OutOfBounds issue when running with data containing many sites

[jiaweiliu0727]

Hi everyone! Thanks for developing these tool. I am recently using it to try to reconstruct the haplotypes from sequencing data of Malaria patients. I am inputting the BAM file and vcf file. However, PoolHapX cannot run and reports the OutOfBounds error all the time, maybe because there are more than 19000 sites in the data (The error information is attached below). I have tried running PoolHapX with less than 100 sites and it generates output, so it might be an issue of not enough length in certain variables, I guess. Does anyone have an idea on where I need to change in the java script or anywhere else to solve this OutOfBounds issue? Thank you!

Best,
Jiawei

Exception in thread "main" java.lang.ArrayIndexOutOfBoundsException: 19887
at PoolHap.GraphColoring.gc_solver(GraphColoring.java:1267)
at PoolHap.GraphColoring.(GraphColoring.java:77)
at PoolHap.Entrance.main(Entrance.java:225)
java.io.FileNotFoundException: /home/liu3594/PoolHapX/Pf241/intermediate/aem/Pf241_level_7_region_0.inter_freq_haps.txt (No such file or directory)
at java.io.FileInputStream.open0(Native Method)
at java.io.FileInputStream.open(FileInputStream.java:195)
at java.io.FileInputStream.(FileInputStream.java:138)
at java.io.FileInputStream.(FileInputStream.java:93)
at java.io.FileReader.(FileReader.java:58)
at PoolHap.HapConfig.(HapConfig.java:400)
at PoolHap.Entrance.main(Entrance.java:393)
......
Exception in thread "main" java.lang.NullPointerException
at PoolHap.GraphColoring.(GraphColoring.java:447)
at PoolHap.Entrance.main(Entrance.java:423)