Version Release date Notes

MapSplice 1.15.2

MapSplice 1.15.2_macos



Bugs fix:

(1) fix wrong --, -+ original fusion alignment, and original fusion junction in fusion.junction

(2) In a rare case, few normal junctions are generated

MapSplice 1.15.1


Fix possbile failure of single anchored fusion mapping step when --cluster, --fusion, --paired are specified at same time, and --non-canonical or --semi-canonical are not specified (output only canonical normal junction)  

MapSplice 1.15



1. Find fusion alignments with a single anchored method ( Option --cluster | do_cluster)
2. Add two new kinds of fusion alignments
    (1) Read alignment contain both fusion splice and normal splice
    (2) Fusion alignment across same chromosome, same strand, with short intron length. It is similar to normal splice alignment but the order of aligned segment is reversed. An example is given below.
3. Add fusion remap step
4. Filter fusion junction if doner sequence and acceptor sequence appear repeatedly in the genome. (Option --filter-fusion-by-repeat | filter_fusion_by_repeat)
5. Annotate fusion junction and normal junction to provided transcript file (Option --annotgene | do_annot_gene)
6. Add an option to output fusion non-canonical and semi-canonical junction
7. Support variable read length, read length option (-w | read_length) is no longer needed
8. Support bowtie 0.12.7, use -best option and remove -m option to report best segment alignments if there are repeated segment alignments (more than the threshold set by -max-hits)
9. Output XS:A tag in sam file.  Splice with flank string GTAG, ATAC, GCAG are XS:A:+ , and  CTAC, GTAT, CTGC are XS:A:-. Non-canonical splice is XS:A:+
10.  Support input reads file from bam file and sam file (-M and -bam | sam_file and BAM)
11. Add read format checking
    (1) two ends of a paired end read have same base read name
    (2) pair end read's name end with /1 or /2
    (3) quality string and read sequence length matches
(4) read name don't contain blank string
12. Bug fixes:
    (1) Quality string not correct in unmapped read in alignment.sam
    (2) Temp directory not created when the input data is large

MapSplice 1.14.1


MapPER supports all bits of flag tag in input sam files

MapSplice 1.14 2010-09-20

1. Add the alignment with small indels
2. Integrate MapPER v0.12
3. Standardize SAM file format. The alignments are in sorted order, forward alignments come before reverse alignments. Unaligned reads are included as part of the SAM file. IH/HI tags are used to indicate when a read is aligned to multiple places.  Use all bits in flag tag for paired-end reads
4. More filtering added for paired multiple aligned reads.
5. Add chromosome file format checking
6. Fix a few minor bugs

MapSplice 2010-08-18

Minor bug fix: filter multiple unspliced alignments when map_segment_directly = no for single end reads

  MapPER fix wrong boundaries of some alignments in output sam file


MapSplice 1.13.5 2010-07-19

support running MapSplice with a configuration file

MapSplice 1.13.4 2010-07-14

fix bug of fasta reads

add -t/--avoid-regions option, not search alignments in specified regions in gff format

add -T/--interested-regions option, search alignments in specified regions in gff format

MapSplice 1.13.3 2010-07-8

Support paired end reads. Specify --pairend option if input reads are paired end reads. 

Integrate  MapPer. Specify --run-MapPER option to run MapPER and generate reads mapping based on probabilistic framework  

Filter reads' multiple alignments by paired alignments. Filter multiple alignments between unspliced and spliced mapped reads. 

Add --map-segments-directly option to map segments of reads directly to chromosomes, instead of mapping whole reads to chromosomes. It wil find spliced alignments and unspliced alignments of a read, and then select best alignments

Add --search-whole-chromosome option to search whole chromosomes regions, instead of searching exonic regions. It can discover small exons(< segment length) at head or tail of a read.

Output Unspliced alignments in the result sam file

  MapSplice 1.12 2010-05-28

improved junction coverage in raw junction produced by MapSplice

improved compatibility with g++ 4.1.1 and 4.1.2.

fix bug if an output file exist.

MapSplice 1.11 2010-05-18

add -R/--remap-mismatch option for mismatch of remapping

add --semi-canonical option to control output of semi-canonical junction

specificity improvement for high depth data

MapSplice 1.10 2010-05-13

redirect all programs' stdout to log files

add --not-rem-temp not remove tmp directory after finished

--non-canonical, --not-rem-temp, --full-running only need to be specified without followed by a value

MapSplice 1.9.1 2010-05-11 Added junction filtering in the default configuration
MapSplice 1.9 2010-05-08

Add the option -f for output canonical junctions only.

Memory and performance improvement, all programs should use less than 4G memory

MapSplice 1.8 2010-05-02

Add --format-chromos option and programs to replace blank space or tab with '_' if there are blank space or tab in read name or chromosome name

MapSplice 1.7.1

Improved memory usage in filtering.

Allow user to run the pipeline when not in the bin path.

 MapSplice 1.7  
2010-04-30 Add --rerun-all option to rerun all steps if output files exist.
 MapSplice 1.6 2010-04-28 Add read sequence and quality string in sam file.
 MapSplice 1.5 2010-04-26