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DB2ONE -w information fixed for .dam DB's
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@thegenemyers
thegenemyers committed May 15, 2023
1 parent aad3a46 commit 8662b7d
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12 changes: 9 additions & 3 deletions DB2ONE.c
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Original file line number Diff line number Diff line change
Expand Up @@ -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";

Expand Down Expand Up @@ -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");
Expand Down Expand Up @@ -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);
Expand Down
31 changes: 27 additions & 4 deletions README.md
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Original file line number Diff line number Diff line change
Expand Up @@ -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> ... )
```
Expand All @@ -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>
```
Expand All @@ -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> ... )
```
Expand All @@ -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>
```
Expand All @@ -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> ... )
```
Expand All @@ -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>
```
Expand All @@ -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> ... )
```
Expand All @@ -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>
```
Expand All @@ -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>
```
Expand All @@ -288,13 +297,15 @@ 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>
```

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>
```
Expand All @@ -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> ...
```
Expand All @@ -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> ... ]
Expand Down Expand Up @@ -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> ... ]
Expand Down Expand Up @@ -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.
Expand All @@ -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.
Expand All @@ -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>
```
Expand All @@ -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> ...
```
Expand All @@ -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>
```
Expand All @@ -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>
```
Expand All @@ -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>
```
Expand All @@ -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)>]
Expand Down Expand Up @@ -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>]
```
Expand Down

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