It seems that some BGZipped files may need Tabix Index files for IGB to properly open the complete file. We should examine ways to improve this.

David's seems to think that it is not a problem with our parser but rather a problem in the way the SamTools library handles BGzipped files that do not have associated tabix index files (ask David for clarification).

See below for am exception that can arise when this problem happens:

May 13, 2015 1:28:58 PM com.affymetrix.genometry.quickload.QuickLoadSymLoader logException
WARNING: For input string: "AT4G12610.1"
java.lang.NumberFormatException: For input string: "AT4G12610.1"
at java.lang.NumberFormatException.forInputString(Unknown Source)
at java.lang.Integer.parseInt(Unknown Source)
at java.lang.Integer.valueOf(Unknown Source)
at com.affymetrix.genometry.util.SortTabFile$LineComparator.minimum(SortTabFile.java:148)
at com.affymetrix.genometry.util.SortTabFile$LineComparator.compare(SortTabFile.java:120)
at com.affymetrix.genometry.util.SortTabFile$LineComparator.compare(SortTabFile.java:99)
at java.util.TimSort.countRunAndMakeAscending(Unknown Source)
at java.util.TimSort.sort(Unknown Source)
at java.util.Arrays.sort(Unknown Source)
at java.util.ArrayList.sort(Unknown Source)
at java.util.Collections.sort(Unknown Source)
at com.affymetrix.genometry.util.SortTabFile.sort(SortTabFile.java:54)
at com.affymetrix.genometry.symloader.SymLoader.sortCreatedFiles(SymLoader.java:109)
at com.affymetrix.genometry.symloader.BED.init(BED.java:97)
at com.affymetrix.genometry.symloader.BED.getChromosomeList(BED.java:104)
at com.affymetrix.genometry.quickload.QuickLoadSymLoader.loadAndAddSymmetries(QuickLoadSymLoader.java:152)
at com.affymetrix.genometry.quickload.QuickLoadSymLoader.loadSymmetriesThread(QuickLoadSymLoader.java:138)
at com.affymetrix.genometry.quickload.QuickLoadSymLoader.loadFeatures(QuickLoadSymLoader.java:118)
at com.affymetrix.igb.view.load.GeneralLoadUtils.loadFeaturesForSym(GeneralLoadUtils.java:783)
at com.affymetrix.igb.view.load.GeneralLoadUtils$1.loadOnSequence(GeneralLoadUtils.java:698)
at com.affymetrix.igb.view.load.GeneralLoadUtils$1.lambda$multiThreadedLoad$81(GeneralLoadUtils.java:641)
at com.affymetrix.igb.view.load.GeneralLoadUtils$1$$Lambda$277/1623074565.run(Unknown Source)
at java.util.concurrent.Executors$RunnableAdapter.call(Unknown Source)
at java.util.concurrent.FutureTask.run(Unknown Source)
at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
at java.lang.Thread.run(Unknown Source)

