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comparison srf2fastq/io_lib-1.12.2/README @ 0:d901c9f41a6a default tip
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
author | dawe |
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date | Tue, 07 Jun 2011 17:48:05 -0400 |
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1 IO_LIB VERSION 1.12.2 | |
2 ===================== | |
3 | |
4 Io_lib is a library of file reading and writing code to provide a general | |
5 purpose trace file (and Experiment File) reading interface. The programmer | |
6 simply calls the (eg) read_reading to create a "Read" C structure with the | |
7 data loaded into memory. It has been compiled and tested on a variety | |
8 of unix systems, MacOS X and MS Windows. | |
9 | |
10 The directories below here contain the io_lib code. These support the | |
11 following file formats: | |
12 | |
13 SCF trace files | |
14 ABI trace files | |
15 ALF trace files | |
16 CTF trace files | |
17 ZTR trace files | |
18 SFF trace archives | |
19 SRF trace archives | |
20 Experiment files | |
21 Plain text files | |
22 | |
23 These link together to form a single "libstaden-read" library supporting | |
24 all the file formats via a single read_reading (or fread_reading or | |
25 mfread_reading) function call and analogous write_reading functions | |
26 too. See the file include/Read.h for the generic 'Read' structure. | |
27 | |
28 | |
29 | |
30 What's new in 1.12.2 | |
31 ==================== | |
32 | |
33 Extra options in srf2fastq: | |
34 -S to output split regions sequentially to stdout. | |
35 -r to request a region to be reverse complemented before output. | |
36 | |
37 API changes in HashTable code: | |
38 We now support HASH_POOL_ITEMS flag to reduce memory usage and | |
39 fragmentation, while speeding it up too. The pooled_alloc | |
40 methods implementing this may be useful in other places too. | |
41 (This change does not break the existing ABI.) | |
42 | |
43 Minor bug fixes (see CHANGES file). | |
44 | |
45 | |
46 What's new in 1.12.1 | |
47 ==================== | |
48 | |
49 Library renaming: | |
50 The final object is no longer libread.so (or read.dll), but | |
51 libstaden-read.so. This had already been done by the Fedora bundled | |
52 version and work was in progress to do this in Debian too. | |
53 | |
54 Illumina2srf/srf2illumina: | |
55 Both of these tools have now been removed. Illumina itself should | |
56 now be supporting these tools and shipping appropriate versions | |
57 compatible with each GA-pipeline release. | |
58 | |
59 Libtool: | |
60 We now create dynamic library too, in addition to the static | |
61 versions, using the autoconf "libtool" program. Furthermore we now | |
62 have proper library versioning, starting with an soname of | |
63 libstaden-read.so.1 for this release. | |
64 | |
65 INCOMPATIBILITY: | |
66 The Array data type and Array* functions now use size_t instead of | |
67 int for the array sizes. This means programs linked against the old | |
68 io_lib releases are not binary compatible with this version. | |
69 | |
70 See CHANGES and ChangeLog for a full list of changes and for older release | |
71 notes. | |
72 | |
73 | |
74 Older comments | |
75 ============== | |
76 | |
77 In 1.11.x the SRF support was added. The SRF v1.3 format specification can | |
78 be found here: | |
79 | |
80 http://www.bcgsc.ca/pipermail/ssrformat/attachments/20071209/b0f865a0/ShortSequenceFormatDec9th_v_1_3-0001.doc | |
81 | |
82 The ZTR specification changes involve adding some new compression | |
83 types (the general purpose XRLE2 plus some more solexa specific TSHIT | |
84 and QSHIFT methods), a region chunk (REGN) to indicate the location of | |
85 paired-end data stored in a single trace, improved meta-data support | |
86 for SMP4/SAMP chunks including specifying the baseline (OFFS meta-data | |
87 tag) and various minor tweaks. There's still a few questions in the | |
88 ZTR format itself (pending feedback), but what is implemented | |
89 currently is also what has been described in the docs/ZTR_format | |
90 file. | |
91 | |
92 Finally the directory layout has been greatly simplified with the | |
93 merging of all the format directories into a single "io_lib" | |
94 directory and the programs utilising it remaining in the "progs" | |
95 subdirectory. | |
96 | |
97 | |
98 Building | |
99 ======== | |
100 | |
101 We use the GNU autoconf build mechanism. | |
102 | |
103 To build: | |
104 | |
105 1. ./configure | |
106 | |
107 "./configure --help" will give a list of the options for GNU autoconf. For | |
108 modifying the compiler options or flags you may wish to redefine the CC or | |
109 CFLAGS variable. | |
110 | |
111 Eg (in sh or bash): | |
112 CC=cc CFLAGS=-g ./configure | |
113 | |
114 2. make (or gmake) | |
115 | |
116 This will build the sources. | |
117 | |
118 CFLAGS may also be changed a build time using (eg): | |
119 make 'CFLAGS=-g ...' | |
120 | |
121 3. make install | |
122 | |
123 The default installation location is /usr/local/bin and /usr/local/lib. These | |
124 can be changed with the --prefix option to "configure". | |
125 | |
126 | |
127 Under Microsoft Windows we recommend the use of MSYS and MINGW as a | |
128 build environment. These contain enough tools to build using the | |
129 configure script. Visit http://sourceforge.net/projects/mingw/files/ | |
130 and download/install Automated MinGW Installer (eg MinGW-5.1.4.exe), | |
131 MSYS Base System (eg MSYS-1.0.11.exe) and MSYS Supplementary Tools (eg | |
132 msysDTK-1.0.1.exe). | |
133 | |
134 |