -0000
+
dazzdb (1.0+git20221215.aad3a46-1) unstable; urgency=medium
* New upstream version
diff --git a/debian/patches/append-cflags.patch b/debian/patches/append-cflags.patch
index 19a2fbe..b7b04ea 100644
--- a/debian/patches/append-cflags.patch
+++ b/debian/patches/append-cflags.patch
@@ -2,8 +2,10 @@ Description: Make upstream build system append to CFLAGS
Author: Afif Elghraoui <afif@ghraoui.name>
Forwarded: no
Last-Update: 2015-09-13
---- a/Makefile
-+++ b/Makefile
+Index: dazzdb.git/Makefile
+===================================================================
+--- dazzdb.git.orig/Makefile
++++ dazzdb.git/Makefile
@@ -1,6 +1,6 @@
DEST_DIR = ~/bin
diff --git a/debian/patches/compiler-flags.patch b/debian/patches/compiler-flags.patch
index ae4f384..bbb1293 100644
--- a/debian/patches/compiler-flags.patch
+++ b/debian/patches/compiler-flags.patch
@@ -3,8 +3,10 @@ Author: Afif Elghraoui <afif@debian.org>
Forwarded: https://github.com/thegenemyers/DAZZ_DB/pull/26
Reviewed-By: Étienne Mollier <emollier@debian.org>
Last-Update: 2022-06-08
---- a/Makefile
-+++ b/Makefile
+Index: dazzdb.git/Makefile
+===================================================================
+--- dazzdb.git.orig/Makefile
++++ dazzdb.git/Makefile
@@ -1,6 +1,7 @@
DEST_DIR = ~/bin
diff --git a/debian/patches/destdir.patch b/debian/patches/destdir.patch
index 4af4dc3..0d6d9fb 100644
--- a/debian/patches/destdir.patch
+++ b/debian/patches/destdir.patch
@@ -3,8 +3,10 @@ Description: Set destination directory in upstream Makefile
Author: Afif Elghraoui <afif@ghraoui.name>
Forwarded: no
Last-Update: 2015-09-13
---- a/Makefile
-+++ b/Makefile
+Index: dazzdb.git/Makefile
+===================================================================
+--- dazzdb.git.orig/Makefile
++++ dazzdb.git/Makefile
@@ -60,7 +60,8 @@ clean:
rm -f dazz.db.tar.gz
diff --git a/debian/patches/use-after-free.patch b/debian/patches/use-after-free.patch
index 72d17f0..8c30b01 100644
--- a/debian/patches/use-after-free.patch
+++ b/debian/patches/use-after-free.patch
@@ -3,8 +3,10 @@ Author: Aurelien Jarno <aurel32@debian.org>
Forwarded: https://github.com/thegenemyers/DAZZ_DB/issues/41
Last-Update: 2021-09-14
---- dazzdb-1.0+git20201103.8d98c37.orig/DBstats.c
-+++ dazzdb-1.0+git20201103.8d98c37/DBstats.c
+Index: dazzdb.git/DBstats.c
+===================================================================
+--- dazzdb.git.orig/DBstats.c
++++ dazzdb.git/DBstats.c
@@ -346,8 +346,6 @@ int main(int argc, char *argv[])
}
}
Debdiff
[The following lists of changes regard files as different if they have different names, permissions or owners.]
Files in second set of .debs but not in first
-rw-r--r-- root/root /usr/lib/debug/.build-id/fd/513ec6be2495b406c0ac982efe2a4f5a53202e.debug
Files in first set of .debs but not in second
-rw-r--r-- root/root /usr/lib/debug/.build-id/80/3fa39bb1076bb978e7c62c6cae704c80792129.debug
No differences were encountered between the control files of package dazzdb
Control files of package dazzdb-dbgsym: lines which differ (wdiff format)
Build-Ids: 00422f9da4b1ef42571435203e165f553daf4002 33f035b8a81475005e584a8322e79974325ea635 42ba2663c7aabd840c7d54d3035d3cd249e2d1b0 432ef3f88000723615e50e5085c9ec541e23dc06 4540cb56c49cd2309c6f6e13e35289959c959181 45f0c95405b6721c74ecafe11282af26fc7783d7 4f693b953dca1c19fc83df49d07a6dee345bc5d1 803fa39bb1076bb978e7c62c6cae704c80792129 846f6b4900782c878e220445d2863b949dfd54ec 9b55cd171dd1eac1a704bcb82c51263ccc184aab a0e5da0345c81ff68a656e263bb34d0b5b3cf715 b6577a0590cf9b9601af020b7df58938c6d5f8d2 b75f6e582cf989e26c82be0b1056847fc7d8b3d9 c1fcfef648be307c4f05eb9df6961a5a18256e49 c215f9ddd07e0ba5800f1ae336a3ca4fdf5e9c3a ce2cc25a5a4ad4b6ff3ada4dc304f0c9f4ff9eec ce54af3f28647b3db44dd9ec62431e08953890cb cf568121c1727690376edcc2916447b9fb7cf460 eb43d24d214f92bdb39eaa1fd7037a2f3274577a eb9464f3b82463bcb937958e160d654a75c52f01 fd513ec6be2495b406c0ac982efe2a4f5a53202e ff3d6a3b0250c8f465617b851311f2339f43456c