13:28:58.331 INFO c.a.igb.view.load.GeneralLoadUtils - Loaded TAIR10 mRNA in 937.5 ms
13:28:58.337 ERROR c.a.igb.view.load.GeneralLoadUtils - Error in loadOnSequence
java.lang.NumberFormatException: For input string: "AT4G12610.1"
at java.lang.NumberFormatException.forInputString(Unknown Source) ~[na:1.8.0_40]
at java.lang.Integer.parseInt(Unknown Source) ~[na:1.8.0_40]
at java.lang.Integer.valueOf(Unknown Source) ~[na:1.8.0_40]
at com.affymetrix.genometry.util.SortTabFile$LineComparator.minimum(SortTabFile.java:148) ~[genometry-8.4.0.jar:na]
at com.affymetrix.genometry.util.SortTabFile$LineComparator.compare(SortTabFile.java:120) ~[genometry-8.4.0.jar:na]
at com.affymetrix.genometry.util.SortTabFile$LineComparator.compare(SortTabFile.java:99) ~[genometry-8.4.0.jar:na]
at java.util.TimSort.countRunAndMakeAscending(Unknown Source) ~[na:1.8.0_40]
at java.util.TimSort.sort(Unknown Source) ~[na:1.8.0_40]
at java.util.Arrays.sort(Unknown Source) ~[na:1.8.0_40]
at java.util.ArrayList.sort(Unknown Source) ~[na:1.8.0_40]
at java.util.Collections.sort(Unknown Source) ~[na:1.8.0_40]
at com.affymetrix.genometry.util.SortTabFile.sort(SortTabFile.java:54) ~[genometry-8.4.0.jar:na]
at com.affymetrix.genometry.symloader.SymLoader.sortCreatedFiles(SymLoader.java:109) ~[genometry-8.4.0.jar:na]
at com.affymetrix.genometry.symloader.BED.init(BED.java:97) ~[genometry-8.4.0.jar:na]
at com.affymetrix.genometry.symloader.BED.getChromosomeList(BED.java:104) ~[genometry-8.4.0.jar:na]
at com.affymetrix.genometry.quickload.QuickLoadSymLoader.loadAndAddSymmetries(QuickLoadSymLoader.java:152) ~[genometry-8.4.0.jar:na]
at com.affymetrix.genometry.quickload.QuickLoadSymLoader.loadSymmetriesThread(QuickLoadSymLoader.java:138) ~[genometry-8.4.0.jar:na]
at com.affymetrix.genometry.quickload.QuickLoadSymLoader.loadFeatures(QuickLoadSymLoader.java:118) ~[genometry-8.4.0.jar:na]
at com.affymetrix.igb.view.load.GeneralLoadUtils.loadFeaturesForSym(GeneralLoadUtils.java:783) ~[igb-8.4.0.jar:na]
at com.affymetrix.igb.view.load.GeneralLoadUtils$1.loadOnSequence(GeneralLoadUtils.java:698) [igb-8.4.0.jar:na]
at com.affymetrix.igb.view.load.GeneralLoadUtils$1.lambda$multiThreadedLoad$81(GeneralLoadUtils.java:641) [igb-8.4.0.jar:na]
at com.affymetrix.igb.view.load.GeneralLoadUtils$1$$Lambda$277/1623074565.run(Unknown Source) [igb-8.4.0.jar:na]
at java.util.concurrent.Executors$RunnableAdapter.call(Unknown Source) [na:1.8.0_40]
at java.util.concurrent.FutureTask.run(Unknown Source) [na:1.8.0_40]
at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source) [na:1.8.0_40]
at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source) [na:1.8.0_40]
at java.lang.Thread.run(Unknown Source) [na:1.8.0_40]
May 13, 2015 1:28:58 PM com.affymetrix.genometry.quickload.QuickLoadSymLoader logException
WARNING: For input string: "ATCYSC1|ARATH;BSAS3;1|CYSC1"
java.lang.NumberFormatException: For input string: "ATCYSC1|ARATH;BSAS3;1|CYSC1"
at java.lang.NumberFormatException.forInputString(Unknown Source)
at java.lang.Integer.parseInt(Unknown Source)
at java.lang.Integer.valueOf(Unknown Source)
at com.affymetrix.genometry.util.SortTabFile$LineComparator.minimum(SortTabFile.java:147)
at com.affymetrix.genometry.util.SortTabFile$LineComparator.compare(SortTabFile.java:120)
at com.affymetrix.genometry.util.SortTabFile$LineComparator.compare(SortTabFile.java:99)
at java.util.TimSort.countRunAndMakeAscending(Unknown Source)
at java.util.TimSort.sort(Unknown Source)
at java.util.Arrays.sort(Unknown Source)
at java.util.ArrayList.sort(Unknown Source)
at java.util.Collections.sort(Unknown Source)
at com.affymetrix.genometry.util.SortTabFile.sort(SortTabFile.java:54)
at com.affymetrix.genometry.symloader.SymLoader.sortCreatedFiles(SymLoader.java:109)
at com.affymetrix.genometry.symloader.BED.init(BED.java:97)
at com.affymetrix.genometry.symloader.BED.getChromosomeList(BED.java:104)
at com.affymetrix.genometry.quickload.QuickLoadSymLoader.loadAndAddSymmetries(QuickLoadSymLoader.java:152)
at com.affymetrix.genometry.quickload.QuickLoadSymLoader.loadSymmetriesThread(QuickLoadSymLoader.java:138)
at com.affymetrix.genometry.quickload.QuickLoadSymLoader.loadFeatures(QuickLoadSymLoader.java:118)
at com.affymetrix.igb.view.load.GeneralLoadUtils.loadFeaturesForSym(GeneralLoadUtils.java:783)
at com.affymetrix.igb.view.load.GeneralLoadUtils$1.loadOnSequence(GeneralLoadUtils.java:698)
at com.affymetrix.igb.view.load.GeneralLoadUtils$1.lambda$multiThreadedLoad$81(GeneralLoadUtils.java:641)
at com.affymetrix.igb.view.load.GeneralLoadUtils$1$$Lambda$277/1623074565.run(Unknown Source)
at java.util.concurrent.Executors$RunnableAdapter.call(Unknown Source)
at java.util.concurrent.FutureTask.run(Unknown Source)
at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
at java.lang.Thread.run(Unknown Source)

13:28:58.886 ERROR c.a.igb.view.load.GeneralLoadUtils - Error in loadOnSequence
java.lang.NumberFormatException: For input string: "ATCYSC1|ARATH;BSAS3;1|CYSC1"
at java.lang.NumberFormatException.forInputString(Unknown Source) ~[na:1.8.0_40]
at java.lang.Integer.parseInt(Unknown Source) ~[na:1.8.0_40]
at java.lang.Integer.valueOf(Unknown Source) ~[na:1.8.0_40]
at com.affymetrix.genometry.util.SortTabFile$LineComparator.minimum(SortTabFile.java:147) ~[genometry-8.4.0.jar:na]
at com.affymetrix.genometry.util.SortTabFile$LineComparator.compare(SortTabFile.java:120) ~[genometry-8.4.0.jar:na]
at com.affymetrix.genometry.util.SortTabFile$LineComparator.compare(SortTabFile.java:99) ~[genometry-8.4.0.jar:na]
at java.util.TimSort.countRunAndMakeAscending(Unknown Source) ~[na:1.8.0_40]
at java.util.TimSort.sort(Unknown Source) ~[na:1.8.0_40]
at java.util.Arrays.sort(Unknown Source) ~[na:1.8.0_40]
at java.util.ArrayList.sort(Unknown Source) ~[na:1.8.0_40]
at java.util.Collections.sort(Unknown Source) ~[na:1.8.0_40]
at com.affymetrix.genometry.util.SortTabFile.sort(SortTabFile.java:54) ~[genometry-8.4.0.jar:na]
at com.affymetrix.genometry.symloader.SymLoader.sortCreatedFiles(SymLoader.java:109) ~[genometry-8.4.0.jar:na]
at com.affymetrix.genometry.symloader.BED.init(BED.java:97) ~[genometry-8.4.0.jar:na]
at com.affymetrix.genometry.symloader.BED.getChromosomeList(BED.java:104) ~[genometry-8.4.0.jar:na]
at com.affymetrix.genometry.quickload.QuickLoadSymLoader.loadAndAddSymmetries(QuickLoadSymLoader.java:152) ~[genometry-8.4.0.jar:na]
at com.affymetrix.genometry.quickload.QuickLoadSymLoader.loadSymmetriesThread(QuickLoadSymLoader.java:138) ~[genometry-8.4.0.jar:na]
at com.affymetrix.genometry.quickload.QuickLoadSymLoader.loadFeatures(QuickLoadSymLoader.java:118) ~[genometry-8.4.0.jar:na]
at com.affymetrix.igb.view.load.GeneralLoadUtils.loadFeaturesForSym(GeneralLoadUtils.java:783) ~[igb-8.4.0.jar:na]
at com.affymetrix.igb.view.load.GeneralLoadUtils$1.loadOnSequence(GeneralLoadUtils.java:698) [igb-8.4.0.jar:na]
at com.affymetrix.igb.view.load.GeneralLoadUtils$1.lambda$multiThreadedLoad$81(GeneralLoadUtils.java:641) [igb-8.4.0.jar:na]
at com.affymetrix.igb.view.load.GeneralLoadUtils$1$$Lambda$277/1623074565.run(Unknown Source) [igb-8.4.0.jar:na]
at java.util.concurrent.Executors$RunnableAdapter.call(Unknown Source) [na:1.8.0_40]
at java.util.concurrent.FutureTask.run(Unknown Source) [na:1.8.0_40]
at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source) [na:1.8.0_40]
at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source) [na:1.8.0_40]
at java.lang.Thread.run(Unknown Source) [na:1.8.0_40]